Starting phenix.real_space_refine on Tue Apr 9 21:07:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dxo_27771/04_2024/8dxo_27771.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dxo_27771/04_2024/8dxo_27771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dxo_27771/04_2024/8dxo_27771.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dxo_27771/04_2024/8dxo_27771.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dxo_27771/04_2024/8dxo_27771.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dxo_27771/04_2024/8dxo_27771.pdb" } resolution = 3.6 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= 0.029 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 147 5.16 5 C 11561 2.51 5 N 2760 2.21 5 O 3031 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 369": "OD1" <-> "OD2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 243": "OE1" <-> "OE2" Residue "G TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 17499 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2481 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 7, 'TRANS': 290} Chain breaks: 2 Chain: "B" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2501 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 7, 'TRANS': 292} Chain breaks: 2 Chain: "C" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2507 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 7, 'TRANS': 293} Chain breaks: 2 Chain: "D" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2497 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 7, 'TRANS': 292} Chain breaks: 2 Chain: "E" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2507 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 7, 'TRANS': 293} Chain breaks: 2 Chain: "F" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2516 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 7, 'TRANS': 294} Chain breaks: 2 Chain: "G" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2490 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 7, 'TRANS': 291} Chain breaks: 2 Time building chain proxies: 9.32, per 1000 atoms: 0.53 Number of scatterers: 17499 At special positions: 0 Unit cell: (122.1, 114.4, 130.9, 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 147 16.00 O 3031 8.00 N 2760 7.00 C 11561 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 293 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 115 " - pdb=" SG CYS B 293 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 115 " - pdb=" SG CYS C 293 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 308 " distance=2.03 Simple disulfide: pdb=" SG CYS D 115 " - pdb=" SG CYS D 293 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 308 " distance=2.03 Simple disulfide: pdb=" SG CYS E 115 " - pdb=" SG CYS E 293 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 308 " distance=2.03 Simple disulfide: pdb=" SG CYS G 115 " - pdb=" SG CYS G 293 " distance=2.03 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: 6.58 Conformation dependent library (CDL) restraints added in 3.2 seconds 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4062 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 7 sheets defined 72.1% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 22 through 48 removed outlier: 4.063A pdb=" N VAL A 26 " --> pdb=" O PRO A 22 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE A 27 " --> pdb=" O TRP A 23 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N THR A 28 " --> pdb=" O TRP A 24 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 117 removed outlier: 3.614A pdb=" N TYR A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU A 117 " --> pdb=" O GLN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 removed outlier: 3.702A pdb=" N LYS A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR A 126 " --> pdb=" O TRP A 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 121 through 126' Processing helix chain 'A' and resid 126 through 148 removed outlier: 3.682A pdb=" N TRP A 145 " --> pdb=" O CYS A 141 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 Processing helix chain 'A' and resid 169 through 176 removed outlier: 4.396A pdb=" N ARG A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 253 Processing helix chain 'A' and resid 259 through 283 removed outlier: 3.764A pdb=" N ALA A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 342 Processing helix chain 'A' and resid 352 through 359 Processing helix chain 'A' and resid 368 through 381 removed outlier: 4.149A pdb=" N GLN A 379 " --> pdb=" O HIS A 375 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 393 removed outlier: 3.543A pdb=" N ARG A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 405 removed outlier: 4.515A pdb=" N GLU A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 Proline residue: B 22 - end of helix Processing helix chain 'B' and resid 23 through 48 removed outlier: 5.311A pdb=" N ASP B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 47 " --> pdb=" O CYS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 120 removed outlier: 3.856A pdb=" N TYR B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 120 " --> pdb=" O TYR B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.654A pdb=" N LYS B 125 " --> pdb=" O HIS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 143 