Starting phenix.real_space_refine on Thu Jun 19 23:47:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ptm_17874/06_2025/8ptm_17874.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ptm_17874/06_2025/8ptm_17874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ptm_17874/06_2025/8ptm_17874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ptm_17874/06_2025/8ptm_17874.map" model { file = "/net/cci-nas-00/data/ceres_data/8ptm_17874/06_2025/8ptm_17874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ptm_17874/06_2025/8ptm_17874.cif" } resolution = 2.9 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= 0.008 sd= 0.055 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 117 5.16 5 C 14461 2.51 5 N 4065 2.21 5 O 4413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23064 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "B" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "C" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "D" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "E" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "F" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "a" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "b" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "c" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "d" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "e" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.67, per 1000 atoms: 0.68 Number of scatterers: 23064 At special positions: 0 Unit cell: (132.288, 143.104, 164.736, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 117 16.00 P 6 15.00 Mg 2 11.99 O 4413 8.00 N 4065 7.00 C 14461 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: 6.02 Conformation dependent library (CDL) restraints added in 3.1 seconds 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5458 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 29 sheets defined 44.9% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.12 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 30 through 45 removed outlier: 3.748A pdb=" N ILE A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 90 Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 155 through 166 removed outlier: 4.067A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 199 Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 235 through 255 removed outlier: 3.553A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 276 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 325 through 335 removed outlier: 3.862A pdb=" N GLU A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.508A pdb=" N LYS A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 removed outlier: 3.527A pdb=" N SER A 363 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.431A pdb=" N LEU A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 388 Processing helix chain 'A' and resid 392 through 406 removed outlier: 3.532A pdb=" N GLU A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR A 406 " --> pdb=" O LYS A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 417 removed outlier: 3.517A pdb=" N LYS A 417 " --> pdb=" O PHE A 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 9 Processing helix chain 'B' and resid 10 through 22 Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.699A pdb=" N SER B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 89 Processing helix chain 'B' and resid 126 through 130 removed outlier: 3.677A pdb=" N ASN B 129 " --> pdb=" O ASN B 126 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS B 130 " --> pdb=" O ALA B 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 126 through 130' Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 155 through 166 removed outlier: 4.283A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 Processing helix chain 'B' and resid 212 through 223 removed outlier: 3.507A pdb=" N THR B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 255 Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 285 through 289 removed outlier: 3.816A pdb=" N VAL B 289 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 325 through 335 removed outlier: 3.510A pdb=" N GLU B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.089A pdb=" N LEU B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 388 Processing helix chain 'B' and resid 391 through 405 removed outlier: 4.021A pdb=" N MET B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 418 removed outlier: 3.781A pdb=" N ARG B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 123 through 128 removed outlier: 3.742A pdb=" N ARG C 128 " --> pdb=" O PRO C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 155 through 166 removed outlier: 4.153A pdb=" N ALA C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 Processing helix chain 'C' and resid 212 through 223 removed outlier: 3.553A pdb=" N THR C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 255 removed outlier: 3.567A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 278 Processing helix chain 'C' and resid 294 through 302 Processing helix chain 'C' and resid 325 through 335 Processing helix chain 'C' and resid 346 through 352 removed outlier: 3.588A pdb=" N LYS C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 388 Processing helix chain 'C' and resid 391 through 405 removed outlier: 3.708A pdb=" N MET C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 418 Processing helix chain 'D' and resid 2 through 8 removed outlier: 3.622A pdb=" N ASN D 8 " --> pdb=" O THR D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 21 removed outlier: 3.621A pdb=" N THR D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET D 21 " --> pdb=" O LEU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 45 removed outlier: 4.191A pdb=" N SER D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 90 Processing helix chain 'D' and resid 123 through 128 removed outlier: 3.672A pdb=" N ARG D 128 " --> pdb=" O PRO D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 166 removed outlier: 4.091A pdb=" N THR D 158 " --> pdb=" O THR D 154 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 Processing helix chain 'D' and resid 212 through 223 removed outlier: 3.586A pdb=" N THR D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 255 removed outlier: 3.558A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 278 Processing helix chain 'D' and resid 285 through 289 removed outlier: 3.866A pdb=" N VAL D 289 " --> pdb=" O THR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 302 Processing helix chain 'D' and resid 325 through 334 removed outlier: 3.565A pdb=" N GLU D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 352 Processing helix chain 'D' and resid 367 through 372 removed outlier: 4.260A pdb=" N LEU D 371 " --> pdb=" O LYS D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 388 Processing helix chain 'D' and resid 391 through 405 removed outlier: 3.641A pdb=" N MET D 396 " --> pdb=" O GLU D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 418 Processing helix chain 'E' and resid 2 through 8 Processing helix chain 'E' and resid 10 through 22 Processing helix chain 'E' and resid 30 through 46 removed outlier: 3.535A pdb=" N GLY E 46 " --> pdb=" O HIS E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 89 Processing helix chain 'E' and resid 123 through 129 removed outlier: 3.788A pdb=" N ASN E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 166 removed outlier: 3.953A pdb=" N ALA E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 199 Processing helix chain 'E' and resid 212 through 223 removed outlier: 3.656A pdb=" N THR E 217 " --> pdb=" O PRO E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 256 removed outlier: 3.525A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS E 256 " --> pdb=" O ARG E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 278 Processing helix chain 'E' and resid 290 through 303 removed outlier: 3.629A pdb=" N HIS E 295 " --> pdb=" O ALA E 291 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG E 296 " --> pdb=" O ASN E 292 " (cutoff:3.500A) Proline residue: E 297 - end of helix Processing helix chain 'E' and resid 325 through 335 removed outlier: 3.823A pdb=" N GLU E 329 " --> pdb=" O SER E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 352 removed outlier: 3.559A pdb=" N LYS E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'E' and resid 373 through 388 Processing helix chain 'E' and resid 391 through 406 removed outlier: 4.072A pdb=" N MET E 405 " --> pdb=" O ASN E 401 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR E 406 " --> pdb=" O LYS E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 417 Processing helix chain 'F' and resid 2 through 9 removed outlier: 3.547A pdb=" N LEU F 6 " --> pdb=" O ASN F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 22 Processing helix chain 'F' and resid 30 through 44 Processing helix chain 'F' and resid 82 through 89 Processing helix chain 'F' and resid 123 through 128 Processing helix chain 'F' and resid 155 through 166 removed outlier: 3.654A pdb=" N ALA F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 199 Processing helix chain 'F' and resid 212 through 223 Processing helix chain 'F' and resid 235 through 256 removed outlier: 3.560A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 278 Processing helix chain 'F' and resid 294 through 302 Processing helix chain 'F' and resid 325 through 335 removed outlier: 3.519A pdb=" N GLU F 329 " --> pdb=" O SER F 325 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE F 335 " --> pdb=" O ILE F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 352 removed outlier: 3.558A pdb=" N LYS F 352 " --> pdb=" O LYS F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 372 removed outlier: 4.327A pdb=" N LEU F 371 " --> pdb=" O LYS