Starting phenix.real_space_refine on Tue Jul 23 16:54:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptm_17874/07_2024/8ptm_17874_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptm_17874/07_2024/8ptm_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptm_17874/07_2024/8ptm_17874.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptm_17874/07_2024/8ptm_17874.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptm_17874/07_2024/8ptm_17874_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptm_17874/07_2024/8ptm_17874_neut.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 Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 13.04, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 8.40 Conformation dependent library (CDL) restraints added in 3.9 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: 3.23 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: 8.20 Time building geometry restraints manager: 9.15 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: 100.19 - 107.37: 748 107.37 - 114.54: 14141 114.54 - 121.72: 11531 121.72 - 128.90: 5039 128.90 - 136.08: 93 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 2.440 nonbonded pdb=" OG1 THR F 231 " pdb=" OD1 ASP F 233 " model vdw 2.226 2.440 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 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: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 60.720 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.030 ------------------------------------------------------------------------------- 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= 0.171 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 *********************** 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 fitting. rotamer outliers: 43 poor density : 399 time to evaluate : 2.477 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: 1.4571 time to fit residues: 716.3956 Evaluate side-chains 320 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 300 time to evaluate : 2.557 ------------------------------------------------------------------------------- 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: 6.9990 chunk 216 optimal weight: 10.0000 chunk 120 optimal weight: 0.0670 chunk 74 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 224 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 259 optimal weight: 9.9990 overall best weight: 1.9524 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN C 2 ASN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS D 8 ASN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN D 292 ASN D 374 GLN F 378 GLN a 73 HIS d 9 ASN d 15 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 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 0.045 23402 Z= 0.320 Angle : 0.607 10.238 31552 Z= 0.301 Chirality : 0.043 0.205 3609 Planarity : 0.004 0.043 4105 Dihedral : 5.903 129.702 3229 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.78 % Allowed : 10.84 % Favored : 86.38 % 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: 1.84 (0.15), residues: 1215 sheet: 0.35 (0.24), residues: 494 loop : 0.76 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 381 HIS 0.006 0.001 HIS F 256 PHE 0.012 0.001 PHE c 71 TYR 0.022 0.002 TYR b 13 ARG 0.010 0.001 ARG A 212 *********************** 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 414 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 344 time to evaluate : 2.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8548 (mp0) REVERT: A 342 GLU cc_start: 0.7884 (pm20) cc_final: 0.7346 (pm20) REVERT: A 415 MET cc_start: 0.9406 (pp-130) cc_final: 0.9127 (ppp) REVERT: B 30 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7381 (mtm-85) REVERT: B 244 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8150 (mm-30) REVERT: B 333 GLU cc_start: 0.8920 (tt0) cc_final: 0.8688 (tt0) REVERT: C 186 MET cc_start: 0.8994 (mmm) cc_final: 0.8653 (mtm) REVERT: C 342 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7985 (pt0) REVERT: C 362 ARG cc_start: 0.9256 (mmm-85) cc_final: 0.9006 (mmm-85) REVERT: D 147 MET cc_start: 0.9421 (OUTLIER) cc_final: 0.8759 (mmp) REVERT: D 244 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8118 (mp0) REVERT: D 333 GLU cc_start: 0.8807 (tp30) cc_final: 0.8450 (tp30) REVERT: D 334 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8246 (mp0) REVERT: D 374 GLN cc_start: 0.8681 (tp40) cc_final: 0.8246 (tp-100) REVERT: D 397 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8558 (mt-10) REVERT: E 210 ASP cc_start: 0.8541 (t70) cc_final: 0.8304 (t0) REVERT: E 244 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8001 (mm-30) REVERT: E 334 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8545 (OUTLIER) REVERT: E 360 TYR cc_start: 0.8459 (t80) cc_final: 0.8191 (t80) REVERT: E 368 GLU cc_start: 0.8528 (tt0) cc_final: 0.8061 (tm-30) REVERT: E 394 ASP cc_start: 0.9183 (m-30) cc_final: 0.8819 (p0) REVERT: F 29 MET cc_start: 0.8707 (mtp) cc_final: 0.8151 (mtp) REVERT: F 41 GLN cc_start: 0.8889 (tp40) cc_final: 0.8542 (pp30) REVERT: F 80 TYR cc_start: 0.8316 (t80) cc_final: 0.8062 (t80) REVERT: F 155 GLU cc_start: 0.7890 (tt0) cc_final: 0.7575 (tm-30) REVERT: F 172 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.6608 (mp10) REVERT: F 181 LYS cc_start: 0.8799 (mmtp) cc_final: 0.8047 (tppt) REVERT: F 189 GLN cc_start: 0.8427 (mt0) cc_final: 0.8085 (mt0) REVERT: F 219 MET cc_start: 0.8775 (tpp) cc_final: 0.8375 (tpp) REVERT: F 341 MET cc_start: 0.3983 (mpt) cc_final: 0.3679 (mpp) REVERT: F 368 GLU cc_start: 0.7378 (pm20) cc_final: 0.7061 (pm20) REVERT: F 396 MET cc_start: 