removed outlier: 3.665A pdb=" N SER B 142 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B 143 " --> pdb=" O MET B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 148 removed outlier: 3.625A pdb=" N LYS B 147 " --> pdb=" O ASN B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 165 Processing helix chain 'B' and resid 168 through 175 removed outlier: 4.426A pdb=" N THR B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 175 " --> pdb=" O THR B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 252 Processing helix chain 'B' and resid 259 through 283 removed outlier: 3.745A pdb=" N LEU B 283 " --> pdb=" O TYR B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 341 removed outlier: 3.687A pdb=" N SER B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS B 318 " --> pdb=" O HIS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 359 Processing helix chain 'B' and resid 367 through 381 removed outlier: 3.628A pdb=" N ALA B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN B 379 " --> pdb=" O HIS B 375 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR B 380 " --> pdb=" O MET B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 391 removed outlier: 3.502A pdb=" N ARG B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 405 removed outlier: 4.106A pdb=" N GLU B 397 " --> pdb=" O SER B 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 47 removed outlier: 4.187A pdb=" N ASP C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR C 30 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 45 " --> pdb=" O PHE C 41 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL C 47 " --> pdb=" O CYS C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 119 removed outlier: 3.855A pdb=" N TYR C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 143 removed outlier: 3.708A pdb=" N LYS C 125 " --> pdb=" O HIS C 121 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR C 126 " --> pdb=" O TRP C 122 " (cutoff:3.500A) Proline residue: C 128 - end of helix Processing helix chain 'C' and resid 152 through 167 removed outlier: 3.844A pdb=" N ASP C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 175 removed outlier: 4.398A pdb=" N THR C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU C 175 " --> pdb=" O THR C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 252 removed outlier: 4.185A pdb=" N GLU C 236 " --> pdb=" O LYS C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 283 removed outlier: 4.212A pdb=" N TYR C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL C 263 " --> pdb=" O TYR C 259 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG C 264 " --> pdb=" O ALA C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 287 removed outlier: 4.074A pdb=" N VAL C 287 " --> pdb=" O VAL C 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 284 through 287' Processing helix chain 'C' and resid 313 through 343 removed outlier: 3.628A pdb=" N PHE C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR C 343 " --> pdb=" O TYR C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 359 Processing helix chain 'C' and resid 367 through 379 removed outlier: 3.829A pdb=" N ALA C 371 " --> pdb=" O LYS C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 393 through 405 Processing helix chain 'D' and resid 22 through 47 removed outlier: 3.548A pdb=" N VAL D 26 " --> pdb=" O PRO D 22 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL D 47 " --> pdb=" O CYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 120 removed outlier: 3.718A pdb=" N GLU D 117 " --> pdb=" O GLN D 113 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU D 120 " --> pdb=" O TYR D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 removed outlier: 3.528A pdb=" N LYS D 125 " --> pdb=" O HIS D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 142 removed outlier: 3.971A pdb=" N LEU D 130 " --> pdb=" O TYR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 167 removed outlier: 3.949A pdb=" N LYS D 154 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 177 removed outlier: 4.153A pdb=" N THR D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 252 removed outlier: 3.891A pdb=" N LEU D 250 " --> pdb=" O LYS D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 282 removed outlier: 3.632A pdb=" N VAL D 263 " --> pdb=" O TYR D 259 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR D 266 " --> pdb=" O TYR D 262 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL D 267 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU D 268 " --> pdb=" O ARG D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 341 removed outlier: 3.990A pdb=" N LYS D 318 " --> pdb=" O HIS D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 359 removed outlier: 3.869A pdb=" N GLN D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 380 Processing helix chain 'D' and resid 383 through 390 removed outlier: 3.515A pdb=" N ARG D 387 " --> pdb=" O LEU D 383 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL D 390 " --> pdb=" O LYS D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 405 removed outlier: 3.953A pdb=" N GLU D 397 " --> pdb=" O SER D 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 21 Processing helix chain 'E' and resid 22 through 50 removed outlier: 3.759A pdb=" N VAL E 26 " --> pdb=" O PRO E 22 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET E 48 " --> pdb=" O THR E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 119 removed outlier: 3.634A pdb=" N TYR E 108 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER E 109 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU E 117 " --> pdb=" O GLN E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 Processing helix chain 'E' and resid 127 through 142 removed outlier: 3.511A pdb=" N VAL E 131 " --> pdb=" O PHE E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 167 removed outlier: 3.952A pdb=" N PHE E 158 " --> pdb=" O LYS E 154 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP E 167 " --> pdb=" O GLY E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 176 removed outlier: 3.778A pdb=" N THR E 172 " --> pdb=" O SER E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 253 removed outlier: 4.008A pdb=" N GLU E 253 " --> pdb=" O ARG E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 284 Processing helix chain 'E' and resid 285 through 287 No H-bonds generated for 'chain 'E' and resid 285 through 287' Processing helix chain 'E' and resid 312 through 344 removed outlier: 3.743A pdb=" N PHE E 316 " --> pdb=" O MET E 312 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS E 318 " --> pdb=" O HIS E 314 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG E 344 " --> pdb=" O TRP E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 359 Processing helix chain 'E' and resid 367 through 381 removed outlier: 3.625A pdb=" N ALA E 371 " --> pdb=" O LYS E 367 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN E 379 " --> pdb=" O HIS E 375 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYR E 380 " --> pdb=" O MET E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 391 removed outlier: 3.924A pdb=" N PHE E 391 " --> pdb=" O ARG E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 405 removed outlier: 3.604A pdb=" N GLU E 397 " --> pdb=" O SER E 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 49 removed outlier: 3.889A pdb=" N THR F 28 " --> pdb=" O TRP F 24 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 119 removed outlier: 3.689A pdb=" N TYR F 108 " --> pdb=" O ASP F 104 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 126 Processing helix chain 'F' and resid 127 through 143 Processing helix chain 'F' and resid 152 through 167 removed outlier: 3.599A pdb=" N GLU F 156 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP F 167 " --> pdb=" O GLY F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 177 removed outlier: 3.583A pdb=" N THR F 172 " --> pdb=" O SER F 168 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU F 177 " --> pdb=" O ARG F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 253 removed outlier: 3.614A pdb=" N LEU F 250 " --> pdb=" O LYS F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 283 removed outlier: 3.718A pdb=" N ALA F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET F 261 " --> pdb=" O ILE F 257 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TYR F 262 " --> pdb=" O LEU F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 342 removed outlier: 3.835A pdb=" N PHE F 316 " --> pdb=" O MET F 312 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE F 342 " --> pdb=" O LEU F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 359 removed outlier: 3.552A pdb=" N ARG F 355 " --> pdb=" O PHE F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 379 removed outlier: 3.674A pdb=" N ALA F 371 " --> pdb=" O LYS F 367 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN F 379 " --> pdb=" O HIS F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 391 removed outlier: 3.957A pdb=" N PHE F 391 " --> pdb=" O ARG F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 405 removed outlier: 3.724A pdb=" N LEU F 405 " --> pdb=" O LYS F 401 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 47 removed outlier: 3.827A pdb=" N VAL G 26 " --> pdb=" O PRO G 22 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL G 47 " --> pdb=" O CYS G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 119 removed outlier: 3.767A pdb=" N GLU G 117 " --> pdb=" O GLN G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 126 removed outlier: 3.820A pdb=" N LYS G 125 " --> pdb=" O HIS G 121 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR G 126 " --> pdb=" O TRP G 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 121 through 126' Processing helix chain 'G' and resid 126 through 142 removed outlier: 3.643A pdb=" N LEU G 130 " --> pdb=" O TYR G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 165 removed outlier: 3.849A pdb=" N ILE G 155 " --> pdb=" O SER G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 177 Processing helix chain 'G' and resid 235 through 253 removed outlier: 3.561A pdb=" N ALA G 240 " --> pdb=" O GLU G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 283 removed outlier: 3.696A pdb=" N VAL G 263 " --> pdb=" O TYR G 259 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER G 281 " --> pdb=" O ILE G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 287 removed outlier: 3.679A pdb=" N VAL G 287 " --> pdb=" O VAL G 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 284 through 287' Processing