Starting phenix.real_space_refine on Sun Feb 18 11:04:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spv_40687/02_2024/8spv_40687.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spv_40687/02_2024/8spv_40687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spv_40687/02_2024/8spv_40687.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spv_40687/02_2024/8spv_40687.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spv_40687/02_2024/8spv_40687.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spv_40687/02_2024/8spv_40687.pdb" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 13782 2.51 5 N 3795 2.21 5 O 4158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21804 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3644 Classifications: {'peptide': 475} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 452} Chain: "B" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3644 Classifications: {'peptide': 475} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 452} Chain: "C" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3644 Classifications: {'peptide': 475} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 452} Chain: "D" Number of atoms: 3624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3624 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "E" Number of atoms: 3624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3624 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3624 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Time building chain proxies: 11.75, per 1000 atoms: 0.54 Number of scatterers: 21804 At special positions: 0 Unit cell: (131.88, 125.16, 108.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 4158 8.00 N 3795 7.00 C 13782 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: 8.38 Conformation dependent library (CDL) restraints added in 4.5 seconds 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5148 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 24 sheets defined 45.0% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 216 through 219 removed outlier: 4.279A pdb=" N ASP A 219 " --> pdb=" O GLY A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 219' Processing helix chain 'A' and resid 231 through 251 removed outlier: 3.746A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.763A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 Processing helix chain 'A' and resid 288 through 299 removed outlier: 4.512A pdb=" N TYR A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 336 Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 372 through 397 removed outlier: 4.506A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 420 Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 451 through 467 removed outlier: 4.281A pdb=" N ARG A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 483 through 498 Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 216 through 219 removed outlier: 4.280A pdb=" N ASP B 219 " --> pdb=" O GLY B 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 216 through 219' Processing helix chain 'B' and resid 231 through 251 removed outlier: 3.746A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.762A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 277 Processing helix chain 'B' and resid 288 through 299 removed outlier: 4.512A pdb=" N TYR B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 345 through 352 Processing helix chain 'B' and resid 372 through 397 removed outlier: 4.506A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 Processing helix chain 'B' and resid 429 through 442 Processing helix chain 'B' and resid 451 through 467 removed outlier: 4.281A pdb=" N ARG B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 479 Processing helix chain 'B' and resid 483 through 498 Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 216 through 219 removed outlier: 4.280A pdb=" N ASP C 219 " --> pdb=" O GLY C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 216 through 219' Processing helix chain 'C' and resid 231 through 251 removed outlier: 3.746A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.762A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 277 Processing helix chain 'C' and resid 288 through 299 removed outlier: 4.511A pdb=" N TYR C 292 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 345 through 352 Processing helix chain 'C' and resid 372 through 397 removed outlier: 4.507A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN C 397 " --> pdb=" O GLU C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 420 Processing helix chain 'C' and resid 429 through 442 Processing helix chain 'C' and resid 451 through 467 removed outlier: 4.282A pdb=" N ARG C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 479 Processing helix chain 'C' and resid 483 through 498 Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.527A pdb=" N THR D 91 " --> pdb=" O GLY D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 163 through 178 Processing helix chain 'D' and resid 191 through 204 Processing helix chain 'D' and resid 205 through 206 No H-bonds generated for 'chain 'D' and resid 205 through 206' Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 221 through 243 removed outlier: 5.311A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 269 removed outlier: 3.759A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 277 Processing helix chain 'D' and resid 280 through 290 Processing helix chain 'D' and resid 315 through 325 removed outlier: 3.795A pdb=" N HIS D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 325 " --> pdb=" O THR D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 339 removed outlier: 3.688A pdb=" N ALA D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 387 removed outlier: 3.523A pdb=" N THR D 373 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 410 removed outlier: 3.702A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 419 removed outlier: 4.002A pdb=" N GLN D 419 " --> pdb=" O VAL D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 443 Processing helix chain 'D' and resid 451 through 455 removed outlier: 4.155A pdb=" N LEU D 455 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 470 removed outlier: 3.907A pdb=" N VAL D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.527A pdb=" N THR E 91 " --> pdb=" O GLY E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 163 through 178 Processing helix chain 