0.8248 (mmt) cc_final: 0.7924 (mmm) REVERT: F 398 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.7077 (t80) REVERT: F 415 MET cc_start: 0.6680 (OUTLIER) cc_final: 0.6471 (pmt) REVERT: b 6 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8504 (mm-40) REVERT: b 15 ASN cc_start: 0.9109 (m-40) cc_final: 0.8793 (m-40) REVERT: b 25 MET cc_start: 0.8945 (mmm) cc_final: 0.8686 (mpp) REVERT: b 39 LYS cc_start: 0.9007 (ttpp) cc_final: 0.8660 (tmmm) REVERT: b 46 ARG cc_start: 0.8648 (mtm-85) cc_final: 0.8347 (mtm-85) REVERT: c 34 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8372 (tm-30) REVERT: c 73 HIS cc_start: 0.8546 (t70) cc_final: 0.7981 (t70) REVERT: d 27 THR cc_start: 0.8982 (p) cc_final: 0.8713 (t) REVERT: d 30 LEU cc_start: 0.8344 (mm) cc_final: 0.8018 (mp) REVERT: e 46 ARG cc_start: 0.8623 (mtm110) cc_final: 0.8288 (mtm110) outliers start: 70 outliers final: 28 residues processed: 380 average time/residue: 1.4122 time to fit residues: 609.2451 Evaluate side-chains 325 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 289 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 147 MET 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 137 THR Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 233 ASP 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 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 27 THR 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 b residue 82 SER Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 63 LEU 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 144 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 216 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 260 optimal weight: 4.9990 chunk 281 optimal weight: 10.0000 chunk 231 optimal weight: 7.9990 chunk 258 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 208 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN D 374 GLN b 9 ASN c 15 ASN d 9 ASN d 15 ASN e 15 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 23402 Z= 0.488 Angle : 0.653 9.630 31552 Z= 0.322 Chirality : 0.045 0.209 3609 Planarity : 0.004 0.055 4105 Dihedral : 5.879 118.532 3220 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.85 % Allowed : 12.43 % Favored : 83.72 % 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: 1.34 (0.16), residues: 2896 helix: 1.63 (0.15), residues: 1224 sheet: 0.21 (0.24), residues: 498 loop : 0.58 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 381 HIS 0.006 0.001 HIS d 73 PHE 0.013 0.002 PHE E 398 TYR 0.025 0.002 TYR e 13 ARG 0.008 0.001 ARG D 109 *********************** 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 409 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 312 time to evaluate : 2.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8566 (mp0) REVERT: A 342 GLU cc_start: 0.7921 (pm20) cc_final: 0.7382 (pm20) REVERT: A 415 MET cc_start: 0.9431 (OUTLIER) cc_final: 0.9169 (ppp) REVERT: B 30 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7444 (mtm-85) REVERT: B 244 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8179 (mm-30) REVERT: B 289 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8245 (m) REVERT: C 147 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.8144 (mmt) REVERT: C 186 MET cc_start: 0.9022 (mmm) cc_final: 0.8533 (mtm) REVERT: C 342 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8048 (pt0) REVERT: D 244 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: D 334 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8299 (mm-30) REVERT: D 374 GLN cc_start: 0.8684 (tp-100) cc_final: 0.8268 (tp-100) REVERT: D 397 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8565 (mt-10) REVERT: E 210 ASP cc_start: 0.8528 (t70) cc_final: 0.8262 (t0) REVERT: E 234 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8747 (mt-10) REVERT: E 244 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8018 (mm-30) REVERT: E 334 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8568 (OUTLIER) REVERT: E 360 TYR cc_start: 0.8490 (t80) cc_final: 0.8199 (t80) REVERT: E 368 GLU cc_start: 0.8525 (tt0) cc_final: 0.8041 (tm-30) REVERT: F 29 MET cc_start: 0.8682 (mtp) cc_final: 0.8269 (mtp) REVERT: F 80 TYR cc_start: 0.8280 (t80) cc_final: 0.8050 (t80) REVERT: F 155 GLU cc_start: 0.7983 (tt0) cc_final: 0.7690 (tm-30) REVERT: F 172 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6667 (mp10) REVERT: F 181 LYS cc_start: 0.8819 (mmtp) cc_final: 0.8056 (tppt) REVERT: F 189 GLN cc_start: 0.8448 (mt0) cc_final: 0.8169 (mt0) REVERT: F 219 MET cc_start: 0.8799 (tpp) cc_final: 0.8533 (tpp) REVERT: F 245 MET cc_start: 0.7482 (mtp) cc_final: 0.7192 (ttp) REVERT: F 341 MET cc_start: 0.4191 (mpt) cc_final: 0.3811 (mpp) REVERT: F 368 GLU cc_start: 0.7361 (pm20) cc_final: 0.7032 (pm20) REVERT: F 398 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7272 (t80) REVERT: F 415 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.6704 (pmt) REVERT: b 15 ASN cc_start: 0.9181 (m-40) cc_final: 0.8860 (m-40) REVERT: b 35 LYS cc_start: 0.9226 (mptt) cc_final: 0.8978 (mppt) REVERT: b 39 LYS cc_start: 0.9000 (ttpp) cc_final: 0.8644 (tmmm) REVERT: b 46 ARG cc_start: 0.8628 (mtm-85) cc_final: 0.8403 (mtm-85) REVERT: c 34 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8339 (tm-30) REVERT: d 18 LEU cc_start: 0.9232 (tm) cc_final: 0.8973 (pp) REVERT: d 26 LEU cc_start: 0.8920 (mt) cc_final: 0.8690 (mt) REVERT: d 27 THR cc_start: 0.8939 (p) cc_final: 0.8665 (t) REVERT: d 30 LEU cc_start: 0.8495 (mm) cc_final: 0.8181 (mp) REVERT: e 46 ARG cc_start: 0.8599 (mtm110) cc_final: 0.8388 (mtm110) outliers start: 97 outliers final: 44 residues processed: 366 average