helix chain 'G' and resid 312 through 343 removed outlier: 3.908A pdb=" N PHE G 316 " --> pdb=" O MET G 312 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER G 317 " --> pdb=" O ALA G 313 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LYS G 318 " --> pdb=" O HIS G 314 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE G 321 " --> pdb=" O SER G 317 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE G 342 " --> pdb=" O LEU G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 359 Processing helix chain 'G' and resid 367 through 379 removed outlier: 3.958A pdb=" N GLN G 379 " --> pdb=" O HIS G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 390 removed outlier: 3.553A pdb=" N LYS G 386 " --> pdb=" O PRO G 382 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL G 390 " --> pdb=" O LYS G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 393 through 405 removed outlier: 3.743A pdb=" N LEU G 405 " --> pdb=" O LYS G 401 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 56 Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 56 Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 56 Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 56 Processing sheet with id=AA7, first strand: chain 'G' and resid 53 through 56 1049 hydrogen bonds defined for protein. 3117 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: 4.65 Time building geometry restraints manager: 7.22 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: 5197 1.34 - 1.46: 4695 1.46 - 1.58: 7853 1.58 - 1.70: 0 1.70 - 1.81: 224 Bond restraints: 17969 Sorted by residual: bond pdb=" N ASN B 368 " pdb=" CA ASN B 368 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.38e+00 bond pdb=" C ASP E 381 " pdb=" N PRO E 382 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.31e+00 bond pdb=" CB PHE A 273 " pdb=" CG PHE A 273 " ideal model delta sigma weight residual 1.502 1.479 0.023 2.30e-02 1.89e+03 9.84e-01 bond pdb=" C ASP A 381 " pdb=" N PRO A 382 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 9.57e-01 bond pdb=" C VAL A 327 " pdb=" O VAL A 327 " ideal model delta sigma weight residual 1.237 1.227 0.010 1.17e-02 7.31e+03 7.72e-01 ... (remaining 17964 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.44: 363 106.44 - 113.36: 9493 113.36 - 120.29: 7192 120.29 - 127.22: 7030 127.22 - 134.14: 180 Bond angle restraints: 24258 Sorted by residual: angle pdb=" N LEU G 315 " pdb=" CA LEU G 315 " pdb=" C LEU G 315 " ideal model delta sigma weight residual 113.18 108.63 4.55 1.33e+00 5.65e-01 1.17e+01 angle pdb=" N MET G 48 " pdb=" CA MET G 48 " pdb=" C MET G 48 " ideal model delta sigma weight residual 113.18 108.98 4.20 1.33e+00 5.65e-01 9.99e+00 angle pdb=" N GLU E 254 " pdb=" CA GLU E 254 " pdb=" C GLU E 254 " ideal model delta sigma weight residual 114.56 110.69 3.87 1.27e+00 6.20e-01 9.29e+00 angle pdb=" C ALA F 278 " pdb=" N TYR F 279 " pdb=" CA TYR F 279 " ideal model delta sigma weight residual 120.68 115.61 5.07 1.70e+00 3.46e-01 8.91e+00 angle pdb=" C ALA A 278 " pdb=" N TYR A 279 " pdb=" CA TYR A 279 " ideal model delta sigma weight residual 122.06 116.58 5.48 1.86e+00 2.89e-01 8.68e+00 ... (remaining 24253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 9417 17.93 - 35.87: 958 35.87 - 53.80: 166 53.80 - 71.74: 22 71.74 - 89.67: 19 Dihedral angle restraints: 10582 sinusoidal: 4307 harmonic: 6275 Sorted by residual: dihedral pdb=" CA ASP B 25 " pdb=" C ASP B 25 " pdb=" N VAL B 26 " pdb=" CA VAL B 26 " ideal model delta harmonic sigma weight residual 180.00 150.02 29.98 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA VAL G 47 " pdb=" C VAL G 47 " pdb=" N MET G 48 " pdb=" CA MET G 48 " ideal model delta harmonic sigma weight residual 180.00 154.29 25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA ILE B 257 " pdb=" C ILE B 257 " pdb=" N LEU B 258 " pdb=" CA LEU B 258 " ideal model delta harmonic sigma weight residual 180.00 157.87 22.13 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 10579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1953 0.035 - 0.070: 516 0.070 - 0.105: 138 0.105 - 0.140: 38 0.140 - 0.174: 2 Chirality restraints: 2647 Sorted by residual: chirality pdb=" CG LEU B 392 " pdb=" CB LEU B 392 " pdb=" CD1 LEU B 392 " pdb=" CD2 LEU B 392 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.60e-01 chirality pdb=" CA ILE A 53 " pdb=" N ILE A 53 " pdb=" C ILE A 53 " pdb=" CB ILE A 53 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA ILE G 363 " pdb=" N ILE G 363 " pdb=" C ILE G 363 " pdb=" CB ILE G 363 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 2644 not shown) Planarity restraints: 2955 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 148 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO C 149 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET C 37 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.79e+00 pdb=" C MET C 37 " -0.029 2.00e-02 2.50e+03 pdb=" O MET C 37 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE C 38 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 145 " -0.013 2.00e-02 2.50e+03 1.00e-02 2.52e+00 pdb=" CG TRP D 145 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP D 145 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP D 145 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 