'E' and resid 191 through 204 Processing helix chain 'E' and resid 205 through 206 No H-bonds generated for 'chain 'E' and resid 205 through 206' Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 221 through 243 removed outlier: 5.312A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 269 removed outlier: 3.760A pdb=" N THR E 258 " --> pdb=" O ILE E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 277 Processing helix chain 'E' and resid 280 through 290 Processing helix chain 'E' and resid 315 through 325 removed outlier: 3.796A pdb=" N HIS E 324 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU E 325 " --> pdb=" O THR E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 339 removed outlier: 3.689A pdb=" N ALA E 336 " --> pdb=" O GLU E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 360 through 387 removed outlier: 3.523A pdb=" N THR E 373 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 410 removed outlier: 3.703A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 419 removed outlier: 4.002A pdb=" N GLN E 419 " --> pdb=" O VAL E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 443 Processing helix chain 'E' and resid 451 through 455 removed outlier: 4.156A pdb=" N LEU E 455 " --> pdb=" O ALA E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 470 removed outlier: 3.907A pdb=" N VAL E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 removed outlier: 3.527A pdb=" N THR F 91 " --> pdb=" O GLY F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 163 through 178 Processing helix chain 'F' and resid 191 through 204 Processing helix chain 'F' and resid 205 through 206 No H-bonds generated for 'chain 'F' and resid 205 through 206' Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'F' and resid 221 through 243 removed outlier: 5.312A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 269 removed outlier: 3.759A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 277 Processing helix chain 'F' and resid 280 through 290 Processing helix chain 'F' and resid 315 through 325 removed outlier: 3.796A pdb=" N HIS F 324 " --> pdb=" O THR F 320 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU F 325 " --> pdb=" O THR F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 339 removed outlier: 3.688A pdb=" N ALA F 336 " --> pdb=" O GLU F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 360 through 387 removed outlier: 3.524A pdb=" N THR F 373 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.703A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 419 removed outlier: 4.002A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 443 Processing helix chain 'F' and resid 451 through 455 removed outlier: 4.156A pdb=" N LEU F 455 " --> pdb=" O ALA F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 470 removed outlier: 3.907A pdb=" N VAL F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 35 removed outlier: 6.522A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN A 65 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 3.546A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.537A pdb=" N VAL A 256 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU A 316 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL A 258 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N PHE A 318 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR A 260 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLU A 320 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU A 344 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE A 168 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 146 removed outlier: 4.764A pdb=" N ILE A 159 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 28 through 35 removed outlier: 6.522A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN B 65 " --> pdb=" O GLY B 72 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.545A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.537A pdb=" N VAL B 256 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU B 316 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL B 258 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N PHE B 318 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR B 260 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLU B 320 " --> pdb=" O TYR B 260 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 145 through 146 removed outlier: 4.765A pdb=" N ILE B 159 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 28 through 35 removed outlier: 6.522A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN C 65 " --> pdb=" O GLY C 72 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.545A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.537A pdb=" N VAL C 256 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU C 316 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL C 258 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N PHE C 318 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR C 260 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLU C 320 " --> pdb=" O TYR C 260 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU C 344 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE C 168 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 145 through 146 removed outlier: 4.764A pdb=" N ILE C 159 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 3 through 10 removed outlier: 5.728A pdb=" N VAL D 6 " --> pdb=" O LYS D 17 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LYS D 17 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN D 8 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB6, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.511A pdb=" N PHE D 96 " --> pdb=" O PHE D 215 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL D 184 " --> pdb=" O PHE D 250 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.451A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 3 through 10 removed outlier: 5.728A pdb=" N VAL E 6 " --> pdb=" O LYS E 17 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LYS E 17 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN E 8 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AC1, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.511A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL E 184 " --> pdb=" O PHE E 250 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE E 154 " --> pdb=" O GLN E 304 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.450A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 3 through 10 removed outlier: 5.728A pdb=" N VAL F 6 " --> pdb=" O LYS F 17 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LYS F 17 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN F 8 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AC5, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.512A pdb=" N PHE F 96 " --> pdb=" O PHE F 215 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.451A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) 1026 hydrogen bonds defined for protein. 