time/residue: 1.3857 time to fit residues: 578.0208 Evaluate side-chains 351 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 296 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 1 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 285 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 60 ASP 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 D residue 394 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 52 ASP 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 228 VAL Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 259 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 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 27 THR Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 69 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 257 optimal weight: 20.0000 chunk 195 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 chunk 261 optimal weight: 7.9990 chunk 276 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23402 Z= 0.237 Angle : 0.583 12.414 31552 Z= 0.279 Chirality : 0.042 0.193 3609 Planarity : 0.004 0.052 4105 Dihedral : 5.539 113.490 3220 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.49 % Allowed : 13.70 % Favored : 82.80 % 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: 1.86 (0.15), residues: 1218 sheet: 0.30 (0.24), residues: 482 loop : 0.60 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 381 HIS 0.008 0.001 HIS d 73 PHE 0.018 0.001 PHE b 71 TYR 0.024 0.001 TYR e 13 ARG 0.009 0.000 ARG D 109 *********************** 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 398 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 310 time to evaluate : 2.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.9202 (tpp) cc_final: 0.8960 (tpp) REVERT: A 342 GLU cc_start: 0.7914 (pm20) cc_final: 0.7342 (pm20) REVERT: A 415 MET cc_start: 0.9457 (OUTLIER) cc_final: 0.9210 (ppp) REVERT: B 30 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7399 (mtm-85) REVERT: B 244 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8167 (mm-30) REVERT: C 186 MET cc_start: 0.8992 (mmm) cc_final: 0.8479 (mtm) REVERT: C 342 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7981 (pt0) REVERT: D 155 GLU cc_start: 0.8493 (mp0) cc_final: 0.8279 (pm20) REVERT: D 244 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7734 (mp0) REVERT: D 374 GLN cc_start: 0.8575 (tp-100) cc_final: 0.8079 (tp-100) REVERT: D 397 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8602 (mt-10) REVERT: E 210 ASP cc_start: 0.8457 (t70) cc_final: 0.8210 (t0) REVERT: E 234 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8678 (mt-10) REVERT: E 244 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7942 (mm-30) REVERT: E 334 GLU cc_start: 0.8806 (mp0) cc_final: 0.8475 (mp0) REVERT: E 360 TYR cc_start: 0.8410 (t80) cc_final: 0.8143 (t80) REVERT: E 368 GLU cc_start: 0.8543 (tt0) cc_final: 0.8063 (tm-30) REVERT: F 21 MET cc_start: 0.8806 (tmm) cc_final: 0.8246 (tmt) REVERT: F 29 MET cc_start: 0.8667 (mtp) cc_final: 0.8075 (mtp) REVERT: F 80 TYR cc_start: 0.8158 (t80) cc_final: 0.7932 (t80) REVERT: F 155 GLU cc_start: 0.7941 (tt0) cc_final: 0.7530 (tm-30) REVERT: F 172 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.6528 (mp10) REVERT: F 181 LYS cc_start: 0.8817 (mmtp) cc_final: 0.8112 (mmmt) REVERT: F 189 GLN cc_start: 0.8450 (mt0) cc_final: 0.8116 (mt0) REVERT: F 219 MET cc_start: 0.8779 (tpp) cc_final: 0.8403 (tpp) REVERT: F 341 MET cc_start: 0.4002 (mpt) cc_final: 0.3598 (mpp) REVERT: F 368 GLU cc_start: 0.7331 (pm20) cc_final: 0.6985 (pm20) REVERT: F 396 MET cc_start: 0.7863 (mmm) cc_final: 0.7515 (mmm) REVERT: F 415 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6739 (pmt) REVERT: b 15 ASN cc_start: 0.9218 (m-40) cc_final: 0.8861 (m-40) REVERT: b 25 MET cc_start: 0.8886 (mmm) cc_final: 0.8594 (mmm) REVERT: b 39 LYS cc_start: 0.9022 (ttpp) cc_final: 0.8716 (tmmm) REVERT: b 46 ARG cc_start: 0.8612 (mtm-85) cc_final: 0.8349 (mtm-85) REVERT: c 34 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8366 (tm-30) REVERT: c 73 HIS cc_start: 0.8363 (t70) cc_final: 0.7639 (t70) REVERT: d 18 LEU cc_start: 0.9264 (tm) cc_final: 0.8929 (pp) REVERT: d 26 LEU cc_start: 0.8946 (mt) cc_final: 0.8563 (mm) REVERT: d 27 THR cc_start: 0.8965 (p) cc_final: 0.8696 (t) REVERT: d 30 LEU cc_start: 0.8646 (mm) cc_final: 0.8277 (mp) REVERT: e 46 ARG cc_start: 0.8613 (mtm110) cc_final: 0.8409 (mtm110) outliers start: 88 outliers final: 38 residues processed: 372 average time/residue: 1.3071 time to fit residues: 557.0954 Evaluate side-chains 335 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 290 time to evaluate : 2.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 292 ASN 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 26 LEU Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 60 ASP 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 394 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 69 ASP 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 234 GLU Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 365 THR 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 79 VAL Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 45 SER Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 80 VAL Chi-restraints excluded: chain e residue 52 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 230 optimal weight: 9.9990 chunk 156 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 205 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 235 optimal weight: 6.9990 chunk 191 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 141 optimal weight: 0.6980 chunk 248 optimal weight: 0.0020 chunk 69 optimal weight: 8.