F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 388 Processing helix chain 'F' and resid 392 through 405 removed outlier: 3.677A pdb=" N GLU F 397 " --> pdb=" O ILE F 393 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU F 403 " --> pdb=" O LEU F 399 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET F 405 " --> pdb=" O ASN F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 418 removed outlier: 3.691A pdb=" N ARG F 418 " --> pdb=" O GLU F 414 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 22 Processing helix chain 'b' and resid 9 through 23 Processing helix chain 'c' and resid 9 through 23 Processing helix chain 'c' and resid 56 through 59 Processing helix chain 'd' and resid 9 through 23 Processing helix chain 'e' and resid 9 through 23 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 57 removed outlier: 3.630A pdb=" N ILE A 79 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N TYR A 80 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N LYS A 115 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU A 114 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ARG A 102 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL A 116 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LYS A 100 " --> pdb=" O VAL A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.580A pdb=" N ASN A 306 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU A 204 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N VAL A 228 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL A 206 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N SER A 230 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU A 208 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.580A pdb=" N ASN A 306 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY A 174 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ALA A 319 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE A 176 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET A 341 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 284 through 285 removed outlier: 3.940A pdb=" N VAL A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 49 through 57 removed outlier: 6.328A pdb=" N LYS B 100 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N VAL B 116 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N SER B 98 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLU B 118 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR B 96 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE B 49 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.539A pdb=" N ASN B 306 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL B 203 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU B 263 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N MET B 205 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP B 265 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU B 207 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU B 204 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL B 228 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL B 206 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N SER B 230 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 208 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.539A pdb=" N ASN B 306 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY B 174 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ALA B 319 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE B 176 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 144 through 145 removed outlier: 4.421A pdb=" N ILE B 168 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 118 through 119 removed outlier: 3.895A pdb=" N ILE C 79 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE C 49 " --> pdb=" O ILE C 101 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.571A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL C 203 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LEU C 263 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N MET C 205 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ASP C 265 " --> pdb=" O MET C 205 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU C 207 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.571A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLY C 174 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ALA C 319 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE C 176 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET C 341 " --> pdb=" O ARG C 173 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 144 through 145 removed outlier: 4.526A pdb=" N ILE C 168 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 284 through 285 removed outlier: 3.811A pdb=" N VAL C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 49 through 57 removed outlier: 3.730A pdb=" N ILE D 79 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS D 100 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VAL D 116 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N SER D 98 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU D 118 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR D 96 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE D 49 " --> pdb=" O ILE D 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 144 through 145 removed outlier: 4.496A pdb=" N ILE D 168 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 226 through 231 removed outlier: 6.221A pdb=" N VAL D 203 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N LEU D 263 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N MET D 205 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ASP D 265 " --> pdb=" O MET D 205 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU D 207 " --> pdb=" O ASP D 265 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 226 through 231 removed outlier: 6.221A pdb=" N VAL D 203 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N LEU D 263 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N MET D 205 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ASP D 265 " --> pdb=" O MET D 205 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU D 207 " --> pdb=" O ASP D 265 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLY D 174 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ALA D 319 " --> pdb=" O GLY D 174 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE D 176 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG D 173 " --> pdb=" O MET D 341 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N LEU D 343 " --> pdb=" O ARG D 173 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU D 175 " --> pdb=" O LEU D 343 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 49 through 57 removed outlier: 3.810A pdb=" N ILE E 79 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N TYR E 80 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 9.269A pdb=" N LYS E 115 " --> pdb=" O TYR E 80 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS E 100 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL E 116 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N SER E 98 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLU E 118 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR E 96 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE E 49 " --> pdb=" O ILE E 101 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 138 through 139 Processing sheet with id=AC2, first strand: chain 'E' and resid 138 through 139 Processing sheet with id=AC3, first strand: chain 'F' and resid 49 through 57 removed outlier: 4.166A pdb=" N ILE F 79 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N TYR F 80 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 9.130A pdb=" N LYS F 115 " --> pdb=" O TYR F 80 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LYS F 100 " --> pdb=" O LEU F 114 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N VAL F 116 " --> pdb=" O SER F 98 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N SER F 98 " --> pdb=" O VAL F 116 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLU F 118 " --> pdb=" O THR F 96 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N THR F 96 " --> pdb=" O GLU F 118 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE F 49 " --> pdb=" O ILE F 101 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 138 through 139 removed outlier: 3.844A pdb=" N ASN F 306 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU F 204 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N VAL F 228 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL F 206 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N SER F 230 " --> pdb=" O VAL F 206 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU F 208 " --> pdb=" O SER F 230 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 138 through 139 removed outlier: 3.844A pdb=" N ASN F 306 " --> pdb=" O LEU F 139 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'a' and resid 35 through 38 removed outlier: 3.840A pdb=" N THR a 27 " --> pdb=" O SER a 72 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER a 72 " --> pdb=" O THR a 27 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'a' and resid 40 through 46 removed outlier: 5.177A pdb=" N ASP a 42 " --> pdb=" O VAL a 53 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL a 53 " --> pdb=" O ASP a 42 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'b' and resid 61 through 64 removed outlier: 3.880A pdb=" N ASP b 42 " --> pdb=" O VAL b 53 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLU b 55 " --> pdb=" O ALA b 40 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ALA b 40 " --> pdb=" O GLU b 55 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR b 27 " --> pdb=" O PHE b 71 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE b 71 " --> pdb=" O THR b 27 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N GLU b 29 " --> pdb=" O THR b 69 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'c' and resid 61 through 64 removed outlier: 3.578A pdb=" N VAL c 53 " --> pdb=" O ASP c 42 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP c 42 " --> pdb=" O VAL c 53 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU c 26 " --> pdb=" O ALA c 38 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'd' and resid 25 through 29 removed outlier: 3.925A pdb=" N LEU d 26 " --> pdb=" O ALA d 38 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA d 38 " --> pdb=" O LEU d 26 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ALA d 40 " --> pdb=" O GLU d 55 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLU d 55 " --> pdb=" O ALA d 40 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP d 42 " --> pdb=" O VAL d 53 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'e' and resid 61 through 64 removed outlier: 4.068A pdb=" N VAL e 53 " --> pdb=" O ASP e 42 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ASP e 42 " --> pdb=" O VAL e 53 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE e 71 " --> pdb=" O VAL e 79 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL e 79 " --> pdb=" O PHE e 71 " (cutoff:3.500A) 1131 hydrogen bonds defined for protein. 