2952 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: 7.13 Time building geometry restraints manager: 9.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7443 1.34 - 1.46: 3000 1.46 - 1.57: 11589 1.57 - 1.69: 0 1.69 - 1.81: 138 Bond restraints: 22170 Sorted by residual: bond pdb=" N GLU C 284 " pdb=" CA GLU C 284 " ideal model delta sigma weight residual 1.457 1.476 -0.018 1.29e-02 6.01e+03 1.97e+00 bond pdb=" N GLU A 284 " pdb=" CA GLU A 284 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.92e+00 bond pdb=" N GLU B 284 " pdb=" CA GLU B 284 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.75e+00 bond pdb=" CA ILE A 94 " pdb=" CB ILE A 94 " ideal model delta sigma weight residual 1.538 1.549 -0.011 1.10e-02 8.26e+03 1.06e+00 bond pdb=" CA ILE B 94 " pdb=" CB ILE B 94 " ideal model delta sigma weight residual 1.538 1.549 -0.011 1.10e-02 8.26e+03 1.05e+00 ... (remaining 22165 not shown) Histogram of bond angle deviations from ideal: 100.22 - 106.49: 666 106.49 - 112.75: 11646 112.75 - 119.02: 6166 119.02 - 125.29: 11351 125.29 - 131.56: 201 Bond angle restraints: 30030 Sorted by residual: angle pdb=" C GLU A 284 " pdb=" N ALA A 285 " pdb=" CA ALA A 285 " ideal model delta sigma weight residual 121.54 131.30 -9.76 1.91e+00 2.74e-01 2.61e+01 angle pdb=" C GLU C 284 " pdb=" N ALA C 285 " pdb=" CA ALA C 285 " ideal model delta sigma weight residual 121.54 131.28 -9.74 1.91e+00 2.74e-01 2.60e+01 angle pdb=" C GLU B 284 " pdb=" N ALA B 285 " pdb=" CA ALA B 285 " ideal model delta sigma weight residual 121.54 131.26 -9.72 1.91e+00 2.74e-01 2.59e+01 angle pdb=" C VAL A 136 " pdb=" N MET A 137 " pdb=" CA MET A 137 " ideal model delta sigma weight residual 121.54 127.04 -5.50 1.91e+00 2.74e-01 8.28e+00 angle pdb=" C VAL C 136 " pdb=" N MET C 137 " pdb=" CA MET C 137 " ideal model delta sigma weight residual 121.54 126.98 -5.44 1.91e+00 2.74e-01 8.12e+00 ... (remaining 30025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 12591 17.53 - 35.07: 687 35.07 - 52.60: 144 52.60 - 70.13: 45 70.13 - 87.67: 12 Dihedral angle restraints: 13479 sinusoidal: 5424 harmonic: 8055 Sorted by residual: dihedral pdb=" CA ALA C 285 " pdb=" C ALA C 285 " pdb=" N TYR C 286 " pdb=" CA TYR C 286 " ideal model delta harmonic sigma weight residual 180.00 159.76 20.24 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA ALA B 285 " pdb=" C ALA B 285 " pdb=" N TYR B 286 " pdb=" CA TYR B 286 " ideal model delta harmonic sigma weight residual 180.00 159.77 20.23 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA ALA A 285 " pdb=" C ALA A 285 " pdb=" N TYR A 286 " pdb=" CA TYR A 286 " ideal model delta harmonic sigma weight residual 180.00 159.82 20.18 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 13476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1919 0.028 - 0.056: 964 0.056 - 0.084: 277 0.084 - 0.112: 204 0.112 - 0.140: 95 Chirality restraints: 3459 Sorted by residual: chirality pdb=" CA VAL E 14 " pdb=" N VAL E 14 " pdb=" C VAL E 14 " pdb=" CB VAL E 14 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA VAL D 456 " pdb=" N VAL D 456 " pdb=" C VAL D 456 " pdb=" CB VAL D 456 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA VAL D 14 " pdb=" N VAL D 14 " pdb=" C VAL D 14 " pdb=" CB VAL D 14 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.87e-01 ... (remaining 3456 not shown) Planarity restraints: 3957 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 284 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C GLU B 284 " 0.028 2.00e-02 2.50e+03 pdb=" O GLU B 284 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA B 285 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 232 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO B 233 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 233 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 233 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 232 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO A 233 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 233 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 233 " 0.022 5.00e-02 4.00e+02 ... (remaining 3954 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 447 2.71 - 3.26: 21957 3.26 - 3.80: 31944 3.80 - 4.35: 42882 4.35 - 4.90: 72349 Nonbonded interactions: 169579 Sorted by model distance: nonbonded pdb=" OG SER D 411 " pdb=" O ARG D 454 " model vdw 2.159 2.440 nonbonded pdb=" OG SER E 411 " pdb=" O ARG E 454 " model vdw 2.159 2.440 nonbonded pdb=" OG SER F 411 " pdb=" O ARG F 454 " model vdw 2.160 2.440 nonbonded pdb=" O ASP A 170 " pdb=" OG1 THR A 173 " model vdw 2.236 2.440 nonbonded pdb=" O ASP C 170 " pdb=" OG1 THR C 173 " model vdw 2.236 2.440 ... (remaining 169574 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' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 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: 4.780 Check model and map are aligned: 0.350 Set scattering table: 0.230 Process input model: 58.520 Find NCS groups from input model: 1.450 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: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 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 0.032 22170 Z= 0.197 Angle : 0.568 9.764 30030 Z= 0.323 Chirality : 0.044 0.140 3459 Planarity : 0.004 0.040 3957 Dihedral : 12.146 87.667 8331 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.32 % Allowed : 1.13 % Favored : 98.55 % Rotamer: Outliers : 0.78 % Allowed : 7.63 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % 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: 0.32 (0.15), residues: 2823 helix: 0.88 (0.15), residues: 1092 sheet: 0.91 (0.25), residues: 426 loop : -0.55 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 401 PHE 0.022 0.002 PHE B 236 TYR 0.011 0.002 TYR F 364 ARG 0.003 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 594 time to evaluate : 2.