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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 ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN E 193 GLN b 9 ASN c 15 ASN d 15 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23402 Z= 0.165 Angle : 0.569 13.024 31552 Z= 0.270 Chirality : 0.042 0.198 3609 Planarity : 0.004 0.056 4105 Dihedral : 5.249 110.965 3220 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.02 % Allowed : 14.81 % Favored : 82.17 % 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: 2.01 (0.15), residues: 1225 sheet: 0.29 (0.24), residues: 474 loop : 0.63 (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 0.020 0.001 PHE b 71 TYR 0.023 0.001 TYR e 13 ARG 0.009 0.000 ARG D 299 *********************** 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 375 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 299 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.7905 (pm20) cc_final: 0.7368 (pm20) REVERT: A 415 MET cc_start: 0.9464 (OUTLIER) cc_final: 0.9234 (ppp) REVERT: B 244 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8202 (mm-30) REVERT: C 186 MET cc_start: 0.8988 (mmm) cc_final: 0.8477 (mtm) REVERT: C 342 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8007 (pt0) REVERT: D 155 GLU cc_start: 0.8461 (mp0) cc_final: 0.8238 (pm20) REVERT: D 244 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: D 374 GLN cc_start: 0.8516 (tp-100) cc_final: 0.8006 (tp-100) REVERT: E 21 MET cc_start: 0.8718 (ttm) cc_final: 0.8197 (ttt) REVERT: E 210 ASP cc_start: 0.8387 (t70) cc_final: 0.8168 (t0) REVERT: E 234 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8646 (mt-10) REVERT: E 244 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7814 (mm-30) REVERT: E 368 GLU cc_start: 0.8524 (tt0) cc_final: 0.7994 (tm-30) REVERT: E 384 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8183 (tpt90) REVERT: F 21 MET cc_start: 0.8776 (tmm) cc_final: 0.8182 (tmt) REVERT: F 29 MET cc_start: 0.8668 (mtp) cc_final: 0.8080 (mtp) REVERT: F 80 TYR cc_start: 0.8153 (t80) cc_final: 0.7936 (t80) REVERT: F 172 GLN cc_start: 0.6960 (OUTLIER) cc_final: 0.6400 (mp10) REVERT: F 181 LYS cc_start: 0.8822 (mmtp) cc_final: 0.8057 (tppt) REVERT: F 189 GLN cc_start: 0.8449 (mt0) cc_final: 0.7793 (mt0) REVERT: F 219 MET cc_start: 0.8769 (tpp) cc_final: 0.8373 (tpp) REVERT: F 341 MET cc_start: 0.4058 (mpt) cc_final: 0.3656 (mpp) REVERT: F 368 GLU cc_start: 0.7402 (pm20) cc_final: 0.7088 (pm20) REVERT: F 396 MET cc_start: 0.7961 (mmm) cc_final: 0.7741 (mmm) REVERT: F 415 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6732 (pmt) REVERT: b 25 MET cc_start: 0.8866 (mmm) cc_final: 0.8558 (mmm) REVERT: b 39 LYS cc_start: 0.9030 (ttpp) cc_final: 0.8746 (tmmm) REVERT: b 46 ARG cc_start: 0.8618 (mtm-85) cc_final: 0.8310 (mtm-85) REVERT: c 17 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7895 (tp30) REVERT: c 34 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8428 (tm-30) REVERT: d 27 THR cc_start: 0.8994 (p) cc_final: 0.8761 (t) REVERT: e 46 ARG cc_start: 0.8617 (mtm110) cc_final: 0.8392 (mtm110) REVERT: e 64 ARG cc_start: 0.7865 (mtm180) cc_final: 0.7032 (ptp-170) outliers start: 76 outliers final: 37 residues processed: 347 average time/residue: 1.3868 time to fit residues: 547.8087 Evaluate side-chains 336 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 291 time to evaluate : 2.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 233 ASP 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 394 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 69 ASP 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 234 GLU Chi-restraints excluded: chain E residue 259 ASP 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 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 27 THR 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 45 SER 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 93 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 276 optimal weight: 0.0970 chunk 229 optimal weight: 5.9990 chunk 128 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN b 9 ASN d 15 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2225 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= 0.255 Angle : 0.596 8.911 31552 Z= 0.282 Chirality : 0.042 0.194 3609 Planarity : 0.004 0.058 4105 Dihedral : 5.179 110.953 3219 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.18 % Allowed : 15.29 % Favored : 81.53 % 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: 2.03 (0.15), residues: 1223 sheet: 0.27 (0.24), residues: 474 loop : 0.60 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 381 HIS 0.006 0.001 HIS d 73 PHE 0.010 0.001 PHE E 398 TYR 0.027 0.001 TYR e 13 ARG 0.010 0.000 ARG c 46 *********************** 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 379 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 299 time to evaluate : 2.