145 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 145 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 145 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 145 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 145 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 145 " -0.001 2.00e-02 2.50e+03 ... (remaining 2952 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1326 2.74 - 3.28: 17965 3.28 - 3.82: 28083 3.82 - 4.36: 31371 4.36 - 4.90: 55105 Nonbonded interactions: 133850 Sorted by model distance: nonbonded pdb=" O LYS C 239 " pdb=" OE1 GLU C 243 " model vdw 2.195 3.040 nonbonded pdb=" OH TYR D 123 " pdb=" OD1 ASN D 280 " model vdw 2.199 2.440 nonbonded pdb=" NE2 HIS F 134 " pdb=" OH TYR F 279 " model vdw 2.201 2.520 nonbonded pdb=" NH2 ARG C 355 " pdb=" OD1 ASP C 365 " model vdw 2.212 2.520 nonbonded pdb=" OH TYR G 123 " pdb=" OD1 ASN G 280 " model vdw 2.233 2.440 ... (remaining 133845 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' and (resid 16 through 175 or resid 234 through 405)) selection = (chain 'B' and (resid 16 through 175 or resid 234 through 405)) selection = (chain 'C' and (resid 16 through 175 or resid 234 through 405)) selection = (chain 'D' and (resid 16 through 175 or resid 177 or resid 235 through 405)) selection = (chain 'E' and (resid 16 through 175 or resid 234 through 405)) selection = (chain 'F' and (resid 16 through 175 or resid 177 or resid 235 through 405)) selection = (chain 'G' and (resid 16 through 175 or resid 177 or resid 235 through 405)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.790 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: 0.000 Extract box with map and model: 9.830 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 45.400 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.070 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 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 : 0.002 0.029 17969 Z= 0.151 Angle : 0.525 8.061 24258 Z= 0.293 Chirality : 0.035 0.174 2647 Planarity : 0.003 0.050 2955 Dihedral : 14.798 89.672 6478 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.20), residues: 2059 helix: 1.45 (0.15), residues: 1328 sheet: -0.14 (0.46), residues: 139 loop : -2.52 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 145 HIS 0.008 0.001 HIS B 375 PHE 0.023 0.001 PHE G 289 TYR 0.015 0.001 TYR C 343 ARG 0.003 0.000 ARG B 344 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 355 time to evaluate : 2.625 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: D 143 ASN cc_start: 0.7896 (t0) cc_final: 0.7519 (t0) REVERT: F 363 ILE cc_start: 0.7979 (mm) cc_final: 0.7625 (mm) REVERT: G 377 ILE cc_start: 0.8882 (tp) cc_final: 0.8544 (tp) outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 0.3264 time to fit residues: 169.4351 Evaluate side-chains 281 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 106 optimal weight: 0.6980 chunk 84 optimal weight: 0.1980 chunk 163 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 188 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 265 GLN A 309 ASN A 310 HIS B 46 GLN B 237 GLN C 49 GLN C 113 GLN C 251 HIS C 314 HIS D 112 ASN D 157 HIS E 106 GLN E 112 ASN F 309 ASN G 298 GLN G 310 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17969 Z= 0.180 Angle : 0.510 8.423 24258 Z= 0.272 Chirality : 0.038 0.130 2647 Planarity : 0.003 0.054 2955 Dihedral : 4.055 30.300 2283 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.49 % Allowed : 10.31 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.83 (0.20), residues: 2059 helix: 1.79 (0.15), residues: 1366 sheet: -0.26 (0.46), residues: 141 loop : -2.54 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 145 HIS 0.010 0.001 HIS C 251 PHE 0.030 0.002 PHE A 158 TYR 0.028 0.001 TYR A 279 ARG 0.009 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 306 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 143 ASN cc_start: 0.7879 (t0) cc_final: 0.7609 (t0) REVERT: D 158 PHE cc_start: 0.6938 (t80) cc_final: 0.6665 (t80) REVERT: F 363 ILE cc_start: 0.8016 (mm) cc_final: 0.7632 (mm) REVERT: G 140 LEU cc_start: 0.8435 (tt) cc_final: 0.8221 (tp) REVERT: G 242 PHE cc_start: 0.8160 (m-80) cc_final: 0.7954 (m-80) outliers start: 29 outliers final: 23 residues processed: 319 average time/residue: 0.3176 time to fit residues: 149.4157 Evaluate side-chains 298 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 275 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 305 ASN Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 141 CYS Chi-restraints excluded: chain G residue 290 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 52 optimal weight: 0.3980 chunk 189 optimal weight: 0.8980 chunk 204 optimal weight: 0.0020 chunk 168 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 64 optimal weight: 0.2980 chunk 151 optimal weight: 1.