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.4447 (mpp) cc_final: 0.3244 (pmm) REVERT: A 349 PHE cc_start: 0.4449 (t80) cc_final: 0.4100 (t80) REVERT: A 474 HIS cc_start: 0.7070 (t-90) cc_final: 0.6865 (t70) REVERT: B 137 MET cc_start: 0.4798 (mpp) cc_final: 0.3332 (pmm) REVERT: B 474 HIS cc_start: 0.7113 (t-90) cc_final: 0.6765 (t70) REVERT: C 137 MET cc_start: 0.4823 (mpp) cc_final: 0.3370 (pmm) REVERT: C 349 PHE cc_start: 0.4475 (t80) cc_final: 0.4122 (t80) REVERT: C 460 PHE cc_start: 0.7797 (t80) cc_final: 0.7313 (t80) REVERT: F 234 THR cc_start: 0.7064 (t) cc_final: 0.6854 (p) outliers start: 18 outliers final: 3 residues processed: 603 average time/residue: 0.4026 time to fit residues: 348.1901 Evaluate side-chains 355 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 352 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 62 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 238 optimal weight: 9.9990 chunk 213 optimal weight: 0.0060 chunk 118 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 144 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 85 optimal weight: 30.0000 chunk 134 optimal weight: 7.9990 chunk 164 optimal weight: 7.9990 chunk 256 optimal weight: 8.9990 overall best weight: 4.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 474 HIS D 365 GLN F 253 ASN F 365 GLN F 407 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 22170 Z= 0.420 Angle : 0.749 9.419 30030 Z= 0.400 Chirality : 0.053 0.189 3459 Planarity : 0.006 0.063 3957 Dihedral : 5.814 66.767 3090 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.61 % Allowed : 14.23 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % 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: -0.16 (0.15), residues: 2823 helix: 0.63 (0.15), residues: 1110 sheet: 0.81 (0.25), residues: 399 loop : -1.02 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS E 401 PHE 0.017 0.002 PHE B 456 TYR 0.028 0.003 TYR A 240 ARG 0.008 0.001 ARG F 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 356 time to evaluate : 2.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6007 (mp0) REVERT: A 137 MET cc_start: 0.4523 (tpp) cc_final: 0.3503 (pmm) REVERT: A 290 ILE cc_start: 0.6527 (OUTLIER) cc_final: 0.5851 (mm) REVERT: A 415 ARG cc_start: 0.7900 (mtt90) cc_final: 0.7198 (mpt-90) REVERT: A 460 PHE cc_start: 0.7866 (t80) cc_final: 0.7243 (t80) REVERT: A 474 HIS cc_start: 0.7285 (t-90) cc_final: 0.7070 (t70) REVERT: B 57 ASN cc_start: 0.6857 (OUTLIER) cc_final: 0.6577 (p0) REVERT: B 290 ILE cc_start: 0.6725 (OUTLIER) cc_final: 0.6058 (mm) REVERT: B 474 HIS cc_start: 0.7250 (t-90) cc_final: 0.7045 (t70) REVERT: C 95 MET cc_start: 0.6539 (mtp) cc_final: 0.6299 (mmm) REVERT: C 459 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6498 (mt-10) REVERT: C 460 PHE cc_start: 0.7853 (t80) cc_final: 0.7312 (t80) REVERT: D 237 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6922 (pt0) REVERT: D 248 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8076 (tt) REVERT: D 406 ILE cc_start: 0.8787 (tp) cc_final: 0.8435 (tp) REVERT: D 469 MET cc_start: 0.6430 (mmt) cc_final: 0.5957 (mpp) REVERT: E 237 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6976 (pt0) REVERT: E 465 LYS cc_start: 0.7101 (tttt) cc_final: 0.6633 (ttmm) REVERT: F 237 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6888 (pt0) REVERT: F 285 MET cc_start: 0.6988 (ttm) cc_final: 0.6762 (ttt) REVERT: F 325 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7940 (mp) outliers start: 107 outliers final: 67 residues processed: 441 average time/residue: 0.3398 time to fit residues: 227.6678 Evaluate side-chains 379 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 303 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 326 ASP Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 375 GLN Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 237 GLU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 326 ASP Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 413 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 142 optimal weight: 0.8980 chunk 79 optimal weight: 0.0030 chunk 213 optimal weight: 1.9990 chunk 174 optimal weight: 20.0000 chunk 70 optimal weight: 0.9980 chunk 256 optimal weight: 0.9980 chunk 277 optimal weight: 7.9990 chunk 228 optimal weight: 5.9990 chunk 254 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 474 HIS D 22 HIS D 259 GLN E 169 GLN E 179 HIS E 259 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22170 Z= 0.159 Angle : 0.534 9.084 30030 Z= 0.283 Chirality : 0.044 0.197 3459 Planarity : 0.004 0.040 3957 Dihedral : 5.112 68.228 3088 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.98 % Allowed : 17.81 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % 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: 0.46 (0.16), residues: 2823 helix: 1.25 (0.16), residues: 1125 sheet: 0.98 (0.25), residues: 411 loop : -0.75 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 401 PHE 0.035 0.002 PHE F 409 TYR 0.012 0.001 TYR A 240 ARG 0.005 0.000 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 327 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.5967 (mp0) REVERT: A 306 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.7077 (m-30) REVERT: A 460 PHE cc_start: 0.7841 (t80) cc_final: 0.7514 (t80) REVERT: A 476 ARG cc_start: 0.7745 (mtm-85) cc_final: 0.7443 (ttm170) REVERT: B 57 ASN cc_start: 0.6903 (OUTLIER) cc_final: 0.6527 (p0) REVERT: B 108 VAL cc_start: 0.7791 (p) cc_final: 0.7512 (m) REVERT: D 237 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6672 (pt0) REVERT: D 379 GLU cc_start: 0.5912 (OUTLIER) cc_final: 0.5445 (tt0) REVERT: D 406 ILE cc_start: 0.8710 (tp) cc_final: 0.8411 (tp) REVERT: D 469 MET cc_start: 0.6426 (mmt) cc_final: 0.5730 (ptm) REVERT: E 202 MET cc_start: 0.6225 (mmt) cc_final: 0.5325 (mmp) REVERT: E 237 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6657 (pt0) REVERT: E 418 GLU cc_start: 0.6722 (pm20) cc_final: 0.6337 (pm20) REVERT: F 237 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6642 (pt0) REVERT: F 285 MET cc_start: 0.6714 (ttm) cc_final: 0.6327 (ttt) REVERT: F 418 GLU cc_start: 0.6616 (pm20) cc_final: 0.6372 (pm20) outliers start: 69 outliers final: 33 residues processed: 379 average time/residue: 0.3484 time to fit residues: 200.1181 Evaluate side-chains 332 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 292 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 