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8123 (mt-10) REVERT: A 342 GLU cc_start: 0.7952 (pm20) cc_final: 0.7416 (pm20) REVERT: A 390 MET cc_start: 0.8428 (ppp) cc_final: 0.8228 (ppp) REVERT: A 415 MET cc_start: 0.9466 (OUTLIER) cc_final: 0.9214 (ppp) REVERT: B 25 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8509 (t0) REVERT: B 30 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7333 (mtm-85) REVERT: B 244 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8196 (mm-30) REVERT: C 21 MET cc_start: 0.8708 (mtp) cc_final: 0.8195 (ttm) REVERT: C 186 MET cc_start: 0.8993 (mmm) cc_final: 0.8475 (mtm) REVERT: C 342 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8060 (pt0) REVERT: D 155 GLU cc_start: 0.8469 (mp0) cc_final: 0.8239 (pm20) REVERT: D 244 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8108 (mp0) REVERT: D 374 GLN cc_start: 0.8523 (tp-100) cc_final: 0.8024 (tp-100) REVERT: E 210 ASP cc_start: 0.8389 (t70) cc_final: 0.8161 (t0) REVERT: E 234 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8666 (mt-10) REVERT: E 244 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7864 (mm-30) REVERT: E 368 GLU cc_start: 0.8544 (tt0) cc_final: 0.8040 (tm-30) REVERT: E 405 MET cc_start: 0.9093 (pmm) cc_final: 0.8873 (pmm) REVERT: F 21 MET cc_start: 0.8716 (tmm) cc_final: 0.8083 (tmt) REVERT: F 29 MET cc_start: 0.8669 (mtp) cc_final: 0.8077 (mtp) REVERT: F 80 TYR cc_start: 0.8141 (t80) cc_final: 0.7901 (t80) REVERT: F 172 GLN cc_start: 0.6983 (OUTLIER) cc_final: 0.6436 (mp10) REVERT: F 181 LYS cc_start: 0.8826 (mmtp) cc_final: 0.8050 (tppt) REVERT: F 189 GLN cc_start: 0.8226 (mt0) cc_final: 0.7307 (mt0) REVERT: F 219 MET cc_start: 0.8788 (tpp) cc_final: 0.8377 (tpp) REVERT: F 341 MET cc_start: 0.4039 (mpt) cc_final: 0.3643 (mpp) REVERT: F 368 GLU cc_start: 0.7358 (pm20) cc_final: 0.6996 (pm20) REVERT: F 396 MET cc_start: 0.7961 (mmm) cc_final: 0.7744 (mmm) REVERT: F 415 MET cc_start: 0.7037 (OUTLIER) cc_final: 0.6802 (pmt) REVERT: b 25 MET cc_start: 0.8845 (mmm) cc_final: 0.8563 (mmm) REVERT: b 39 LYS cc_start: 0.9022 (ttpp) cc_final: 0.8736 (tmmm) REVERT: b 46 ARG cc_start: 0.8613 (mtm-85) cc_final: 0.8288 (mtm-85) REVERT: c 17 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7929 (tp30) REVERT: c 34 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8441 (tm-30) REVERT: d 18 LEU cc_start: 0.9287 (tm) cc_final: 0.8911 (pp) REVERT: d 26 LEU cc_start: 0.8930 (mt) cc_final: 0.8507 (mm) REVERT: d 27 THR cc_start: 0.8915 (p) cc_final: 0.8688 (t) REVERT: e 64 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7390 (ptp-170) outliers start: 80 outliers final: 42 residues processed: 347 average time/residue: 1.3561 time to fit residues: 537.2405 Evaluate side-chains 341 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 289 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 233 ASP 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 394 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 69 ASP 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 234 GLU Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 365 THR 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 365 THR 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 27 THR 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 45 SER 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 64 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 266 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 157 optimal weight: 0.8980 chunk 202 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 chunk 232 optimal weight: 6.9990 chunk 154 optimal weight: 0.8980 chunk 275 optimal weight: 5.9990 chunk 172 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN E 193 GLN b 9 ASN d 15 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23402 Z= 0.242 Angle : 0.606 10.416 31552 Z= 0.287 Chirality : 0.042 0.161 3609 Planarity : 0.004 0.056 4105 Dihedral : 5.152 112.904 3219 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.14 % Allowed : 15.65 % Favored : 81.22 % 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: 1.64 (0.16), residues: 2896 helix: 2.04 (0.15), residues: 1223 sheet: 0.27 (0.24), residues: 474 loop : 0.58 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 381 HIS 0.007 0.001 HIS d 73 PHE 0.032 0.001 PHE b 71 TYR 0.030 0.001 TYR e 13 ARG 0.011 0.000 ARG b 61 *********************** 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 379 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 300 time to evaluate : 2.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.9154 (tpp) cc_final: 0.8850 (tpp) REVERT: A 244 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8120 (mt-10) REVERT: A 342 GLU cc_start: 0.7993 (pm20) cc_final: 0.7423 (pm20) REVERT: A 415 MET cc_start: 0.9442 (OUTLIER) cc_final: 0.9219 (ppp) REVERT: B 25 ASN cc_start: 0.8779 (OUTLIER) cc_final: 0.8570 (t0) REVERT: B 30 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7337 (mtm-85) REVERT: B 244 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8176 (mm-30) REVERT: C 21 MET cc_start: 0.8716 (mtp) cc_final: 0.8232 (ttm) REVERT: C 186 MET cc_start: 0.8988 (mmm) cc_final: 0.8466 (mtm) REVERT: C 342 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8002 (pt0) REVERT: D 155 GLU cc_start: 0.8475 (mp0) cc_final: 0.8222 (pm20) REVERT: D 244 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: D 374 GLN cc_start: 0.8503 (tp-100) cc_final: 0.8007 (tp-100) REVERT: E 210 ASP cc_start: 0.8388 (t70) cc_final: 0.8152 (t0) REVERT: E 234 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8662 (mt-10) REVERT: E 244 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7849 (mm-30) REVERT: E 368 GLU cc_start: 0.8516 (tt0) cc_final: 0.8029 (tm-30) REVERT: F 21 MET cc_start: 0.8708 (tmm) cc_final: 0.8050 (tmt) REVERT: F 29 MET cc_start: 0.8666 (mtp) cc_final: 0.8086 (mtp) REVERT: F 80 TYR cc_start: 0.8119 (t80) cc_final: 0.7884 (t80) REVERT: F 172 GLN cc_start: 0.6965 (OUTLIER) cc_final: 0.6372 (mp10) REVERT: F 181 LYS cc_start: 0.8825 (mmtp) cc_final: 0.8048 (tppt) REVERT: F 189 GLN cc_start: 0.8033 (mt0) cc_final: 0.7094 (mt0) REVERT: F 219 MET cc_start: 0.8779 (tpp) cc_final: 0.8378 (tpp) REVERT: F 341 MET cc_start: 0.4100 (mpt) cc_final: 0.3669 (mpp) REVERT: F 368 GLU cc_start: 0.7313 (pm20) cc_final: 