3204 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: 8.54 Time building geometry restraints manager: 7.14 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: 7853 1.34 - 1.46: 3055 1.46 - 1.57: 12267 1.57 - 1.69: 9 1.69 - 1.81: 218 Bond restraints: 23402 Sorted by residual: bond pdb=" N ASN c 48 " pdb=" CA ASN c 48 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.49e-02 4.50e+03 3.71e+00 bond pdb=" N LYS B 283 " pdb=" CA LYS B 283 " ideal model delta sigma weight residual 1.462 1.475 -0.013 1.35e-02 5.49e+03 9.93e-01 bond pdb=" C4 ADP C1000 " pdb=" C5 ADP C1000 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.89e-01 bond pdb=" C4 ADP D1000 " pdb=" C5 ADP D1000 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 9.39e-01 bond pdb=" C4 ADP E1000 " pdb=" C5 ADP E1000 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 9.31e-01 ... (remaining 23397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 31091 1.20 - 2.41: 269 2.41 - 3.61: 134 3.61 - 4.81: 38 4.81 - 6.02: 20 Bond angle restraints: 31552 Sorted by residual: angle pdb=" C GLU a 59 " pdb=" N THR a 60 " pdb=" CA THR a 60 " ideal model delta sigma weight residual 122.46 126.20 -3.74 1.41e+00 5.03e-01 7.04e+00 angle pdb=" CA ASN c 48 " pdb=" C ASN c 48 " pdb=" O ASN c 48 " ideal model delta sigma weight residual 120.81 117.76 3.05 1.24e+00 6.50e-01 6.05e+00 angle pdb=" C GLU b 59 " pdb=" N THR b 60 " pdb=" CA THR b 60 " ideal model delta sigma weight residual 121.54 126.17 -4.63 1.91e+00 2.74e-01 5.89e+00 angle pdb=" C GLY B 282 " pdb=" N LYS B 283 " pdb=" CA LYS B 283 " ideal model delta sigma weight residual 122.85 119.51 3.34 1.39e+00 5.18e-01 5.78e+00 angle pdb=" O GLY B 282 " pdb=" C GLY B 282 " pdb=" N LYS B 283 " ideal model delta sigma weight residual 122.46 125.40 -2.94 1.23e+00 6.61e-01 5.72e+00 ... (remaining 31547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.41: 14197 25.41 - 50.83: 300 50.83 - 76.24: 5 76.24 - 101.66: 2 101.66 - 127.07: 4 Dihedral angle restraints: 14508 sinusoidal: 6086 harmonic: 8422 Sorted by residual: dihedral pdb=" O2A ADP E1000 " pdb=" O3A ADP E1000 " pdb=" PA ADP E1000 " pdb=" PB ADP E1000 " ideal model delta sinusoidal sigma weight residual -60.00 67.07 -127.07 1 2.00e+01 2.50e-03 3.85e+01 dihedral pdb=" O1B ADP E1000 " pdb=" O3A ADP E1000 " pdb=" PB ADP E1000 " pdb=" PA ADP E1000 " ideal model delta sinusoidal sigma weight residual -60.00 64.58 -124.58 1 2.00e+01 2.50e-03 3.76e+01 dihedral pdb=" C5' ADP E1000 " pdb=" O5' ADP E1000 " pdb=" PA ADP E1000 " pdb=" O2A ADP E1000 " ideal model delta sinusoidal sigma weight residual -60.00 56.44 -116.43 1 2.00e+01 2.50e-03 3.47e+01 ... (remaining 14505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2109 0.025 - 0.050: 906 0.050 - 0.075: 292 0.075 - 0.100: 160 0.100 - 0.125: 142 Chirality restraints: 3609 Sorted by residual: chirality pdb=" CA PRO B 180 " pdb=" N PRO B 180 " pdb=" C PRO B 180 " pdb=" CB PRO B 180 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA ILE D 49 " pdb=" N ILE D 49 " pdb=" C ILE D 49 " pdb=" CB ILE D 49 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA ILE C 49 " pdb=" N ILE C 49 " pdb=" C ILE C 49 " pdb=" CB ILE C 49 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 3606 not shown) Planarity restraints: 4105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS e 73 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO e 74 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO e 74 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO e 74 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 9 " -0.021 5.00e-02 4.00e+02 3.11e-02 1.54e+00 pdb=" N PRO F 10 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO F 10 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 10 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 278 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO C 279 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 279 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 279 " 0.017 5.00e-02 4.00e+02 ... (remaining 4102 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 213 2.60 - 3.18: 19755 3.18 - 3.75: 35018 3.75 - 4.33: 49087 4.33 - 4.90: 81181 Nonbonded interactions: 185254 Sorted by model distance: nonbonded pdb=" O3B ADP C1000 " pdb="MG MG C1001 " model vdw 2.027 2.170 nonbonded pdb=" OG1 THR C 185 " pdb="MG MG C1001 " model vdw 2.139 2.170 nonbonded pdb=" OG SER C 84 " pdb=" OD1 ASP c 14 " model vdw 2.222 3.040 nonbonded pdb=" OG1 THR F 231 " pdb=" OD1 ASP F 233 " model vdw 2.226 3.040 nonbonded pdb=" OG1 THR D 185 " pdb="MG MG D1001 " model vdw 2.228 2.170 ... (remaining 185249 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 'B' selection = (chain 'C' and resid 1 through 418) selection = (chain 'D' and resid 1 through 418) selection = (chain 'E' and resid 1 through 418) selection = chain 'F' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } 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: 3.670 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: 1.140 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 56.370 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.120 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:14.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 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 : 0.003 0.029 23402 Z= 0.116 Angle : 0.426 6.015 31552 Z= 0.211 Chirality : 0.039 0.125 3609 Planarity : 0.003 0.039 4105 Dihedral : 10.040 127.073 9050 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.71 % Allowed : 5.36 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.16), residues: 2896 helix: 1.64 (0.15), residues: 1185 sheet: 0.56 (0.24), residues: 524 loop : 0.74 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 381 HIS 0.002 0.000 HIS c 73 PHE 0.007 0.001 PHE D 232 TYR 0.005 0.001 TYR C 197 ARG 0.003 0.000 ARG D 66 Details of bonding type rmsd hydrogen bonds : bond 0.24302 ( 1103) hydrogen bonds : angle 7.05366 ( 3204) covalent geometry : bond 0.00261 (23402) covalent geometry : angle 0.42582 (31552) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 399 time to evaluate : 2.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 LYS cc_start: 0.8774 (ptmt) cc_final: 0.8566 (ptmt) REVERT: A 327 MET cc_start: 0.8735 (ttm) cc_final: 0.8290 (ttp) REVERT: A 334 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8632 (mm-30) REVERT: A 342 GLU cc_start: 0.8205 (pm20) cc_final: 0.7588 (pm20) REVERT: A 390 MET cc_start: 0.8472 (ppp) cc_final: 0.8181 (ppp) REVERT: A 415 MET cc_start: 0.9358 (pp-130) cc_final: 0.8961 (pp-130) REVERT: B 21 MET cc_start: 0.8935 (mtt) cc_final: 0.8708 (mtp) REVERT: B 244 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8136 (mm-30) REVERT: B 296 ARG cc_start: 0.8616 (mmm-85) cc_final: 0.8333 (mmm160) REVERT: B 326 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8674 (mmmm) REVERT: B 334 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8890 (mm-30) REVERT: B 378 GLN cc_start: 0.9124 (tp-100) cc_final: 0.8854 (tp-100) REVERT: C 85 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8822 (tp40) REVERT: C 186 MET cc_start: 0.9030 (mmm) cc_final: 0.8777 (mtm) REVERT: C 244 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8447 (mm-30) REVERT: C 362 ARG cc_start: 0.9220 (mmm-85) cc_final: 0.8946 (mmm-85) REVERT: C 374 GLN cc_start: 0.8953 (tp-100) cc_final: 0.8521 (tp-100) REVERT: D 244 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8201 (mp0) REVERT: D 333 GLU cc_start: 0.8920 (tp30) cc_final: 0.8583 (mm-30) REVERT: D 334 GLU cc_start: 0.8787 (mp0) cc_final: 0.8476 (mp0) REVERT: D 374 GLN cc_start: 0.9004 (tp-100) cc_final: 0.8797 (tp-100) REVERT: D 397 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8680 (mt-10) REVERT: E 210 ASP cc_start: 0.8481 (t70) cc_final: 0.8212 (t0) REVERT: E 244 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8056 (mm-30) REVERT: E 334 GLU cc_start: 0.8973 (mp0) cc_final: 0.8494 (mp0) REVERT: E 338 THR cc_start: 0.9467 (m) cc_final: 0.9263 (m) REVERT: E 368 GLU cc_start: 0.8409 (tt0) cc_final: 0.7789 (tm-30) REVERT: E 378 GLN cc_start: 0.9189 (tp40) cc_final: 0.8963 (tp-100) REVERT: E 394 ASP cc_start: 0.9157 (m-30) cc_final: 0.8741 (p0) REVERT: F 21 MET cc_start: 0.8353 (tmt) cc_final: 0.7932 (tmt) REVERT: F 29 MET cc_start: 0.8744 (mtp) cc_final: 0.8174 (mtp) REVERT: F 80 TYR cc_start: 0.8403 (t80) cc_final: 0.8200 (t80) REVERT: F 181 LYS cc_start: 0.8784 (mmtp) cc_final: 0.8058 (tppt) REVERT: F 186 MET cc_start: 0.8601 (ptp) cc_final: 0.8377 (ptp) REVERT: F 189 GLN cc_start: 0.8281 (mt0) cc_final: 0.7984 (mt0) REVERT: F 219 MET cc_start: 0.8737 (tpp) cc_final: 0.8461 (tpp) REVERT: F 329 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8306 (mm-30) REVERT: F 368 GLU cc_start: 0.7416 (pm20) cc_final: 0.7105 (pm20) REVERT: b 25 MET cc_start: 0.8955 (mmm) cc_final: 0.8751 (mpp) REVERT: b 35 LYS cc_start: 0.9414 (mttt) cc_final: 0.9179 (mmtm) REVERT: b 39 LYS cc_start: 0.9013 (ttpp) cc_final: 0.8679 (tmmm) REVERT: b 46 ARG cc_start: 0.8671 (mtm-85) cc_final: 0.8343 (mtm-85) REVERT: b 71 PHE cc_start: 0.9196 (p90) cc_final: 0.8955 (p90) REVERT: c 12 ASP cc_start: 0.8536 (m-30) cc_final: 0.8283 (m-30) REVERT: c 15 ASN cc_start: 0.9316 (m-40) cc_final: 0.8838 (m110) REVERT: c 34 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8167 (tm-30) REVERT: d 26 LEU cc_start: 0.8804 (mt) cc_final: 0.8502 (mt) REVERT: d 27 THR cc_start: 0.8756 (p) cc_final: 0.8539 (t) outliers start: 43 outliers final: 19 residues processed: 436 average time/residue: 1.5139 time to fit residues: 743.7059 Evaluate side-chains 320 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 300 time to evaluate : 2.