22 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 179 HIS Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 237 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 253 optimal weight: 9.9990 chunk 192 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 257 optimal weight: 0.9980 chunk 272 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS A 345 GLN B 255 HIS B 345 GLN C 255 HIS C 345 GLN C 474 HIS D 22 HIS E 245 GLN F 169 GLN F 401 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 22170 Z= 0.434 Angle : 0.727 10.356 30030 Z= 0.387 Chirality : 0.052 0.224 3459 Planarity : 0.006 0.061 3957 Dihedral : 5.611 63.453 3084 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 5.39 % Allowed : 17.59 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % 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: -0.21 (0.15), residues: 2823 helix: 0.69 (0.15), residues: 1119 sheet: 0.66 (0.24), residues: 399 loop : -1.11 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS E 179 PHE 0.023 0.002 PHE F 409 TYR 0.028 0.003 TYR B 240 ARG 0.007 0.001 ARG E 193 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 307 time to evaluate : 2.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6111 (mp0) REVERT: A 236 PHE cc_start: 0.7249 (OUTLIER) cc_final: 0.6711 (p90) REVERT: A 306 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7126 (m-30) REVERT: A 448 ILE cc_start: 0.7389 (OUTLIER) cc_final: 0.7120 (mp) REVERT: A 460 PHE cc_start: 0.7873 (t80) cc_final: 0.7317 (t80) REVERT: B 57 ASN cc_start: 0.6890 (OUTLIER) cc_final: 0.6616 (p0) REVERT: B 95 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.6421 (mmm) REVERT: B 290 ILE cc_start: 0.6816 (OUTLIER) cc_final: 0.6273 (mm) REVERT: B 339 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7242 (m-30) REVERT: B 476 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7331 (mtm-85) REVERT: C 62 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.6558 (mtm) REVERT: C 95 MET cc_start: 0.6771 (mtp) cc_final: 0.6438 (mmm) REVERT: C 198 ILE cc_start: 0.5623 (mt) cc_final: 0.5132 (mt) REVERT: D 237 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6986 (pt0) REVERT: D 285 MET cc_start: 0.6650 (ttt) cc_final: 0.6421 (ttm) REVERT: D 406 ILE cc_start: 0.8731 (tp) cc_final: 0.8514 (tp) REVERT: D 469 MET cc_start: 0.6537 (mmt) cc_final: 0.6026 (mpp) REVERT: E 202 MET cc_start: 0.6516 (mmt) cc_final: 0.6023 (mmt) REVERT: E 237 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7055 (pt0) REVERT: F 237 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6921 (pt0) outliers start: 125 outliers final: 74 residues processed: 406 average time/residue: 0.3530 time to fit residues: 218.8367 Evaluate side-chains 374 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 287 time to evaluate : 2.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 33 GLN Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 326 ASP Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 237 GLU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 413 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 227 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 202 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 232 optimal weight: 7.9990 chunk 188 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 244 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 474 HIS E 179 HIS E 245 GLN F 169 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 22170 Z= 0.325 Angle : 0.633 9.814 30030 Z= 0.337 Chirality : 0.048 0.218 3459 Planarity : 0.005 0.053 3957 Dihedral : 5.432 62.947 3084 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 5.00 % Allowed : 19.36 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % 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: -0.13 (0.15), residues: 2823 helix: 0.79 (0.15), residues: 1125 sheet: 0.62 (0.24), residues: 402 loop : -1.09 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS D 401 PHE 0.018 0.002 PHE C 494 TYR 0.020 0.002 TYR B 240 ARG 0.008 0.001 ARG D 405 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 309 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6027 (mp0) REVERT: A 236 PHE cc_start: 0.7183 (OUTLIER) cc_final: 0.6691 (p90) REVERT: A 278 ARG cc_start: 0.6983 (mtp85) cc_final: 0.5982 (mtm-85) REVERT: A 306 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.7031 (m-30) REVERT: A 460 PHE cc_start: 0.7860 (t80) cc_final: 0.7311 (t80) REVERT: A 476 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7288 (mtm-85) REVERT: B 57 ASN cc_start: 0.6832 (OUTLIER) cc_final: 0.6546 (p0) REVERT: B 339 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7199 (m-30) REVERT: C 198 ILE cc_start: 0.5557 (mt) cc_final: 0.5017 (mt) REVERT: C 306 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7342 (m-30) REVERT: C 476 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7535 (mtm-85) REVERT: D 237 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6937 (pt0) REVERT: E 237 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6958 (pt0) REVERT: E 285 MET cc_start: 0.6741 (ttm) cc_final: 0.6464 (ttt) REVERT: E 303 ILE cc_start: 0.6780 (OUTLIER) cc_final: 0.6506 (mm) REVERT: E 418 GLU cc_start: 0.6867 (pm20) cc_final: 0.6532 (pm20) REVERT: F 234 THR cc_start: 0.6543 (OUTLIER) cc_final: 0.6132 (m) REVERT: F 237 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6903 (pt0) REVERT: F 297 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.6978 (ptpp) outliers start: 116 outliers final: 75 residues processed: 403 average time/residue: 0.3454 time to fit residues: 211.2017 Evaluate side-chains 385 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 296 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 476 ARG Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 179 HIS Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 326 ASP Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 237 GLU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 297 LYS Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 326 ASP Chi-restraints excluded: chain F residue 413 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 91 optimal weight: 8.9990 chunk 245 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 272 optimal weight: 5.9990 chunk 226 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 HIS ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS E 179 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22170 