0.6997 (pm20) REVERT: F 396 MET cc_start: 0.7962 (mmm) cc_final: 0.7744 (mmm) REVERT: F 415 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6863 (pmt) REVERT: b 39 LYS cc_start: 0.9015 (ttpp) cc_final: 0.8725 (tmmm) REVERT: b 46 ARG cc_start: 0.8613 (mtm-85) cc_final: 0.8322 (mtm-85) REVERT: c 34 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8409 (tm-30) REVERT: c 48 ASN cc_start: 0.8985 (m-40) cc_final: 0.8701 (p0) REVERT: d 18 LEU cc_start: 0.9311 (tm) cc_final: 0.8963 (pp) REVERT: d 26 LEU cc_start: 0.8918 (mt) cc_final: 0.8683 (mp) REVERT: d 27 THR cc_start: 0.8891 (p) cc_final: 0.8655 (t) REVERT: d 30 LEU cc_start: 0.8526 (mm) cc_final: 0.8146 (mp) REVERT: d 41 SER cc_start: 0.8837 (t) cc_final: 0.8453 (p) REVERT: e 64 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7343 (ptp-170) outliers start: 79 outliers final: 47 residues processed: 347 average time/residue: 1.3077 time to fit residues: 519.3094 Evaluate side-chains 341 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 285 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 292 ASN 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 1 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain C residue 60 ASP 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 60 ASP Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 233 ASP 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 D residue 394 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 69 ASP 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 234 GLU Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 365 THR 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 365 THR 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 27 THR 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 45 SER 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 64 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 170 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 187 optimal weight: 0.7980 chunk 136 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 216 optimal weight: 7.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN F 190 ASN ** F 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 9 ASN d 15 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23402 Z= 0.193 Angle : 0.629 11.918 31552 Z= 0.295 Chirality : 0.042 0.227 3609 Planarity : 0.004 0.056 4105 Dihedral : 5.092 114.381 3219 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.74 % Allowed : 16.56 % Favored : 80.70 % 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: 1.67 (0.16), residues: 2896 helix: 2.08 (0.15), residues: 1223 sheet: 0.29 (0.24), residues: 474 loop : 0.57 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 381 HIS 0.006 0.001 HIS d 73 PHE 0.009 0.001 PHE E 89 TYR 0.030 0.001 TYR e 13 ARG 0.018 0.000 ARG e 46 *********************** 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 375 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 306 time to evaluate : 2.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8059 (mt-10) REVERT: A 245 MET cc_start: 0.9031 (tpp) cc_final: 0.8797 (tpt) REVERT: A 342 GLU cc_start: 0.7980 (pm20) cc_final: 0.7440 (pm20) REVERT: A 415 MET cc_start: 0.9441 (OUTLIER) cc_final: 0.9221 (ppp) REVERT: B 25 ASN cc_start: 0.8758 (m-40) cc_final: 0.8550 (t0) REVERT: B 30 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7325 (mtm-85) REVERT: B 244 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8165 (mm-30) REVERT: C 21 MET cc_start: 0.8697 (mtp) cc_final: 0.8262 (ttm) REVERT: C 186 MET cc_start: 0.8986 (mmm) cc_final: 0.8471 (mtm) REVERT: C 347 ARG cc_start: 0.8410 (tpp80) cc_final: 0.7680 (tpp80) REVERT: D 155 GLU cc_start: 0.8474 (mp0) cc_final: 0.8217 (pm20) REVERT: D 244 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8103 (mp0) REVERT: D 374 GLN cc_start: 0.8469 (tp-100) cc_final: 0.8003 (tp-100) REVERT: E 21 MET cc_start: 0.8704 (ttm) cc_final: 0.8186 (ttt) REVERT: E 210 ASP cc_start: 0.8332 (t70) cc_final: 0.8113 (t0) REVERT: E 234 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8637 (mt-10) REVERT: E 244 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7779 (mm-30) REVERT: E 368 GLU cc_start: 0.8506 (tt0) cc_final: 0.8041 (tm-30) REVERT: F 21 MET cc_start: 0.8715 (tmm) cc_final: 0.8043 (tmt) REVERT: F 29 MET cc_start: 0.8652 (mtp) cc_final: 0.8074 (mtp) REVERT: F 80 TYR cc_start: 0.8069 (t80) cc_final: 0.7842 (t80) REVERT: F 172 GLN cc_start: 0.6925 (OUTLIER) cc_final: 0.6334 (mp10) REVERT: F 181 LYS cc_start: 0.8819 (mmtp) cc_final: 0.8047 (tppt) REVERT: F 219 MET cc_start: 0.8763 (tpp) cc_final: 0.8369 (tpp) REVERT: F 341 MET cc_start: 0.4099 (mpt) cc_final: 0.3670 (mpp) REVERT: F 368 GLU cc_start: 0.7320 (pm20) cc_final: 0.7000 (pm20) REVERT: F 396 MET cc_start: 0.7966 (mmm) cc_final: 0.7745 (mmm) REVERT: F 415 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6891 (pmt) REVERT: b 25 MET cc_start: 0.8881 (mmm) cc_final: 0.8538 (tpp) REVERT: b 39 LYS cc_start: 0.9059 (ttpp) cc_final: 0.8668 (tmmm) REVERT: b 46 ARG cc_start: 0.8591 (mtm-85) cc_final: 0.8290 (mtm-85) REVERT: b 70 SER cc_start: 0.8884 (OUTLIER) cc_final: 0.8356 (m) REVERT: c 34 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8457 (tm-30) REVERT: c 49 VAL cc_start: 0.9027 (t) cc_final: 0.8746 (p) REVERT: d 18 LEU cc_start: 0.9327 (tm) cc_final: 0.8909 (pp) REVERT: d 27 THR cc_start: 0.8915 (p) cc_final: 0.8686 (t) REVERT: d 30 LEU cc_start: 0.8477 (mm) cc_final: 0.8088 (mp) REVERT: e 64 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7317 (ptp-170) outliers start: 69 outliers final: 45 residues processed: 348 average time/residue: 1.3152 time to fit residues: 522.9684 Evaluate side-chains 345 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 292 time to evaluate : 2.