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 112 ASN A 309 ASN A 398 ASN B 106 GLN B 237 GLN C 251 HIS E 49 GLN F 309 ASN G 398 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17969 Z= 0.150 Angle : 0.473 6.872 24258 Z= 0.252 Chirality : 0.037 0.132 2647 Planarity : 0.003 0.054 2955 Dihedral : 3.920 29.470 2283 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.32 % Allowed : 12.84 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.00 (0.20), residues: 2059 helix: 1.93 (0.15), residues: 1365 sheet: -0.22 (0.45), residues: 141 loop : -2.49 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 145 HIS 0.006 0.001 HIS C 251 PHE 0.027 0.001 PHE A 158 TYR 0.025 0.001 TYR A 279 ARG 0.004 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 292 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 248 PHE cc_start: 0.6652 (t80) cc_final: 0.6392 (t80) REVERT: D 19 VAL cc_start: 0.8667 (m) cc_final: 0.8246 (m) REVERT: D 143 ASN cc_start: 0.7806 (t0) cc_final: 0.7549 (t0) REVERT: F 363 ILE cc_start: 0.8029 (mm) cc_final: 0.7642 (mm) REVERT: G 140 LEU cc_start: 0.8323 (tt) cc_final: 0.8119 (tp) outliers start: 45 outliers final: 32 residues processed: 312 average time/residue: 0.3178 time to fit residues: 145.9536 Evaluate side-chains 307 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 275 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 305 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 141 CYS Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 290 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 201 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 309 ASN B 106 GLN C 251 HIS F 305 ASN G 398 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17969 Z= 0.208 Angle : 0.494 8.234 24258 Z= 0.265 Chirality : 0.038 0.134 2647 Planarity : 0.003 0.056 2955 Dihedral : 3.948 29.089 2283 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.73 % Allowed : 15.15 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.91 (0.20), residues: 2059 helix: 1.84 (0.15), residues: 1379 sheet: -0.18 (0.46), residues: 139 loop : -2.57 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 23 HIS 0.006 0.001 HIS C 251 PHE 0.028 0.001 PHE F 41 TYR 0.024 0.001 TYR A 279 ARG 0.006 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 290 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 145 TRP cc_start: 0.6760 (t60) cc_final: 0.6491 (t60) REVERT: D 143 ASN cc_start: 0.7813 (t0) cc_final: 0.7537 (t0) REVERT: F 363 ILE cc_start: 0.8038 (mm) cc_final: 0.7608 (mm) outliers start: 53 outliers final: 40 residues processed: 315 average time/residue: 0.3255 time to fit residues: 151.1211 Evaluate side-chains 306 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 266 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 305 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 141 CYS Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 290 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 167 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 171 optimal weight: 0.5980 chunk 138 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 180 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 ASN C 251 HIS C 368 ASN ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 398 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17969 Z= 0.231 Angle : 0.506 6.910 24258 Z= 0.272 Chirality : 0.039 0.135 2647 Planarity : 0.003 0.055 2955 Dihedral : 3.974 29.198 2283 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.45 % Allowed : 16.13 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.89 (0.20), residues: 2059 helix: 1.80 (0.15), residues: 1378 sheet: -0.14 (0.46), residues: 137 loop : -2.52 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 23 HIS 0.007 0.001 HIS C 251 PHE 0.029 0.001 PHE G 158 TYR 0.022 0.001 TYR A 279 ARG 0.003 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 285 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 145 TRP cc_start: 0.6808 (t60) cc_final: 0.6580 (t60) REVERT: D 143 ASN cc_start: 0.7891 (t0) cc_final: 0.7625 (t0) REVERT: D 158 PHE cc_start: 0.6691 (t80) cc_final: 0.6418 (t80) REVERT: F 363 ILE cc_start: 0.8071 (mm) cc_final: 0.7625 (mm) REVERT: G 108 TYR cc_start: 0.8843 (OUTLIER) cc_final: 0.8544 (m-10) outliers start: 67 outliers final: 53 residues processed: 319 average time/residue: 0.3066 time to fit residues: 146.1683 Evaluate side-chains 326 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 272 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 305 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 370 PHE Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 305 ASN Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 290 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 201 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 309 ASN B 106 GLN C 251 HIS ** D 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 398 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17969 Z= 0.190 Angle : 0.491 7.328 24258 Z= 0.264 Chirality : 0.038 0.199 2647 Planarity : 0.003 0.054 2955 Dihedral : 3.937 29.236 2283 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.40 % Allowed : 17.42 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.91 (0.20), residues: 2059 helix: 1.83 (0.15), residues: 1373 sheet: -0.22 (0.46), residues: 139 loop : -2.48 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 23 HIS 0.007 0.001 HIS C 251 PHE 0.029 0.001 PHE G 158 TYR 0.023 0.001 TYR A 279 ARG 0.003 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 288 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 145 TRP cc_start: 0.6828 (t60) cc_final: 0.6561 (t60) REVERT: C 242 PHE cc_start: 0.6900 (m-80) cc_final: 0.6478 (m-80) REVERT: C 273 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.8114 (t80) REVERT: D 143 ASN cc_start: 0.7872 (t0) cc_final: 0.7597 (t0) REVERT: D 368 ASN cc_start: 0.7696 (p0) cc_final: 0.7367 (p0) REVERT: F 363 ILE cc_start: 0.8073 (mm) cc_final: 0.7659 (mm) REVERT: F 373 MET cc_start: 0.6916 (mmm) cc_final: 0.6694 (mmm) REVERT: G 108 TYR cc_start: 0.8845 (OUTLIER) cc_final: 0.8543 (m-10) outliers start: 66 outliers final: 50 residues processed: 324 average time/residue: 0.2978 time to fit residues: 144.3313 Evaluate side-chains 324 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 272 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 305 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 243 GLU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 305 ASN Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 290 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 114 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 92 optimal weight: 0.0670 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 251 HIS D 309 ASN E 157 HIS F 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17969 Z= 0.160 Angle : 0.490 9.872 24258 Z= 0.260 Chirality : 0.038 0.179 2647 Planarity : 0.003 0.052 2955 Dihedral : 3.874 29.209 2283 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.56 % Allowed : 18.14 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.00 (0.20), residues: 2059 helix: 1.91 (0.15), residues: 1370 sheet: -0.08 (0.46), residues: 137 loop : -2.47 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 23 HIS 0.007 0.001 HIS C 251 PHE 0.033 0.001 PHE F 41 TYR 0.024 0.001 TYR A 279 ARG 0.002 0.000 ARG D 344 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 297 time to evaluate : 2.354 Fit side-chains revert: symmetry clash REVERT: B 145 TRP cc_start: 0.6815 (t60) cc_final: 0.6513 (t60) REVERT: D 143 ASN cc_start: 0.7817 (t0) cc_final: 0.7573 (t0) REVERT: D 347 ARG cc_start: 0.7028 (ttm170) cc_final: 0.6588 (mpp-170) REVERT: D 368 ASN cc_start: 0.7763 (p0) cc_final: 0.7219 (p0) REVERT: F 363 ILE cc_start: 0.8065 (mm) cc_final: 0.7655 (mm) REVERT: F 373 MET cc_start: 0.6932 (mmm) cc_final: 0.6729 (mmm) REVERT: G 108 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.8514 (m-10) REVERT: G 167 ASP cc_start: 0.4720 (OUTLIER) cc_final: 0.4473 (t0) outliers start: 69 outliers final: 54 residues processed: 331 average time/residue: 0.3063 time to fit residues: 152.6655 Evaluate side-chains 339 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 283 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 305 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 370 PHE Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 305 ASN Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 141 CYS Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 290 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 124 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 157 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 ASN C 251 HIS ** D 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 398 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17969 Z= 0.215 Angle : 0.532 12.012 24258 Z= 0.280 Chirality : 0.039 0.174 2647 Planarity : 0.003 0.053 2955 Dihedral : 3.950 29.088 2283 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.45 % Allowed : 19.23 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.88 (0.20), residues: 2059 helix: 1.82 (0.15), residues: 1374 sheet: -0.07 (0.46), residues: 135 loop : -2.57 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 170 HIS 0.007 0.001 HIS C 251 PHE 0.030 0.001 PHE G 158 TYR 0.023 0.001 TYR A 279 ARG 0.002 0.000 ARG D 344 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 284 time to evaluate : 2.193 Fit side-chains revert: symmetry clash REVERT: A 273 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.7038 (t80) REVERT: B 145 TRP cc_start: 0.6693 (t60) cc_final: 0.6444 (t60) REVERT: D 143 ASN cc_start: 0.7875 (t0) cc_final: 0.7611 (t0) REVERT: D 347 ARG cc_start: 0.6992 (ttm170) cc_final: 0.6566 (mpp-170) REVERT: D 351 PHE cc_start: 0.5247 (OUTLIER) cc_final: 0.4964 (m-10) REVERT: D 368 ASN cc_start: 0.7742 (p0) cc_final: 0.7200 (p0) REVERT: F 363 ILE cc_start: 0.8121 (mm) cc_final: 0.7700 (mm) REVERT: G 167 ASP cc_start: 0.4727 (OUTLIER) cc_final: 0.4453 (t0) outliers start: 67 outliers final: 55 residues processed: 322 average time/residue: 0.2988 time to fit residues: 145.4329 Evaluate side-chains 332 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 274 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 305 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 370 PHE Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 305 ASN Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 404 ASN Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 141 CYS Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 290 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 182 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 175 optimal weight: 0.8980 chunk 186 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 146 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 168 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN C 251 HIS ** D 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17969 Z= 0.181 Angle : 0.518 10.932 24258 Z= 0.273 Chirality : 0.038 0.169 2647 