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain a residue 47 LYS Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 80 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 241 optimal weight: 3.9990 chunk 216 optimal weight: 10.0000 chunk 120 optimal weight: 0.1980 chunk 74 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 224 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 259 optimal weight: 9.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 378 GLN B 129 ASN C 2 ASN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN D 85 GLN D 193 GLN D 292 ASN D 374 GLN F 190 ASN F 378 GLN ** a 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 9 ASN d 15 ASN ** e 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.109850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.071371 restraints weight = 55143.521| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.98 r_work: 0.2847 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23402 Z= 0.226 Angle : 0.628 10.471 31552 Z= 0.314 Chirality : 0.044 0.196 3609 Planarity : 0.004 0.049 4105 Dihedral : 5.914 124.832 3229 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.58 % Allowed : 10.68 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.16), residues: 2896 helix: 1.83 (0.15), residues: 1215 sheet: 0.31 (0.24), residues: 494 loop : 0.75 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 381 HIS 0.006 0.001 HIS F 256 PHE 0.011 0.001 PHE c 71 TYR 0.022 0.002 TYR b 13 ARG 0.009 0.001 ARG A 212 Details of bonding type rmsd hydrogen bonds : bond 0.05401 ( 1103) hydrogen bonds : angle 5.10404 ( 3204) covalent geometry : bond 0.00520 (23402) covalent geometry : angle 0.62795 (31552) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 339 time to evaluate : 2.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.7908 (pm20) cc_final: 0.7348 (pm20) REVERT: A 415 MET cc_start: 0.9378 (pp-130) cc_final: 0.9169 (ppp) REVERT: B 244 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8323 (mm-30) REVERT: B 333 GLU cc_start: 0.8983 (tt0) cc_final: 0.8752 (tt0) REVERT: C 186 MET cc_start: 0.9160 (mmm) cc_final: 0.8899 (mtm) REVERT: C 342 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8231 (pt0) REVERT: C 362 ARG cc_start: 0.9318 (mmm-85) cc_final: 0.9079 (mmm-85) REVERT: D 244 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: D 333 GLU cc_start: 0.8969 (tp30) cc_final: 0.8578 (mp0) REVERT: D 334 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8467 (mp0) REVERT: D 374 GLN cc_start: 0.8828 (tp40) cc_final: 0.8447 (tp-100) REVERT: D 397 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8656 (mt-10) REVERT: E 210 ASP cc_start: 0.8518 (t70) cc_final: 0.8281 (t0) REVERT: E 244 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8295 (mm-30) REVERT: E 334 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8578 (mp0) REVERT: E 360 TYR cc_start: 0.8349 (t80) cc_final: 0.8094 (t80) REVERT: E 368 GLU cc_start: 0.8590 (tt0) cc_final: 0.8125 (tm-30) REVERT: E 394 ASP cc_start: 0.9218 (m-30) cc_final: 0.8842 (p0) REVERT: F 29 MET cc_start: 0.8723 (mtp) cc_final: 0.8185 (mtp) REVERT: F 41 GLN cc_start: 0.8864 (tp40) cc_final: 0.8466 (pp30) REVERT: F 155 GLU cc_start: 0.8012 (tt0) cc_final: 0.7587 (tm-30) REVERT: F 172 GLN cc_start: 0.6697 (OUTLIER) cc_final: 0.6259 (mp10) REVERT: F 181 LYS cc_start: 0.8651 (mmtp) cc_final: 0.7774 (tppt) REVERT: F 189 GLN cc_start: 0.8470 (mt0) cc_final: 0.8129 (mt0) REVERT: F 219 MET cc_start: 0.8757 (tpp) cc_final: 0.8421 (tpp) REVERT: F 220 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8466 (tm-30) REVERT: F 341 MET cc_start: 0.3747 (mpt) cc_final: 0.3485 (mpp) REVERT: F 368 GLU cc_start: 0.7436 (pm20) cc_final: 0.7128 (pm20) REVERT: F 396 MET cc_start: 0.8293 (mmt) cc_final: 0.7945 (mmm) REVERT: F 398 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.7384 (t80) REVERT: b 6 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8377 (mm-40) REVERT: b 14 ASP cc_start: 0.8570 (m-30) cc_final: 0.8256 (m-30) REVERT: b 15 ASN cc_start: 0.9093 (m-40) cc_final: 0.8779 (m-40) REVERT: b 25 MET cc_start: 0.9123 (mmm) cc_final: 0.8859 (mpp) REVERT: b 35 LYS cc_start: 0.9397 (mttt) cc_final: 0.9174 (mptt) REVERT: b 39 LYS cc_start: 0.9073 (ttpp) cc_final: 0.8775 (tmmm) REVERT: b 46 ARG cc_start: 0.8684 (mtm-85) cc_final: 0.8441 (mtm-85) REVERT: b 51 TYR cc_start: 0.8741 (m-80) cc_final: 0.8495 (m-80) REVERT: c 34 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8142 (tm-30) REVERT: c 73 HIS cc_start: 0.8553 (t70) cc_final: 0.7995 (t70) REVERT: d 26 LEU cc_start: 0.8739 (mt) cc_final: 0.8503 (pp) REVERT: d 27 THR cc_start: 0.8763 (p) cc_final: 0.8549 (t) REVERT: d 30 LEU cc_start: 0.8099 (mm) cc_final: 0.7797 (mp) REVERT: d 62 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8526 (mt-10) REVERT: e 46 ARG cc_start: 0.8656 (mtm110) cc_final: 0.8338 (mtm110) outliers start: 65 outliers final: 24 residues processed: 375 average time/residue: 1.5094 time to fit residues: 640.6603 Evaluate side-chains 329 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 299 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 172 GLN Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 398 PHE Chi-restraints excluded: chain a residue 47 LYS Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 80 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 chunk 240 optimal weight: 10.0000 chunk 224 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN D 374 GLN F 190 ASN a 37 GLN a 73 HIS b 9 ASN c 15 ASN d 9 ASN d 15 ASN ** e 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.110686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.072120 restraints weight = 55658.994| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.97 r_work: 0.2877 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23402 Z= 0.162 Angle : 0.596 11.102 31552 Z= 0.290 Chirality : 0.043 0.208 3609 Planarity : 0.004 0.052 4105 Dihedral : 5.621 116.364 3216 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.78 % Allowed : 12.03 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.16), residues: 2896 helix: 1.80 (0.15), residues: 1217 sheet: 0.21 (0.24), residues: 493 loop : 0.73 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 381 HIS 0.004 0.001 HIS d 73 PHE 0.011 0.001 PHE E 398 TYR 0.023 0.002 TYR e 13 ARG 0.008 0.000 ARG D 109 Details of bonding type rmsd hydrogen bonds : bond 0.04104 ( 1103) hydrogen bonds : angle 4.68501 ( 3204) covalent geometry : bond 0.00373 (23402) covalent geometry : angle 0.59625 (31552) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 328 time to evaluate : 3.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.7875 (pm20) cc_final: 0.7306 (pm20) REVERT: A 415 MET cc_start: 0.9401 (pp-130) cc_final: 0.9084 (ppp) REVERT: B 30 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7381 (mtm-85) REVERT: B 244 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8357 (mm-30) REVERT: C 186 MET cc_start: 0.9087 (mmm) cc_final: 0.8757 (mtm) REVERT: C 244 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8354 (mm-30) REVERT: C 342 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8232 (pt0) REVERT: C 362 ARG cc_start: 0.9308 (mmm-85) cc_final: 0.9104 (mmm-85) REVERT: D 155 GLU cc_start: 0.8634 (mp0) cc_final: 0.8402 (pm20) REVERT: D 244 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8067 (mp0) REVERT: D 333 GLU cc_start: 0.8992 (tp30) cc_final: 0.8644 (mp0) REVERT: D 334 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8445 (mp0) REVERT: D 397 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8626 (mt-10) REVERT: E 125 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8372 (pm20) REVERT: E 210 ASP cc_start: 0.8477 (t70) cc_final: 0.8211 (t0) REVERT: E 234 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8728 (mt-10) REVERT: E 244 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8315 (mm-30) REVERT: E 334 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8591 (mp0) REVERT: E 360 TYR cc_start: 0.8327 (t80) cc_final: 0.8075 (t80) REVERT: E 368 GLU cc_start: 0.8595 (tt0) cc_final: 0.8046 (tm-30) REVERT: E 394 ASP cc_start: 0.9225 (m-30) cc_final: 0.8823 (p0) REVERT: F 1 MET cc_start: 0.6710 (pmm) cc_final: 0.6409 (ptt) REVERT: F 29 MET cc_start: 0.8690 (mtp) cc_final: 0.8121 (mtp) REVERT: F 155 GLU cc_start: 0.8057 (tt0) cc_final: 0.7644 (tm-30) REVERT: F 172 GLN cc_start: 0.6661 (OUTLIER) cc_final: 0.6421 (mp10) REVERT: F 181 LYS cc_start: 0.8628 (mmtp) cc_final: 0.7735 (tppt) REVERT: F 189 GLN cc_start: 0.8456 (mt0) cc_final: 0.8063 (mt0) REVERT: F 219 MET cc_start: 0.8761 (tpp) cc_final: 0.8395 (tpp) REVERT: F 220 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8482 (tm-30) REVERT: F 245 MET cc_start: 0.7208 (mtp) cc_final: 0.6977 (ttp) REVERT: F 368 GLU cc_start: 0.7414 (pm20) cc_final: 0.7053 (pm20) REVERT: b 14 ASP cc_start: 0.8676 (m-30) cc_final: 0.8465 (m-30) REVERT: b 25 MET cc_start: 0.9123 (mmm) cc_final: 0.8847 (mpp) REVERT: b 35 LYS cc_start: 0.9392 (mttt) cc_final: 0.9165 (mptt) REVERT: b 39 LYS cc_start: 0.9085 (ttpp) cc_final: 0.8842 (tmmm) REVERT: b 55 GLU cc_start: 0.7928 (pm20) cc_final: 0.7566 (pm20) REVERT: c 34 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8161 (tm-30) REVERT: d 18 LEU cc_start: 0.9178 (tm) cc_final: 0.8896 (pp) REVERT: d 26 LEU cc_start: 0.8750 (mt) cc_final: 0.8533 (mt) REVERT: d 27 THR cc_start: 0.8815 (p) cc_final: 0.8497 (t) REVERT: d 30 LEU cc_start: 0.8235 (mm) cc_final: 0.7894 (mp) REVERT: d 62 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8392 (mt-10) REVERT: d 65 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8460 (mp) outliers start: 70 outliers final: 26 residues processed: 364 average time/residue: 1.9445 time to fit residues: 799.3881 Evaluate side-chains 327 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 292 time to evaluate : 3.