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 292 ASN 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 210 ASP Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 233 ASP 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 D residue 394 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 69 ASP 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 234 GLU Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 390 MET Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 172 GLN Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 365 THR 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 68 ILE Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain b residue 29 GLU 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 Chi-restraints excluded: chain e residue 64 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 250 optimal weight: 0.0970 chunk 264 optimal weight: 8.9990 chunk 240 optimal weight: 5.9990 chunk 256 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 111 optimal weight: 0.4980 chunk 201 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 232 optimal weight: 7.9990 chunk 242 optimal weight: 7.9990 chunk 255 optimal weight: 4.9990 overall best weight: 1.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN E 193 GLN F 190 ASN c 9 ASN d 15 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23402 Z= 0.240 Angle : 0.650 11.846 31552 Z= 0.304 Chirality : 0.043 0.189 3609 Planarity : 0.004 0.058 4105 Dihedral : 5.110 116.079 3219 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.74 % Allowed : 17.04 % Favored : 80.22 % 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: 2.04 (0.15), residues: 1223 sheet: 0.28 (0.24), residues: 474 loop : 0.52 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 381 HIS 0.005 0.001 HIS d 73 PHE 0.034 0.001 PHE b 71 TYR 0.031 0.002 TYR e 13 ARG 0.016 0.000 ARG e 46 *********************** 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 360 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 291 time to evaluate : 4.346 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: 0.4137 (pp-130) cc_final: 0.3266 (ttp) REVERT: A 244 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8086 (mt-10) REVERT: A 245 MET cc_start: 0.9021 (tpp) cc_final: 0.8727 (tpt) REVERT: A 342 GLU cc_start: 0.7995 (pm20) cc_final: 0.7448 (pm20) REVERT: A 415 MET cc_start: 0.9446 (OUTLIER) cc_final: 0.9227 (ppp) REVERT: B 30 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7343 (mtm-85) REVERT: B 244 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8177 (mm-30) REVERT: C 21 MET cc_start: 0.8714 (mtp) cc_final: 0.8284 (ttm) REVERT: C 186 MET cc_start: 0.8986 (mmm) cc_final: 0.8458 (mtm) REVERT: C 341 MET cc_start: 0.9350 (ttp) cc_final: 0.9121 (tmt) REVERT: D 155 GLU cc_start: 0.8484 (mp0) cc_final: 0.8234 (pm20) REVERT: D 244 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8106 (mp0) REVERT: D 374 GLN cc_start: 0.8486 (tp-100) cc_final: 0.8006 (tp-100) REVERT: E 210 ASP cc_start: 0.8336 (t70) cc_final: 0.8116 (t0) REVERT: E 234 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8653 (mt-10) REVERT: E 244 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7820 (mm-30) REVERT: E 368 GLU cc_start: 0.8522 (tt0) cc_final: 0.8051 (tm-30) REVERT: F 21 MET cc_start: 0.8710 (tmm) cc_final: 0.8032 (tmt) REVERT: F 29 MET cc_start: 0.8669 (mtp) cc_final: 0.8087 (mtp) REVERT: F 80 TYR cc_start: 0.8063 (t80) cc_final: 0.7849 (t80) REVERT: F 172 GLN cc_start: 0.6952 (OUTLIER) cc_final: 0.6355 (mp10) REVERT: F 181 LYS cc_start: 0.8828 (mmtp) cc_final: 0.8058 (tppt) REVERT: F 189 GLN cc_start: 0.8017 (mt0) cc_final: 0.7563 (mt0) REVERT: F 219 MET cc_start: 0.8780 (tpp) cc_final: 0.8511 (tpp) REVERT: F 341 MET cc_start: 0.4119 (mpt) cc_final: 0.3683 (mpp) REVERT: F 368 GLU cc_start: 0.7299 (pm20) cc_final: 0.6972 (pm20) REVERT: F 396 MET cc_start: 0.8013 (mmm) cc_final: 0.7789 (mmm) REVERT: F 415 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.6922 (pmt) REVERT: b 25 MET cc_start: 0.8852 (mmm) cc_final: 0.8556 (tpp) REVERT: b 39 LYS cc_start: 0.9052 (ttpp) cc_final: 0.8686 (tmmm) REVERT: b 70 SER cc_start: 0.8874 (p) cc_final: 0.8365 (m) REVERT: c 34 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8453 (tm-30) REVERT: d 18 LEU cc_start: 0.9329 (tm) cc_final: 0.8961 (pp) REVERT: d 27 THR cc_start: 0.8920 (p) cc_final: 0.8700 (t) REVERT: d 30 LEU cc_start: 0.8553 (mm) cc_final: 0.8156 (mp) REVERT: e 64 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7289 (ptp-170) outliers start: 69 outliers final: 50 residues processed: 336 average time/residue: 1.3831 time to fit residues: 535.4679 Evaluate side-chains 340 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 283 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 69 ASP 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 234 GLU Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 390 MET Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 172 GLN Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 365 THR 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 68 ILE Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain b residue 29 GLU 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 66 ASP Chi-restraints excluded: chain e residue 52 LEU Chi-restraints excluded: chain e residue 64 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 168 optimal weight: 1.9990 chunk 271 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 chunk 188 optimal