Z= 0.233 Angle : 0.574 8.630 30030 Z= 0.305 Chirality : 0.045 0.212 3459 Planarity : 0.005 0.051 3957 Dihedral : 5.191 64.616 3084 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.66 % Allowed : 20.35 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % 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: 0.03 (0.15), residues: 2823 helix: 0.98 (0.16), residues: 1128 sheet: 0.60 (0.24), residues: 417 loop : -1.04 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.021 0.001 HIS E 179 PHE 0.035 0.002 PHE D 409 TYR 0.015 0.002 TYR B 240 ARG 0.006 0.000 ARG D 3 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 311 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.5954 (mp0) REVERT: A 236 PHE cc_start: 0.7139 (OUTLIER) cc_final: 0.6677 (p90) REVERT: A 278 ARG cc_start: 0.6889 (mtp85) cc_final: 0.5908 (mtm-85) REVERT: A 306 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.7026 (m-30) REVERT: A 460 PHE cc_start: 0.7795 (t80) cc_final: 0.7300 (t80) REVERT: A 476 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7344 (mtm-85) REVERT: B 57 ASN cc_start: 0.6822 (OUTLIER) cc_final: 0.6533 (p0) REVERT: B 219 ASP cc_start: 0.5008 (OUTLIER) cc_final: 0.4769 (p0) REVERT: B 339 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7118 (m-30) REVERT: B 460 PHE cc_start: 0.7462 (t80) cc_final: 0.6972 (t80) REVERT: B 476 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7339 (mtm-85) REVERT: C 198 ILE cc_start: 0.5578 (mt) cc_final: 0.5015 (mt) REVERT: C 219 ASP cc_start: 0.5632 (OUTLIER) cc_final: 0.5409 (p0) REVERT: C 306 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7280 (m-30) REVERT: C 476 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7535 (mtm-85) REVERT: D 237 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6814 (pt0) REVERT: D 285 MET cc_start: 0.6537 (ttt) cc_final: 0.6317 (ttm) REVERT: D 469 MET cc_start: 0.6598 (mmp) cc_final: 0.5934 (mpp) REVERT: E 237 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6846 (pt0) REVERT: F 237 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6802 (pt0) REVERT: F 285 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.6281 (ttm) outliers start: 108 outliers final: 70 residues processed: 400 average time/residue: 0.3411 time to fit residues: 207.0275 Evaluate side-chains 376 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 291 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 476 ARG Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 179 HIS Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 326 ASP Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 237 GLU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 326 ASP Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 413 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 263 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 199 optimal weight: 0.5980 chunk 154 optimal weight: 4.9990 chunk 229 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 271 optimal weight: 2.9990 chunk 170 optimal weight: 8.9990 chunk 165 optimal weight: 0.5980 chunk 125 optimal weight: 9.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS E 179 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22170 Z= 0.227 Angle : 0.572 7.884 30030 Z= 0.303 Chirality : 0.045 0.213 3459 Planarity : 0.005 0.050 3957 Dihedral : 5.112 65.678 3084 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.83 % Allowed : 20.22 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % 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: 0.09 (0.15), residues: 2823 helix: 1.02 (0.15), residues: 1128 sheet: 0.64 (0.24), residues: 417 loop : -1.00 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS E 179 PHE 0.024 0.002 PHE C 494 TYR 0.014 0.001 TYR B 240 ARG 0.008 0.000 ARG D 3 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 305 time to evaluate : 2.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.5916 (mp0) REVERT: A 198 ILE cc_start: 0.5831 (OUTLIER) cc_final: 0.5435 (mt) REVERT: A 236 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6604 (p90) REVERT: A 278 ARG cc_start: 0.6874 (mtp85) cc_final: 0.5915 (mtm-85) REVERT: A 306 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.7016 (m-30) REVERT: A 460 PHE cc_start: 0.7785 (t80) cc_final: 0.7289 (t80) REVERT: A 476 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7325 (mtm-85) REVERT: B 57 ASN cc_start: 0.6863 (OUTLIER) cc_final: 0.6558 (p0) REVERT: B 339 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7121 (m-30) REVERT: B 460 PHE cc_start: 0.7464 (t80) cc_final: 0.6971 (t80) REVERT: C 60 MET cc_start: 0.6408 (mmp) cc_final: 0.6183 (mmp) REVERT: C 95 MET cc_start: 0.6654 (mtp) cc_final: 0.6321 (mmm) REVERT: C 198 ILE cc_start: 0.5624 (mt) cc_final: 0.5055 (mt) REVERT: C 219 ASP cc_start: 0.5553 (OUTLIER) cc_final: 0.5344 (p0) REVERT: C 289 ASP cc_start: 0.5967 (OUTLIER) cc_final: 0.5666 (m-30) REVERT: C 306 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7283 (m-30) REVERT: C 460 PHE cc_start: 0.7402 (t80) cc_final: 0.6984 (t80) REVERT: C 476 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7530 (mtm-85) REVERT: D 285 MET cc_start: 0.6491 (ttt) cc_final: 0.6290 (ttm) REVERT: E 64 MET cc_start: 0.7231 (mmp) cc_final: 0.6938 (mmm) REVERT: E 237 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6786 (pt0) REVERT: E 303 ILE cc_start: 0.6762 (OUTLIER) cc_final: 0.6454 (mm) REVERT: E 418 GLU cc_start: 0.6754 (pm20) cc_final: 0.6486 (pm20) REVERT: F 237 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6827 (pt0) REVERT: F 285 MET cc_start: 0.6889 (OUTLIER) cc_final: 0.6276 (ttm) REVERT: F 297 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.6881 (ptpp) outliers start: 112 outliers final: 80 residues processed: 395 average time/residue: 0.3488 time to fit residues: 210.9942 Evaluate side-chains 394 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 298 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 476 ARG Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 179 HIS Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 326 ASP Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 237 GLU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 297 LYS Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 326 ASP Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 413 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 168 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 162 