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 172 GLN Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain a residue 47 LYS Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain b residue 11 ASP Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 70 SER Chi-restraints excluded: chain c residue 80 VAL Chi-restraints excluded: chain d residue 65 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 79 optimal weight: 0.5980 chunk 174 optimal weight: 0.3980 chunk 183 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 278 optimal weight: 0.5980 chunk 8 optimal weight: 0.1980 chunk 224 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN D 292 ASN E 193 GLN b 9 ASN c 15 ASN d 9 ASN d 15 ASN ** e 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.111357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.073149 restraints weight = 55768.084| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.95 r_work: 0.2901 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23402 Z= 0.121 Angle : 0.582 14.635 31552 Z= 0.279 Chirality : 0.042 0.211 3609 Planarity : 0.004 0.055 4105 Dihedral : 5.378 113.269 3214 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.90 % Allowed : 12.71 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.16), residues: 2896 helix: 1.93 (0.15), residues: 1216 sheet: 0.31 (0.24), residues: 486 loop : 0.68 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 381 HIS 0.007 0.001 HIS d 73 PHE 0.014 0.001 PHE A 62 TYR 0.032 0.001 TYR b 13 ARG 0.009 0.000 ARG D 299 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 1103) hydrogen bonds : angle 4.45072 ( 3204) covalent geometry : bond 0.00276 (23402) covalent geometry : angle 0.58213 (31552) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 304 time to evaluate : 3.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.9136 (tpp) cc_final: 0.8826 (tpp) REVERT: A 244 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8220 (mt-10) REVERT: A 342 GLU cc_start: 0.7825 (pm20) cc_final: 0.7229 (pm20) REVERT: A 415 MET cc_start: 0.9436 (OUTLIER) cc_final: 0.9182 (ppp) REVERT: B 26 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7683 (pp) REVERT: B 30 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7283 (mtm-85) REVERT: B 244 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8350 (mm-30) REVERT: C 186 MET cc_start: 0.9064 (mmm) cc_final: 0.8717 (mtm) REVERT: D 155 GLU cc_start: 0.8634 (mp0) cc_final: 0.8393 (pm20) REVERT: D 244 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8030 (mp0) REVERT: D 333 GLU cc_start: 0.8935 (tp30) cc_final: 0.8587 (mp0) REVERT: D 334 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8390 (mp0) REVERT: D 374 GLN cc_start: 0.8598 (tp-100) cc_final: 0.8394 (tp-100) REVERT: E 125 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8329 (pm20) REVERT: E 210 ASP cc_start: 0.8396 (t70) cc_final: 0.8170 (t0) REVERT: E 234 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8667 (mt-10) REVERT: E 244 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8235 (mm-30) REVERT: E 322 ASP cc_start: 0.8644 (t0) cc_final: 0.8443 (t0) REVERT: E 360 TYR cc_start: 0.8238 (t80) cc_final: 0.7976 (t80) REVERT: E 368 GLU cc_start: 0.8583 (tt0) cc_final: 0.8034 (tm-30) REVERT: E 394 ASP cc_start: 0.9227 (m-30) cc_final: 0.8832 (p0) REVERT: F 1 MET cc_start: 0.6562 (pmm) cc_final: 0.6288 (ptt) REVERT: F 29 MET cc_start: 0.8669 (mtp) cc_final: 0.7823 (mtp) REVERT: F 33 ASP cc_start: 0.8843 (m-30) cc_final: 0.8262 (OUTLIER) REVERT: F 155 GLU cc_start: 0.8045 (tt0) cc_final: 0.7671 (tm-30) REVERT: F 172 GLN cc_start: 0.6522 (OUTLIER) cc_final: 0.6096 (mp10) REVERT: F 181 LYS cc_start: 0.8669 (mmtp) cc_final: 0.7767 (tppt) REVERT: F 189 GLN cc_start: 0.8470 (mt0) cc_final: 0.8093 (mt0) REVERT: F 219 MET cc_start: 0.8758 (tpp) cc_final: 0.8405 (tpp) REVERT: F 226 GLU cc_start: 0.7710 (mp0) cc_final: 0.7244 (pm20) REVERT: F 341 MET cc_start: 0.3525 (mpt) cc_final: 0.3255 (mpp) REVERT: F 368 GLU cc_start: 0.7502 (pm20) cc_final: 0.7144 (pm20) REVERT: F 396 MET cc_start: 0.7740 (mmm) cc_final: 0.7514 (mmm) REVERT: F 415 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6598 (pmm) REVERT: F 416 MET cc_start: 0.2068 (tmm) cc_final: 0.1206 (tmm) REVERT: b 25 MET cc_start: 0.9057 (mmm) cc_final: 0.8779 (mpp) REVERT: b 39 LYS cc_start: 0.9068 (ttpp) cc_final: 0.8837 (tmmm) REVERT: b 55 GLU cc_start: 0.7985 (pm20) cc_final: 0.7630 (pm20) REVERT: c 34 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8194 (tm-30) REVERT: c 73 HIS cc_start: 0.8450 (t70) cc_final: 0.7841 (t70) REVERT: d 18 LEU cc_start: 0.9212 (tm) cc_final: 0.8926 (pp) REVERT: d 26 LEU cc_start: 0.8755 (mt) cc_final: 0.8390 (mm) REVERT: d 27 THR cc_start: 0.8880 (p) cc_final: 0.8595 (t) REVERT: d 30 LEU cc_start: 0.8286 (mm) cc_final: 0.7922 (mp) REVERT: d 62 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8329 (mt-10) REVERT: d 65 LEU cc_start: 0.8691 (mt) cc_final: 0.8489 (mp) outliers start: 73 outliers final: 26 residues processed: 350 average time/residue: 1.5610 time to fit residues: 618.9345 Evaluate side-chains 325 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 291 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 172 GLN Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain a residue 47 LYS Chi-restraints excluded: chain b residue 11 ASP Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 22 HIS Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 70 SER Chi-restraints excluded: chain c residue 80 VAL Chi-restraints excluded: chain d residue 11 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 262 optimal weight: 0.0970 chunk 173 optimal weight: 0.9980 chunk 2 optimal weight: 20.0000 chunk 138 optimal weight: 1.9990 chunk 277 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 274 optimal weight: 8.9990 chunk 233 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 193 optimal weight: 4.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 GLN D 292 ASN b 9 ASN c 15 ASN d 15 ASN ** e 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.110720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.072423 restraints weight = 55539.606| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.97 r_work: 0.2887 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23402 Z= 0.164 Angle : 0.598 13.335 31552 Z= 0.286 Chirality : 0.042 0.180 3609 Planarity : 0.004 0.057 4105 Dihedral : 5.227 112.306 3213 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.62 % Allowed : 13.86 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.16), residues: 2896 helix: 1.94 (0.15), residues: 1221 sheet: 0.26 (0.24), residues: 488 loop : 0.64 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 381 HIS 0.008 0.001 HIS d 73 PHE 0.031 0.001 PHE b 71 TYR 0.022 0.002 TYR d 13 ARG 0.012 0.000 ARG e 46 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 1103) hydrogen bonds : angle 4.42657 ( 3204) covalent geometry : bond 0.00385 (23402) covalent geometry : angle 0.59829 (31552) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 303 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.7904 (pm20) cc_final: 0.7289 (pm20) REVERT: A 415 MET cc_start: 0.9445 (OUTLIER) cc_final: 0.9212 (ppp) REVERT: B 30 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7323 (mtm-85) REVERT: B 244 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8343 (mm-30) REVERT: C 186 MET cc_start: 0.9070 (mmm) cc_final: 0.8706 (mtm) REVERT: C 342 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8143 (pt0) REVERT: D 155 GLU cc_start: 0.8656 (mp0) cc_final: 0.8417 (pm20) REVERT: D 244 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: D 334 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8481 (mm-30) REVERT: D 374 GLN cc_start: 0.8749 (tp-100) cc_final: 0.8444 (tp-100) REVERT: E 125 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8341 (pm20) REVERT: E 210 ASP cc_start: 0.8370 (t70) cc_final: 0.8149 (t0) REVERT: E 234 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8661 (mt-10) REVERT: E 244 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8251 (mm-30) REVERT: E 321 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8795 (pp) REVERT: E 322 ASP cc_start: 0.8652 (t0) cc_final: 0.8389 (t0) REVERT: E 360 TYR cc_start: 0.8262 (t80) cc_final: 0.7941 (t80) REVERT: E 368 GLU cc_start: 0.8565 (tt0) cc_final: 0.8072 (tm-30) REVERT: F 29 MET cc_start: 0.8663 (mtp) cc_final: 0.8095 (mtp) REVERT: F 155 GLU cc_start: 0.8076 (tt0) cc_final: 0.7685 (tm-30) REVERT: F 172 GLN cc_start: 0.6516 (OUTLIER) cc_final: 0.6071 (mp10) REVERT: F 181 LYS cc_start: 0.8640 (mmtp) cc_final: 0.7783 (tppt) REVERT: F 