Planarity : 0.003 0.052 2955 Dihedral : 3.907 29.230 2283 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.20 % Allowed : 19.59 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.95 (0.20), residues: 2059 helix: 1.87 (0.15), residues: 1374 sheet: -0.25 (0.46), residues: 139 loop : -2.50 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 23 HIS 0.007 0.001 HIS C 251 PHE 0.032 0.001 PHE G 158 TYR 0.023 0.001 TYR A 279 ARG 0.003 0.000 ARG F 344 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 286 time to evaluate : 2.131 Fit side-chains revert: symmetry clash REVERT: A 250 LEU cc_start: 0.5711 (pp) cc_final: 0.5426 (mt) REVERT: A 273 PHE cc_start: 0.7421 (OUTLIER) cc_final: 0.7040 (t80) REVERT: B 145 TRP cc_start: 0.6666 (t60) cc_final: 0.6426 (t60) REVERT: B 373 MET cc_start: 0.4925 (ptp) cc_final: 0.4580 (mtm) REVERT: C 241 LEU cc_start: 0.5277 (OUTLIER) cc_final: 0.5054 (tp) REVERT: D 143 ASN cc_start: 0.7786 (t0) cc_final: 0.7545 (t0) REVERT: D 347 ARG cc_start: 0.7013 (ttm170) cc_final: 0.6647 (mpp-170) REVERT: D 368 ASN cc_start: 0.7751 (p0) cc_final: 0.7169 (p0) REVERT: F 342 PHE cc_start: 0.7916 (m-10) cc_final: 0.7588 (m-10) REVERT: F 363 ILE cc_start: 0.8111 (mm) cc_final: 0.7676 (mm) REVERT: G 246 LYS cc_start: 0.7683 (mttp) cc_final: 0.7418 (mtmm) REVERT: G 248 PHE cc_start: 0.7595 (t80) cc_final: 0.7338 (t80) outliers start: 62 outliers final: 51 residues processed: 318 average time/residue: 0.2914 time to fit residues: 139.2282 Evaluate side-chains 334 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 281 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 305 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 370 PHE Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 305 ASN Chi-restraints excluded: chain F residue 334 CYS Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 141 CYS Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 290 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 93 optimal weight: 0.0040 chunk 137 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 131 optimal weight: 0.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 ASN C 251 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17969 Z= 0.179 Angle : 0.515 9.703 24258 Z= 0.270 Chirality : 0.038 0.170 2647 Planarity : 0.003 0.053 2955 Dihedral : 3.893 29.116 2283 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.04 % Allowed : 19.90 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.98 (0.20), residues: 2059 helix: 1.88 (0.15), residues: 1370 sheet: -0.13 (0.46), residues: 137 loop : -2.45 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 23 HIS 0.008 0.001 HIS C 251 PHE 0.032 0.001 PHE G 158 TYR 0.023 0.001 TYR A 279 ARG 0.002 0.000 ARG F 344 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 281 time to evaluate : 2.172 Fit side-chains revert: symmetry clash REVERT: A 250 LEU cc_start: 0.5962 (pp) cc_final: 0.5558 (mt) REVERT: A 273 PHE cc_start: 0.7431 (OUTLIER) cc_final: 0.7053 (t80) REVERT: B 145 TRP cc_start: 0.6636 (t60) cc_final: 0.6358 (t60) REVERT: D 347 ARG cc_start: 0.6900 (ttm170) cc_final: 0.6592 (mpp-170) REVERT: D 368 ASN cc_start: 0.7703 (p0) cc_final: 0.7141 (p0) REVERT: F 342 PHE cc_start: 0.7904 (m-10) cc_final: 0.7572 (m-10) REVERT: F 363 ILE cc_start: 0.7950 (mm) cc_final: 0.7541 (mm) REVERT: G 248 PHE cc_start: 0.7545 (t80) cc_final: 0.7310 (t80) outliers start: 59 outliers final: 56 residues processed: 312 average time/residue: 0.3096 time to fit residues: 146.2764 Evaluate side-chains 335 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 278 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 388 PHE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 145 TRP Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 305 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 370 PHE Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 305 ASN Chi-restraints excluded: chain F residue 334 CYS Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 141 CYS Chi-restraints excluded: chain G residue 273 PHE Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 290 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 45 optimal weight: 0.5980 chunk 165 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 251 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.182670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.141972 restraints weight = 25803.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.140725 restraints weight = 18897.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.141569 restraints weight = 16210.882| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17969 Z= 0.181 Angle : 0.515 9.304 24258 Z= 0.271 Chirality : 0.038 0.167 2647 Planarity : 0.003 0.053 2955 Dihedral : 3.873 29.124 2283 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.04 % Allowed : 19.95 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.97 (0.20), residues: 2059 helix: 1.87 (0.15), residues: 1374 sheet: -0.21 (0.46), residues: 139 loop : -2.47 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 23 HIS 0.007 0.001 HIS C 251 PHE 0.042 0.001 PHE D 158 TYR 0.023 0.001 TYR A 279 ARG 0.002 0.000 ARG F 344 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3523.91 seconds wall clock time: 66 minutes 6.13 seconds (3966.13 seconds total)