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 172 optimal weight: 0.0670 chunk 185 optimal weight: 30.0000 chunk 134 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 213 optimal weight: 0.9990 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS E 179 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22170 Z= 0.199 Angle : 0.559 10.576 30030 Z= 0.294 Chirality : 0.044 0.185 3459 Planarity : 0.005 0.048 3957 Dihedral : 4.998 67.078 3084 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.92 % Allowed : 19.97 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % 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: 0.22 (0.15), residues: 2823 helix: 1.14 (0.15), residues: 1128 sheet: 0.73 (0.25), residues: 411 loop : -0.95 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.001 HIS E 179 PHE 0.037 0.002 PHE D 409 TYR 0.014 0.001 TYR F 199 ARG 0.008 0.000 ARG D 3 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 301 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.5900 (mp0) REVERT: A 236 PHE cc_start: 0.7122 (OUTLIER) cc_final: 0.6625 (p90) REVERT: A 278 ARG cc_start: 0.6820 (mtp85) cc_final: 0.5909 (mtm-85) REVERT: A 279 ARG cc_start: 0.6499 (tpp80) cc_final: 0.6105 (mpt180) REVERT: A 306 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.7032 (m-30) REVERT: A 460 PHE cc_start: 0.7785 (t80) cc_final: 0.7322 (t80) REVERT: A 476 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7295 (mtm-85) REVERT: B 57 ASN cc_start: 0.6846 (OUTLIER) cc_final: 0.6582 (p0) REVERT: B 108 VAL cc_start: 0.8008 (p) cc_final: 0.7691 (m) REVERT: B 219 ASP cc_start: 0.5045 (OUTLIER) cc_final: 0.4774 (p0) REVERT: B 339 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7137 (m-30) REVERT: B 460 PHE cc_start: 0.7472 (t80) cc_final: 0.6970 (t80) REVERT: B 476 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7256 (mtm-85) REVERT: C 38 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7603 (mm) REVERT: C 62 MET cc_start: 0.6724 (OUTLIER) cc_final: 0.6146 (mtm) REVERT: C 95 MET cc_start: 0.6622 (mtp) cc_final: 0.6302 (mmm) REVERT: C 198 ILE cc_start: 0.5671 (mt) cc_final: 0.5093 (mt) REVERT: C 289 ASP cc_start: 0.5891 (OUTLIER) cc_final: 0.5627 (m-30) REVERT: C 306 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.7222 (m-30) REVERT: C 460 PHE cc_start: 0.7395 (t80) cc_final: 0.6882 (t80) REVERT: C 476 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7480 (mtm-85) REVERT: D 418 GLU cc_start: 0.6604 (pm20) cc_final: 0.6368 (pm20) REVERT: D 469 MET cc_start: 0.6549 (mmp) cc_final: 0.5909 (mpp) REVERT: E 64 MET cc_start: 0.7227 (mmp) cc_final: 0.6959 (mmm) REVERT: E 237 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6708 (pt0) REVERT: E 303 ILE cc_start: 0.6749 (OUTLIER) cc_final: 0.6449 (mm) REVERT: E 418 GLU cc_start: 0.6674 (pm20) cc_final: 0.6415 (pm20) REVERT: F 237 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6812 (pt0) REVERT: F 285 MET cc_start: 0.6824 (OUTLIER) cc_final: 0.6150 (ttm) REVERT: F 297 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.6855 (ptpp) REVERT: F 439 GLU cc_start: 0.7696 (tp30) cc_final: 0.7483 (tp30) outliers start: 114 outliers final: 84 residues processed: 394 average time/residue: 0.3510 time to fit residues: 209.0640 Evaluate side-chains 392 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 290 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 476 ARG Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 179 HIS Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 326 ASP Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 237 GLU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 297 LYS Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 326 ASP Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 413 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 247 optimal weight: 5.9990 chunk 260 optimal weight: 0.0670 chunk 237 optimal weight: 0.0570 chunk 253 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 198 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 228 optimal weight: 4.9990 chunk 239 optimal weight: 0.0000 chunk 252 optimal weight: 6.9990 overall best weight: 2.0244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS E 179 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22170 Z= 0.213 Angle : 0.566 9.704 30030 Z= 0.297 Chirality : 0.045 0.179 3459 Planarity : 0.005 0.046 3957 Dihedral : 4.988 67.745 3084 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 5.13 % Allowed : 20.14 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % 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: 0.25 (0.15), residues: 2823 helix: 1.17 (0.15), residues: 1128 sheet: 0.71 (0.24), residues: 417 loop : -0.94 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS E 179 PHE 0.034 0.002 PHE D 409 TYR 0.013 0.001 TYR F 199 ARG 0.009 0.000 ARG D 3 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 290 time to evaluate : 2.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.5900 (mp0) REVERT: A 236 PHE cc_start: 0.7136 (OUTLIER) cc_final: 0.6638 (p90) REVERT: A 278 ARG cc_start: 0.6838 (mtp85) cc_final: 0.5921 (mtm-85) REVERT: A 279 ARG cc_start: 0.6507 (tpp80) cc_final: 0.6070 (mpt180) REVERT: A 306 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.6965 (m-30) REVERT: A 460 PHE cc_start: 0.7746 (t80) cc_final: 0.7311 (t80) REVERT: A 476 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7272 (mtm-85) REVERT: B 57 ASN cc_start: 0.6842 (OUTLIER) cc_final: 0.6579 (p0) REVERT: B 108 VAL cc_start: 0.8016 (p) cc_final: 0.7705 (m) REVERT: B 219 ASP cc_start: 0.5073 (OUTLIER) cc_final: 0.4802 (p0) REVERT: B 339 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7166 (m-30) REVERT: B 476 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7317 (mtm-85) REVERT: C 38 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7591 (mm) REVERT: C 62 MET cc_start: 0.6752 (OUTLIER) cc_final: 0.6118 (mtm) REVERT: C 95 MET cc_start: 0.6572 (mtp) cc_final: 0.6289 (mmm) REVERT: C 198 ILE cc_start: 0.5710 (OUTLIER) cc_final: 0.5123 (mt) REVERT: C 289 ASP cc_start: 0.5911 (OUTLIER) cc_final: 0.5649 (m-30) REVERT: C 306 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7274 (m-30) REVERT: C 460 PHE cc_start: 0.7343 (t80) cc_final: 0.6806 (t80) REVERT: C 476 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7464 (mtm-85) REVERT: D 418 GLU cc_start: 0.6581 (pm20) cc_final: 0.6342 (pm20) REVERT: E 64 MET cc_start: 0.7257 (mmp) cc_final: 