189 GLN cc_start: 0.8476 (mt0) cc_final: 0.8098 (mt0) REVERT: F 219 MET cc_start: 0.8743 (tpp) cc_final: 0.8356 (tpp) REVERT: F 220 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8431 (tm-30) REVERT: F 341 MET cc_start: 0.3514 (mpt) cc_final: 0.3284 (mpp) REVERT: F 368 GLU cc_start: 0.7485 (pm20) cc_final: 0.7103 (pm20) REVERT: F 416 MET cc_start: 0.2115 (tmm) cc_final: 0.1306 (tmm) REVERT: b 55 GLU cc_start: 0.8111 (pm20) cc_final: 0.7901 (pm20) REVERT: c 34 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8158 (tm-30) REVERT: d 18 LEU cc_start: 0.9217 (tm) cc_final: 0.8898 (pp) REVERT: d 26 LEU cc_start: 0.8779 (mt) cc_final: 0.8422 (mm) REVERT: d 27 THR cc_start: 0.8797 (p) cc_final: 0.8548 (t) REVERT: d 30 LEU cc_start: 0.8284 (mm) cc_final: 0.7912 (mp) REVERT: d 62 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8241 (mt-10) outliers start: 66 outliers final: 28 residues processed: 344 average time/residue: 1.3980 time to fit residues: 546.3984 Evaluate side-chains 324 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 287 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 172 GLN Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain a residue 47 LYS Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain b residue 11 ASP Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 22 HIS Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 70 SER Chi-restraints excluded: chain c residue 80 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 155 optimal weight: 0.7980 chunk 197 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 267 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 223 optimal weight: 0.0470 chunk 141 optimal weight: 0.6980 chunk 138 optimal weight: 0.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN D 292 ASN E 193 GLN c 15 ASN d 15 ASN ** e 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.111801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.073370 restraints weight = 55452.496| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.97 r_work: 0.2911 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23402 Z= 0.118 Angle : 0.607 11.240 31552 Z= 0.287 Chirality : 0.042 0.180 3609 Planarity : 0.004 0.057 4105 Dihedral : 5.083 114.789 3213 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.14 % Allowed : 14.85 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.16), residues: 2896 helix: 2.02 (0.15), residues: 1221 sheet: 0.21 (0.24), residues: 478 loop : 0.66 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 381 HIS 0.007 0.001 HIS d 73 PHE 0.011 0.001 PHE F 62 TYR 0.023 0.001 TYR e 13 ARG 0.015 0.000 ARG e 46 Details of bonding type rmsd hydrogen bonds : bond 0.03173 ( 1103) hydrogen bonds : angle 4.29089 ( 3204) covalent geometry : bond 0.00272 (23402) covalent geometry : angle 0.60666 (31552) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 308 time to evaluate : 2.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8205 (mt-10) REVERT: A 341 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8725 (ppp) REVERT: A 342 GLU cc_start: 0.7910 (pm20) cc_final: 0.7328 (pm20) REVERT: A 415 MET cc_start: 0.9448 (OUTLIER) cc_final: 0.9179 (ppp) REVERT: B 244 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8322 (mm-30) REVERT: C 21 MET cc_start: 0.8617 (mtp) cc_final: 0.8130 (ttm) REVERT: C 186 MET cc_start: 0.9069 (mmm) cc_final: 0.8718 (mtm) REVERT: C 342 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8135 (pt0) REVERT: C 347 ARG cc_start: 0.8627 (tpp80) cc_final: 0.8015 (tpp80) REVERT: D 155 GLU cc_start: 0.8660 (mp0) cc_final: 0.8406 (pm20) REVERT: D 244 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8040 (mp0) REVERT: D 374 GLN cc_start: 0.8708 (tp-100) cc_final: 0.8389 (tp-100) REVERT: E 125 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8373 (pm20) REVERT: E 234 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8612 (mt-10) REVERT: E 244 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8175 (mm-30) REVERT: E 322 ASP cc_start: 0.8633 (t0) cc_final: 0.8344 (t0) REVERT: E 347 ARG cc_start: 0.8968 (ptm-80) cc_final: 0.8430 (tpm170) REVERT: E 360 TYR cc_start: 0.8247 (t80) cc_final: 0.7991 (t80) REVERT: E 368 GLU cc_start: 0.8555 (tt0) cc_final: 0.8031 (tm-30) REVERT: F 1 MET cc_start: 0.6640 (pmm) cc_final: 0.6330 (ptt) REVERT: F 21 MET cc_start: 0.8822 (tmm) cc_final: 0.8374 (tmt) REVERT: F 29 MET cc_start: 0.8657 (mtp) cc_final: 0.7817 (mtp) REVERT: F 33 ASP cc_start: 0.8826 (m-30) cc_final: 0.8209 (OUTLIER) REVERT: F 155 GLU cc_start: 0.8076 (tt0) cc_final: 0.7514 (tm-30) REVERT: F 172 GLN cc_start: 0.6506 (OUTLIER) cc_final: 0.6065 (mp10) REVERT: F 181 LYS cc_start: 0.8669 (mmtp) cc_final: 0.7764 (tppt) REVERT: F 189 GLN cc_start: 0.8464 (mt0) cc_final: 0.7729 (mt0) REVERT: F 193 GLN cc_start: 0.9071 (mm110) cc_final: 0.8855 (pt0) REVERT: F 205 MET cc_start: 0.7064 (mtm) cc_final: 0.6763 (mtm) REVERT: F 219 MET cc_start: 0.8738 (tpp) cc_final: 0.8394 (tpp) REVERT: F 248 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8420 (mm-30) REVERT: F 341 MET cc_start: 0.3561 (mpt) cc_final: 0.3351 (mpp) REVERT: F 368 GLU cc_start: 0.7479 (pm20) cc_final: 0.7089 (pm20) REVERT: b 35 LYS cc_start: 0.9354 (mttt) cc_final: 0.8963 (mmmm) REVERT: b 39 LYS cc_start: 0.8907 (tmmm) cc_final: 0.8700 (tmmt) REVERT: b 55 GLU cc_start: 0.8534 (pm20) cc_final: 0.8220 (pm20) REVERT: c 34 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8184 (tm-30) REVERT: d 18 LEU cc_start: 0.9236 (tm) cc_final: 0.8935 (pp) REVERT: d 26 LEU cc_start: 0.8788 (mt) cc_final: 0.8407 (mm) REVERT: d 27 THR cc_start: 0.8806 (p) cc_final: 0.8548 (t) REVERT: d 30 LEU cc_start: 0.8266 (mm) cc_final: 0.7901 (mp) REVERT: d 62 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8263 (mt-10) REVERT: e 46 ARG cc_start: 0.8281 (mtm110) cc_final: 0.8060 (ttp-110) REVERT: e 64 ARG cc_start: 0.8398 (mtm110) cc_final: 0.8156 (mtm180) outliers start: 54 outliers final: 31 residues processed: 343 average time/residue: 1.4967 time to fit residues: 589.1565 Evaluate side-chains 324 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 287 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 172 GLN Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain a residue 47 LYS Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain b residue 11 ASP Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 22 HIS Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 70 SER Chi-restraints excluded: chain c residue 80 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 0 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 214 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 292 ASN c 15 ASN d 15 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.110467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.072029 restraints weight = 55412.879| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.98 r_work: 0.2892 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23402 Z= 0.163 Angle : 0.632 10.225 31552 Z= 0.299 Chirality : 0.043 0.152 3609 Planarity : 0.004 0.056 4105 Dihedral : 5.059 118.177 3213 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.30 % Allowed : 15.21 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.16), residues: 2896 helix: 2.00 (0.15), residues: 1218 sheet: 0.16 (0.24), residues: 478 loop : 0.63 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 381 HIS 0.008 0.001 HIS d 73 PHE 0.032 0.001 PHE b 71 TYR 0.032 0.002 TYR b 13 ARG 0.012 0.000 ARG b 61 Details of bonding type rmsd hydrogen bonds : bond 0.03387 ( 1103) hydrogen bonds : angle 4.31035 ( 3204) covalent geometry : bond 0.00383 (23402) covalent geometry : angle 0.63150 (31552) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 299 time to evaluate : 2.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8177 (mt-10) REVERT: A 342 GLU cc_start: 0.7966 (pm20) cc_final: 0.7376 (pm20) REVERT: A 390 MET cc_start: 0.8440 (pp-130) cc_final: 0.8222 (pp-130) REVERT: A 415 MET cc_start: 0.9446 (OUTLIER) cc_final: 0.9199 (ppp) REVERT: B 30 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7327 (mtm-85) REVERT: B 244 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8321 (mm-30) REVERT: C 21 MET cc_start: 0.8677 (mtp) cc_final: 0.8184 (ttm) REVERT: C 186 MET cc_start: 0.9085 (mmm) cc_final: 0.8701 (mtm) REVERT: C 342 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8193 (pt0) REVERT: D 155 GLU cc_start: 0.8683 (mp0) cc_final: 0.8415 (pm20) REVERT: D 244 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: D 374 GLN cc_start: 0.8732 (tp-100) cc_final: 0.8358 (tp-100) REVERT: E 125 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8390 (pm20) REVERT: E 234 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8605 (mt-10) REVERT: E 244 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8130 (mm-30) REVERT: E 322 ASP cc_start: 0.8675 (t0) cc_final: 0.8357 (t0) REVERT: E 360 TYR cc_start: 0.8319 (t80) cc_final: 0.8028 (t80) REVERT: E 368 GLU cc_start: 0.8583 (tt0) cc_final: 0.8062 (tm-30) REVERT: F 1 MET cc_start: 0.6606 (pmm) cc_final: 0.6350 (ptt) REVERT: F 21 MET cc_start: 0.8839 (tmm) cc_final: 0.8305 (tmt) REVERT: F 29 MET cc_start: 0.8663 (mtp) cc_final: 0.8091 (mtp) REVERT: F 72 TYR cc_start: 0.8890 (m-10) cc_final: 0.8183 (m-10) REVERT: F 155 GLU cc_start: 0.8066 (tt0) cc_final: 0.7704 (tm-30) REVERT: F 172 GLN cc_start: 0.6572 (OUTLIER) cc_final: 0.6127 (mp10) REVERT: F 181 LYS cc_start: 0.8663 (mmtp) cc_final: 0.7840 (tppt) REVERT: F 189 GLN cc_start: 0.8468 (mt0) cc_final: 0.8110 (mt0) REVERT: F 205 MET cc_start: 0.7086 (mtm) cc_final: 0.6684 (mtm) REVERT: F 219 MET cc_start: 0.8772 (tpp) cc_final: 0.8376 (tpp) REVERT: F 220 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8309 (tm-30) REVERT: F 245 MET cc_start: 0.7454 (ttm) cc_final: 0.7113 (ttp) REVERT: F 341 MET cc_start: 0.3697 (mpt) cc_final: 0.3484 (mpp) REVERT: F 368 GLU cc_start: 0.7510 (pm20) cc_final: 0.7130 (pm20) REVERT: b 15 ASN cc_start: 0.9083 (m-40) cc_final: 0.8627 (m-40) REVERT: b 25 MET cc_start: 0.9151 (mmm) cc_final: 0.8676 (tpp) REVERT: b 35 LYS cc_start: 0.9347 (mttt) cc_final: 0.8947 (mmmm) REVERT: c 17 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7842 (tp30) REVERT: c 34 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8177 (tm-30) REVERT: c 48 ASN cc_start: 0.8933 (m-40) cc_final: 0.8651 (p0) REVERT: d 18 LEU cc_start: 0.9272 (tm) cc_final: 0.8933 (pp) REVERT: d 26 LEU cc_start: 0.8857 (mt) cc_final: 0.8442 (mm) REVERT: d 27 THR cc_start: 0.8785 (p) cc_final: 0.8564 (t) REVERT: d 30 LEU cc_start: 0.8366 (mm) cc_final: 0.7993 (mp) REVERT: d 62 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8297 (mt-10) REVERT: e 46 ARG cc_start: 0.8402 (mtm110) cc_final: 0.8179 (ttp-110) REVERT: e 64 ARG cc_start: 0.8411 (mtm110) cc_final: 0.8143 (mtm180) outliers start: 58 outliers final: 31 residues processed: 339 average time/residue: 1.4829 time to fit residues: 572.4050 Evaluate side-chains 326 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 287 time to evaluate : 2.