weight: 0.6980 chunk 284 optimal weight: 6.9990 chunk 262 optimal weight: 5.9990 chunk 226 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 175 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN c 9 ASN d 15 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23402 Z= 0.192 Angle : 0.673 12.896 31552 Z= 0.312 Chirality : 0.043 0.391 3609 Planarity : 0.004 0.064 4105 Dihedral : 5.068 117.410 3219 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.18 % Allowed : 17.47 % Favored : 80.34 % 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: 2.08 (0.15), residues: 1223 sheet: 0.30 (0.24), residues: 478 loop : 0.52 (0.18), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 381 HIS 0.004 0.000 HIS d 73 PHE 0.018 0.001 PHE A 62 TYR 0.036 0.002 TYR e 13 ARG 0.018 0.000 ARG e 46 ********************** 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 356 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 301 time to evaluate : 2.662 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: 0.4151 (pp-130) cc_final: 0.3218 (ttp) REVERT: A 244 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8048 (mt-10) REVERT: A 245 MET cc_start: 0.9046 (tpp) cc_final: 0.8755 (tpt) REVERT: A 342 GLU cc_start: 0.7976 (pm20) cc_final: 0.7423 (pm20) REVERT: A 353 ARG cc_start: 0.8949 (tpm170) cc_final: 0.8691 (tmm160) REVERT: A 415 MET cc_start: 0.9429 (OUTLIER) cc_final: 0.9193 (ppp) REVERT: B 25 ASN cc_start: 0.8784 (m-40) cc_final: 0.8580 (t0) REVERT: B 244 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8178 (mm-30) REVERT: C 21 MET cc_start: 0.8684 (mtp) cc_final: 0.8299 (ttm) REVERT: C 186 MET cc_start: 0.8980 (mmm) cc_final: 0.8466 (mtm) REVERT: C 341 MET cc_start: 0.9328 (ttp) cc_final: 0.9096 (tmt) REVERT: D 155 GLU cc_start: 0.8481 (mp0) cc_final: 0.8233 (pm20) REVERT: D 244 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8106 (mp0) REVERT: D 374 GLN cc_start: 0.8449 (tp-100) cc_final: 0.7966 (tp-100) REVERT: E 21 MET cc_start: 0.8697 (ttm) cc_final: 0.8184 (ttt) REVERT: E 210 ASP cc_start: 0.8317 (t70) cc_final: 0.8106 (t0) REVERT: E 234 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8630 (mt-10) REVERT: E 244 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7775 (mm-30) REVERT: E 368 GLU cc_start: 0.8515 (tt0) cc_final: 0.8047 (tm-30) REVERT: E 394 ASP cc_start: 0.9167 (m-30) cc_final: 0.8736 (p0) REVERT: F 21 MET cc_start: 0.8713 (tmm) cc_final: 0.8034 (tmt) REVERT: F 29 MET cc_start: 0.8657 (mtp) cc_final: 0.8074 (mtp) REVERT: F 80 TYR cc_start: 0.8045 (t80) cc_final: 0.7843 (t80) REVERT: F 172 GLN cc_start: 0.6914 (OUTLIER) cc_final: 0.6319 (mp10) REVERT: F 181 LYS cc_start: 0.8812 (mmtp) cc_final: 0.8052 (tppt) REVERT: F 189 GLN cc_start: 0.8024 (mt0) cc_final: 0.7582 (mt0) REVERT: F 219 MET cc_start: 0.8794 (tpp) cc_final: 0.8516 (tpp) REVERT: F 341 MET cc_start: 0.4104 (mpt) cc_final: 0.3671 (mpp) REVERT: F 368 GLU cc_start: 0.7298 (pm20) cc_final: 0.7012 (pm20) REVERT: F 396 MET cc_start: 0.8010 (mmm) cc_final: 0.7785 (mmm) REVERT: F 415 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6875 (pmt) REVERT: b 25 MET cc_start: 0.8838 (mmm) cc_final: 0.8529 (tpp) REVERT: b 29 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7772 (mm-30) REVERT: b 39 LYS cc_start: 0.9041 (ttpp) cc_final: 0.8668 (tmmm) REVERT: b 70 SER cc_start: 0.8820 (p) cc_final: 0.8280 (m) REVERT: c 34 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8451 (tm-30) REVERT: c 50 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7608 (mt-10) REVERT: d 18 LEU cc_start: 0.9320 (tm) cc_final: 0.8945 (pp) REVERT: d 27 THR cc_start: 0.8948 (p) cc_final: 0.8717 (t) REVERT: d 30 LEU cc_start: 0.8552 (mm) cc_final: 0.8154 (mp) REVERT: e 64 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7207 (ptp-170) outliers start: 55 outliers final: 44 residues processed: 337 average time/residue: 1.3282 time to fit residues: 511.5219 Evaluate side-chains 342 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 292 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 69 ASP 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 259 ASP Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 172 GLN Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 365 THR 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 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 e residue 64 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 180 optimal weight: 1.9990 chunk 241 optimal weight: 10.0000 chunk 69 optimal weight: 0.3980 chunk 209 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 227 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 233 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3835 r_free = 0.3835 target = 0.110460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.072637 restraints weight = 54463.123| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.92 r_work: 0.2909 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23402 Z= 0.215 Angle : 0.679 13.957 31552 Z= 0.314 Chirality : 0.043 0.417 3609 Planarity : 0.004 0.061 4105 Dihedral : 5.076 118.801 3219 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.26 % Allowed : 17.47 % Favored : 80.26 % 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: 1.64 (0.16), residues: 2896 helix: 2.05 (0.15), residues: 1223 sheet: 0.29 (0.24), residues: 480 loop : 0.54 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 381 HIS 0.006 0.001 HIS F 239 PHE 0.033 0.001 PHE b 71 TYR 0.038 0.001 TYR e 13 ARG 0.018 0.000 ARG e 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8866.44 seconds wall clock time: 155 minutes 34.31 seconds (9334.31 seconds total)