0.6989 (mmm) REVERT: E 237 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6712 (pt0) REVERT: E 303 ILE cc_start: 0.6750 (OUTLIER) cc_final: 0.6452 (mm) REVERT: F 237 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6812 (pt0) REVERT: F 285 MET cc_start: 0.6853 (OUTLIER) cc_final: 0.6198 (ttm) REVERT: F 297 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.6833 (ptpp) outliers start: 119 outliers final: 90 residues processed: 387 average time/residue: 0.3377 time to fit residues: 199.3025 Evaluate side-chains 393 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 284 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 476 ARG Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 179 HIS Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 326 ASP Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 237 GLU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 297 LYS Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 326 ASP Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 413 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 166 optimal weight: 0.9980 chunk 267 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 chunk 127 optimal weight: 20.0000 chunk 186 optimal weight: 4.9990 chunk 280 optimal weight: 6.9990 chunk 258 optimal weight: 4.9990 chunk 223 optimal weight: 0.6980 chunk 23 optimal weight: 9.9990 chunk 172 optimal weight: 0.0030 chunk 137 optimal weight: 10.0000 overall best weight: 1.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 HIS ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS D 423 GLN E 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22170 Z= 0.197 Angle : 0.563 9.598 30030 Z= 0.295 Chirality : 0.044 0.179 3459 Planarity : 0.005 0.045 3957 Dihedral : 4.947 68.970 3084 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.53 % Allowed : 20.61 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % 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: 0.33 (0.16), residues: 2823 helix: 1.23 (0.15), residues: 1128 sheet: 0.67 (0.24), residues: 441 loop : -0.87 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS E 179 PHE 0.030 0.001 PHE D 409 TYR 0.014 0.001 TYR F 199 ARG 0.009 0.000 ARG F 3 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 293 time to evaluate : 2.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.5887 (mp0) REVERT: A 236 PHE cc_start: 0.7123 (OUTLIER) cc_final: 0.6635 (p90) REVERT: A 278 ARG cc_start: 0.6808 (mtp85) cc_final: 0.5885 (mtm-85) REVERT: A 279 ARG cc_start: 0.6534 (tpp80) cc_final: 0.6096 (mpt180) REVERT: A 306 ASP cc_start: 0.7332 (OUTLIER) cc_final: 0.6959 (m-30) REVERT: A 460 PHE cc_start: 0.7762 (t80) cc_final: 0.7332 (t80) REVERT: A 476 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7256 (mtm-85) REVERT: B 57 ASN cc_start: 0.6827 (OUTLIER) cc_final: 0.6602 (p0) REVERT: B 108 VAL cc_start: 0.8005 (p) cc_final: 0.7708 (m) REVERT: B 132 ARG cc_start: 0.7337 (mpp80) cc_final: 0.6363 (tpt170) REVERT: B 198 ILE cc_start: 0.5934 (mt) cc_final: 0.5514 (mt) REVERT: B 219 ASP cc_start: 0.5051 (OUTLIER) cc_final: 0.4783 (p0) REVERT: B 339 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7136 (m-30) REVERT: B 476 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7302 (mtm-85) REVERT: C 38 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7565 (mm) REVERT: C 62 MET cc_start: 0.6688 (OUTLIER) cc_final: 0.6042 (mtm) REVERT: C 132 ARG cc_start: 0.6683 (tpt170) cc_final: 0.6273 (mpp80) REVERT: C 198 ILE cc_start: 0.5721 (OUTLIER) cc_final: 0.5138 (mt) REVERT: C 289 ASP cc_start: 0.5915 (OUTLIER) cc_final: 0.5655 (m-30) REVERT: C 306 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7264 (m-30) REVERT: C 418 GLU cc_start: 0.5729 (tm-30) cc_final: 0.5465 (tm-30) REVERT: C 460 PHE cc_start: 0.7302 (t80) cc_final: 0.6714 (t80) REVERT: C 476 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7461 (mtm-85) REVERT: D 418 GLU cc_start: 0.6587 (pm20) cc_final: 0.6364 (pm20) REVERT: E 64 MET cc_start: 0.7243 (mmp) cc_final: 0.6974 (mmm) REVERT: E 237 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6688 (pt0) REVERT: E 303 ILE cc_start: 0.6749 (OUTLIER) cc_final: 0.6445 (mm) REVERT: F 237 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6809 (pt0) REVERT: F 285 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6161 (ttm) REVERT: F 297 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.6801 (ptpp) outliers start: 105 outliers final: 83 residues processed: 378 average time/residue: 0.3418 time to fit residues: 197.3241 Evaluate side-chains 390 residues out of total 2319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 288 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 476 ARG Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 179 HIS Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 326 ASP Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 237 GLU Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 297 LYS Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 326 ASP Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 413 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 177 optimal weight: 5.9990 chunk 238 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 206 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 62 optimal weight: 6.9990 chunk 224 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 230 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 474 HIS E 179 HIS F 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.203354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.177482 restraints weight = 22072.712| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 1.07 r_work: 0.3888 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 22170 Z= 0.556 Angle : 0.824 10.390 30030 Z= 0.438 Chirality : 0.055 0.244 3459 Planarity : 0.007 0.073 3957 Dihedral : 5.848 64.782 3084 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 5.22 % Allowed : 20.05 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % 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: -0.69 (0.15), residues: 2823 helix: 0.36 (0.15), residues: 1131 sheet: 0.35 (0.25), residues: 378 loop : -1.43 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.022 0.003 HIS E 179 PHE 0.046 0.003 PHE D 409 TYR 0.031 0.003 TYR C 240 ARG 0.010 0.001 ARG D 291 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4953.57 seconds wall clock time: 89 minutes 49.79 seconds (5389.79 seconds total)