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 390 MET Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 172 GLN Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain a residue 47 LYS Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain b residue 11 ASP Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 17 GLU Chi-restraints excluded: chain c residue 22 HIS Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 70 SER Chi-restraints excluded: chain c residue 80 VAL Chi-restraints excluded: chain d residue 65 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 3 optimal weight: 2.9990 chunk 253 optimal weight: 30.0000 chunk 22 optimal weight: 8.9990 chunk 248 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 124 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN E 193 GLN c 15 ASN d 15 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.110775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.072541 restraints weight = 55112.125| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.95 r_work: 0.2889 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23402 Z= 0.158 Angle : 0.647 10.981 31552 Z= 0.306 Chirality : 0.043 0.186 3609 Planarity : 0.004 0.056 4105 Dihedral : 5.061 121.620 3213 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.38 % Allowed : 15.61 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.16), residues: 2896 helix: 1.99 (0.15), residues: 1221 sheet: 0.18 (0.24), residues: 478 loop : 0.63 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 381 HIS 0.008 0.001 HIS d 73 PHE 0.010 0.001 PHE c 71 TYR 0.029 0.001 TYR e 13 ARG 0.012 0.000 ARG E 87 Details of bonding type rmsd hydrogen bonds : bond 0.03345 ( 1103) hydrogen bonds : angle 4.28734 ( 3204) covalent geometry : bond 0.00374 (23402) covalent geometry : angle 0.64736 (31552) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 290 time to evaluate : 3.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4582 (pp-130) cc_final: 0.3614 (tmm) REVERT: A 244 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8181 (mt-10) REVERT: A 245 MET cc_start: 0.9041 (tpp) cc_final: 0.8830 (tpt) REVERT: A 341 MET cc_start: 0.8913 (tmm) cc_final: 0.8712 (ppp) REVERT: A 342 GLU cc_start: 0.7988 (pm20) cc_final: 0.7351 (pm20) REVERT: A 390 MET cc_start: 0.8502 (pp-130) cc_final: 0.8236 (pp-130) REVERT: A 415 MET cc_start: 0.9445 (OUTLIER) cc_final: 0.9180 (ppp) REVERT: B 30 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7333 (mtm-85) REVERT: B 244 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8332 (mm-30) REVERT: C 21 MET cc_start: 0.8706 (mtp) cc_final: 0.8242 (ttm) REVERT: C 186 MET cc_start: 0.9080 (mmm) cc_final: 0.8654 (mtm) REVERT: C 342 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8156 (pt0) REVERT: D 155 GLU cc_start: 0.8692 (mp0) cc_final: 0.8412 (pm20) REVERT: D 244 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: D 374 GLN cc_start: 0.8756 (tp-100) cc_final: 0.8384 (tp-100) REVERT: E 125 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8380 (pm20) REVERT: E 234 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8614 (mt-10) REVERT: E 244 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8114 (mm-30) REVERT: E 322 ASP cc_start: 0.8676 (t0) cc_final: 0.8330 (t0) REVERT: E 360 TYR cc_start: 0.8341 (t80) cc_final: 0.8128 (t80) REVERT: E 368 GLU cc_start: 0.8562 (tt0) cc_final: 0.8053 (tm-30) REVERT: E 384 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.7654 (tpt90) REVERT: F 1 MET cc_start: 0.6601 (pmm) cc_final: 0.6370 (ptt) REVERT: F 21 MET cc_start: 0.8859 (tmm) cc_final: 0.8290 (tmt) REVERT: F 29 MET cc_start: 0.8646 (mtp) cc_final: 0.8067 (mtp) REVERT: F 72 TYR cc_start: 0.8846 (m-10) cc_final: 0.8519 (m-10) REVERT: F 155 GLU cc_start: 0.8085 (tt0) cc_final: 0.7499 (tm-30) REVERT: F 162 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8723 (pt) REVERT: F 172 GLN cc_start: 0.6513 (OUTLIER) cc_final: 0.6083 (mp10) REVERT: F 181 LYS cc_start: 0.8670 (mmtp) cc_final: 0.7824 (tppt) REVERT: F 189 GLN cc_start: 0.8450 (mt0) cc_final: 0.7735 (mt0) REVERT: F 205 MET cc_start: 0.6878 (mtm) cc_final: 0.6367 (mtm) REVERT: F 219 MET cc_start: 0.8748 (tpp) cc_final: 0.8364 (tpp) REVERT: F 220 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8290 (tm-30) REVERT: F 341 MET cc_start: 0.3569 (mpt) cc_final: 0.3327 (mpp) REVERT: F 368 GLU cc_start: 0.7513 (pm20) cc_final: 0.7172 (pm20) REVERT: b 29 GLU cc_start: 0.8209 (mp0) cc_final: 0.7112 (mp0) REVERT: b 35 LYS cc_start: 0.9311 (mttt) cc_final: 0.8904 (mmmm) REVERT: b 39 LYS cc_start: 0.8896 (tmmm) cc_final: 0.8624 (tmmt) REVERT: c 34 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8086 (tm-30) REVERT: c 49 VAL cc_start: 0.8803 (t) cc_final: 0.8543 (p) REVERT: d 18 LEU cc_start: 0.9264 (tm) cc_final: 0.8914 (pp) REVERT: d 26 LEU cc_start: 0.8821 (mt) cc_final: 0.8569 (mp) REVERT: d 27 THR cc_start: 0.8733 (p) cc_final: 0.8489 (t) REVERT: d 30 LEU cc_start: 0.8261 (mm) cc_final: 0.7889 (mp) REVERT: d 62 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8230 (mt-10) REVERT: e 46 ARG cc_start: 0.8442 (mtm110) cc_final: 0.8207 (ttp-110) outliers start: 60 outliers final: 31 residues processed: 331 average time/residue: 1.8327 time to fit residues: 691.4172 Evaluate side-chains 322 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 282 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 384 ARG Chi-restraints excluded: chain E residue 390 MET Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 172 GLN Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain a residue 47 LYS Chi-restraints excluded: chain a residue 68 ILE Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain b residue 11 ASP Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 22 HIS Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 70 SER Chi-restraints excluded: chain c residue 80 VAL Chi-restraints excluded: chain d residue 65 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 163 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 270 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 264 optimal weight: 5.9990 chunk 199 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 281 optimal weight: 20.0000 chunk 166 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 292 ASN b 9 ASN d 15 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.109131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.070959 restraints weight = 54773.490| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.93 r_work: 0.2867 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 23402 Z= 0.230 Angle : 0.684 14.623 31552 Z= 0.326 Chirality : 0.044 0.186 3609 Planarity : 0.004 0.062 4105 Dihedral : 5.159 122.138 3213 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.18 % Allowed : 15.77 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.16), residues: 2896 helix: 1.86 (0.15), residues: 1221 sheet: 0.12 (0.24), residues: 478 loop : 0.57 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 381 HIS 0.007 0.001 HIS d 73 PHE 0.033 0.001 PHE b 71 TYR 0.032 0.002 TYR e 13 ARG 0.014 0.001 ARG b 61 Details of bonding type rmsd hydrogen bonds : bond 0.03760 ( 1103) hydrogen bonds : angle 4.41577 ( 3204) covalent geometry : bond 0.00543 (23402) covalent geometry : angle 0.68401 (31552) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 287 time to evaluate : 2.883 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 1 MET cc_start: 0.4551 (OUTLIER) cc_final: 0.3721 (ttp) REVERT: A 58 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8065 (mm) REVERT: A 219 MET cc_start: 0.9095 (tpp) cc_final: 0.8828 (tpp) REVERT: A 244 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8176 (mt-10) REVERT: A 245 MET cc_start: 0.9044 (tpp) cc_final: 0.8776 (tpt) REVERT: A 342 GLU cc_start: 0.8038 (pm20) cc_final: 0.7441 (pm20) REVERT: A 390 MET cc_start: 0.8549 (pp-130) cc_final: 0.8267 (pp-130) REVERT: A 415 MET cc_start: 0.9439 (OUTLIER) cc_final: 0.9220 (ppp) REVERT: B 30 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7391 (mtm-85) REVERT: B 244 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8347 (mm-30) REVERT: C 21 MET cc_start: 0.8767 (mtp) cc_final: 0.8273 (ttm) REVERT: C 186 MET cc_start: 0.9075 (mmm) cc_final: 0.8656 (mtm) REVERT: C 342 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8200 (pt0) REVERT: D 244 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: D 334 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8493 (mp0) REVERT: D 374 GLN cc_start: 0.8788 (tp-100) cc_final: 0.8427 (tp-100) REVERT: E 21 MET cc_start: 0.8656 (ttm) cc_final: 0.8142 (ttt) REVERT: E 125 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8376 (pm20) REVERT: E 234 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8570 (mt-10) REVERT: E 244 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8224 (mm-30) REVERT: E 322 ASP cc_start: 0.8681 (t0) cc_final: 0.8319 (t0) REVERT: E 360 TYR cc_start: 0.8404 (t80) cc_final: 0.8119 (t80) REVERT: E 368 GLU cc_start: 0.8596 (tt0) cc_final: 0.8083 (tm-30) REVERT: E 384 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.7678 (tpt90) REVERT: E 405 MET cc_start: 0.9165 (pmm) cc_final: 0.8933 (pmm) REVERT: F 1 MET cc_start: 0.6669 (pmm) cc_final: 0.6429 (ptt) REVERT: F 21 MET cc_start: 0.8876 (tmm) cc_final: 0.8340 (tmt) REVERT: F 29 MET cc_start: 0.8650 (mtp) cc_final: 0.8079 (mtp) REVERT: F 172 GLN cc_start: 0.6602 (OUTLIER) cc_final: 0.6150 (mp10) REVERT: F 181 LYS cc_start: 0.8687 (mmtp) cc_final: 0.7835 (tppt) REVERT: F 189 GLN cc_start: 0.8047 (mt0) cc_final: 0.7102 (mt0) REVERT: F 219 MET cc_start: 0.8766 (tpp) cc_final: 0.8378 (tpp) REVERT: F 220 GLN cc_start: 0.8611 (mm-40) cc_final: 0.8318 (tm-30) REVERT: F 341 MET cc_start: 0.3714 (mpt) cc_final: 0.3476 (mpp) REVERT: F 368 GLU cc_start: 0.7516 (pm20) cc_final: 0.7123 (pm20) REVERT: F 415 MET cc_start: 0.7066 (pmm) cc_final: 0.6640 (pmm) REVERT: b 25 MET cc_start: 0.9150 (mmm) cc_final: 0.8670 (tpp) REVERT: b 39 LYS cc_start: 0.8879 (tmmm) cc_final: 0.8540 (tmmt) REVERT: c 34 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8085 (tm-30) REVERT: d 18 LEU cc_start: 0.9280 (tm) cc_final: 0.8924 (pp) REVERT: d 25 MET cc_start: 0.8069 (mmm) cc_final: 0.7858 (tpp) REVERT: d 27 THR cc_start: 0.8727 (p) cc_final: 0.8486 (t) REVERT: d 62 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8183 (mt-10) REVERT: e 46 ARG cc_start: 0.8460 (mtm110) cc_final: 0.8197 (ttp-110) REVERT: e 64 ARG cc_start: 0.8323 (mtm110) cc_final: 0.7777 (mtm110) outliers start: 55 outliers final: 31 residues processed: 325 average time/residue: 1.5111 time to fit residues: 561.4746 Evaluate side-chains 322 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 281 time to evaluate : 3.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 384 ARG Chi-restraints excluded: chain E residue 390 MET Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 172 GLN Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain a residue 47 LYS Chi-restraints excluded: chain a residue 68 ILE Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 22 HIS Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 70 SER Chi-restraints excluded: chain c residue 80 VAL Chi-restraints excluded: chain d residue 11 ASP Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain e residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 261 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 239 optimal weight: 0.0370 chunk 150 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 145 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 292 ASN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 9 ASN d 15 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.110569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.072522 restraints weight = 55001.090| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.96 r_work: 0.2903 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23402 Z= 0.136 Angle : 0.676 13.109 31552 Z= 0.319 Chirality : 0.043 0.184 3609 Planarity : 0.004 0.066 4105 Dihedral : 5.092 120.578 3213 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.87 % Allowed : 16.28 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.16), residues: 2896 helix: 1.92 (0.15), residues: 1221 sheet: 0.17 (0.24), residues: 478 loop : 0.60 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 381 HIS 0.005 0.000 HIS d 73 PHE 0.010 0.001 PHE c 71 TYR 0.033 0.002 TYR e 13 ARG 0.014 0.000 ARG c 46 Details of bonding type rmsd hydrogen bonds : bond 0.03212 ( 1103) hydrogen bonds : angle 4.32099 ( 3204) covalent geometry : bond 0.00319 (23402) covalent geometry : angle 0.67628 (31552) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 296 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4526 (OUTLIER) cc_final: 0.3688 (ttp) REVERT: A 58 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8068 (mm) REVERT: A 244 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8167 (mt-10) REVERT: A 341 MET cc_start: 0.8919 (tmm) cc_final: 0.8711 (ppp) REVERT: A 342 GLU cc_start: 0.7992 (pm20) cc_final: 0.7348 (pm20) REVERT: A 390 MET cc_start: 0.8534 (pp-130) cc_final: 0.8247 (pp-130) REVERT: A 415 MET cc_start: 0.9434 (OUTLIER) cc_final: 0.9210 (ppp) REVERT: B 30 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7396 (mtm-85) REVERT: B 244 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8320 (mm-30) REVERT: C 21 MET cc_start: 0.8690 (mtp) cc_final: 0.8240 (ttm) REVERT: C 186 MET cc_start: 0.9072 (mmm) cc_final: 0.8648 (mtm) REVERT: C 341 MET cc_start: 0.9140 (ttp) cc_final: 0.8804 (ppp) REVERT: C 342 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8186 (pt0) REVERT: D 244 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7786 (mp0) REVERT: D 334 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8445 (mp0) REVERT: D 374 GLN cc_start: 0.8720 (tp-100) cc_final: 0.8337 (tp-100) REVERT: E 125 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8420 (pm20) REVERT: E 234 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8593 (mt-10) REVERT: E 244 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8125 (mm-30) REVERT: E 322 ASP cc_start: 0.8676 (t0) cc_final: 0.8308 (t0) REVERT: E 334 GLU cc_start: 0.9233 (OUTLIER) cc_final: 0.8759 (mp0) REVERT: E 347 ARG cc_start: 0.8947 (ptm-80) cc_final: 0.8440 (tpm170) REVERT: E 360 TYR cc_start: 0.8364 (t80) cc_final: 0.8118 (t80) REVERT: E 368 GLU cc_start: 0.8567 (tt0) cc_final: 0.8054 (tm-30) REVERT: E 384 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.7702 (tpt90) REVERT: E 405 MET cc_start: 0.9164 (pmm) cc_final: 0.8865 (pmm) REVERT: F 1 MET cc_start: 0.6558 (pmm) cc_final: 0.6354 (ptt) REVERT: F 21 MET cc_start: 0.8887 (tmm) cc_final: 0.8350 (tmt) REVERT: F 29 MET cc_start: 0.8640 (mtp) cc_final: 0.8074 (mtp) REVERT: F 155 GLU cc_start: 0.8584 (tt0) cc_final: 0.7972 (tm-30) REVERT: F 172 GLN cc_start: 0.6534 (OUTLIER) cc_final: 0.6077 (mp10) REVERT: F 181 LYS cc_start: 0.8678 (mmtp) cc_final: 0.7817 (tppt) REVERT: F 189 GLN cc_start: 0.7839 (mt0) cc_final: 0.7109 (mt0) REVERT: F 219 MET cc_start: 0.8769 (tpp) cc_final: 0.8382 (tpp) REVERT: F 220 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8319 (tm-30) REVERT: F 341 MET cc_start: 0.3819 (mpt) cc_final: 0.3580 (mpp) REVERT: F 368 GLU cc_start: 0.7552 (pm20) cc_final: 0.7180 (pm20) REVERT: F 415 MET cc_start: 0.7177 (pmm) cc_final: 0.6846 (pmm) REVERT: b 25 MET cc_start: 0.9195 (mmm) cc_final: 0.8764 (tpp) REVERT: b 35 LYS cc_start: 0.9305 (mttt) cc_final: 0.9079 (mptt) REVERT: b 39 LYS cc_start: 0.8873 (tmmm) cc_final: 0.8539 (tmmt) REVERT: c 34 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8121 (tm-30) REVERT: d 18 LEU cc_start: 0.9276 (tm) cc_final: 0.8940 (pp) REVERT: d 27 THR cc_start: 0.8793 (p) cc_final: 0.8575 (t) REVERT: d 30 LEU cc_start: 0.8176 (mm) cc_final: 0.7815 (mp) REVERT: d 41 SER cc_start: 0.8783 (t) cc_final: 0.8493 (p) REVERT: e 46 ARG cc_start: 0.8484 (mtm110) cc_final: 0.8224 (ttp-110) REVERT: e 64 ARG cc_start: 0.8309 (mtm110) cc_final: 0.7756 (mtm110) outliers start: 47 outliers final: 27 residues processed: 329 average time/residue: 1.5243 time to fit residues: 568.8400 Evaluate side-chains 322 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 284 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 384 ARG Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 172 GLN Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain a residue 47 LYS Chi-restraints excluded: chain a residue 68 ILE Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 22 HIS Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 70 SER Chi-restraints excluded: chain c residue 80 VAL Chi-restraints excluded: chain d residue 11 ASP Chi-restraints excluded: chain e residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 237 optimal weight: 0.0050 chunk 212 optimal weight: 0.0170 chunk 63 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 139 optimal weight: 0.0000 chunk 179 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 35 optimal weight: 0.0370 chunk 205 optimal weight: 9.9990 chunk 225 optimal weight: 10.0000 chunk 117 optimal weight: 0.0040 overall best weight: 0.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 85 GLN D 292 ASN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 GLN F 190 ASN F 193 GLN b 9 ASN d 15 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.112210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.074460 restraints weight = 54508.115| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.95 r_work: 0.2948 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23402 Z= 0.114 Angle : 0.688 12.976 31552 Z= 0.324 Chirality : 0.043 0.227 3609 Planarity : 0.004 0.060 4105 Dihedral : 4.984 119.131 3213 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.59 % Allowed : 16.68 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.16), residues: 2896 helix: 1.97 (0.15), residues: 1221 sheet: 0.26 (0.23), residues: 500 loop : 0.61 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 381 HIS 0.004 0.000 HIS d 73 PHE 0.036 0.001 PHE b 71 TYR 0.037 0.001 TYR e 13 ARG 0.015 0.000 ARG c 46 Details of bonding type rmsd hydrogen bonds : bond 0.02823 ( 1103) hydrogen bonds : angle 4.26854 ( 3204) covalent geometry : bond 0.00256 (23402) covalent geometry : angle 0.68774 (31552) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20154.84 seconds wall clock time: 350 minutes 56.44 seconds (21056.44 seconds total)