Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 11:44:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dxp_27772/04_2023/8dxp_27772.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dxp_27772/04_2023/8dxp_27772.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dxp_27772/04_2023/8dxp_27772.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dxp_27772/04_2023/8dxp_27772.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dxp_27772/04_2023/8dxp_27772.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dxp_27772/04_2023/8dxp_27772.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.026 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 11541 2.51 5 N 2756 2.21 5 O 3021 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 104": "OD1" <-> "OD2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 231": "OD1" <-> "OD2" Residue "C PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 25": "OD1" <-> "OD2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 369": "OD1" <-> "OD2" Residue "D PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "E GLU 348": "OE1" <-> "OE2" Residue "E TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 156": "OE1" <-> "OE2" Residue "F GLU 243": "OE1" <-> "OE2" Residue "F PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 243": "OE1" <-> "OE2" Residue "G TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 17465 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: 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: "E" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2498 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 7, 'TRANS': 292} Chain breaks: 2 Chain: "F" 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: "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: 8.84, per 1000 atoms: 0.51 Number of scatterers: 17465 At special positions: 0 Unit cell: (125.4, 117.7, 134.2, 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 3021 8.00 N 2756 7.00 C 11541 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: 6.92 Conformation dependent library (CDL) restraints added in 2.2 seconds 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4054 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 7 sheets defined 71.3% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 22 through 45 Processing helix chain 'A' and resid 106 through 116 Processing helix chain 'A' and resid 122 through 142 removed outlier: 3.510A pdb=" N TYR A 126 " --> pdb=" O TRP A 122 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 151 through 167 removed outlier: 4.084A pdb=" N ILE A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 156 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N HIS A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 159 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 176 removed outlier: 4.070A pdb=" N ARG A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 254 Processing helix chain 'A' and resid 258 through 283 removed outlier: 3.728A pdb=" N TYR A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 283 " --> pdb=" O TYR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 344 removed outlier: 4.262A pdb=" N ARG A 344 " --> pdb=" O TRP A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 367 through 378 Processing helix chain 'A' and resid 383 through 391 removed outlier: 3.621A pdb=" N PHE A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 405 removed outlier: 4.173A pdb=" N GLU A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 21 removed outlier: 3.624A pdb=" N VAL B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 47 removed outlier: 5.080A pdb=" N ASP B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL B 47 " --> pdb=" O CYS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 120 removed outlier: 3.621A pdb=" N GLU B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 120 " --> pdb=" O TYR B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.886A pdb=" N LYS B 125 " --> pdb=" O HIS B 121 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR B 126 " --> pdb=" O TRP B 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 121 through 126' Processing helix chain 'B' and resid 126 through 143 removed outlier: 3.701A pdb=" N ASN B 143 " --> pdb=" O MET B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 165 removed outlier: 4.050A pdb=" N ILE B 155 " --> pdb=" O SER B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 175 removed outlier: 4.290A pdb=" N THR B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) removed outlier: 3.610A 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: 3.521A pdb=" N LEU B 283 " --> pdb=" O TYR B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 343 removed outlier: 3.559A pdb=" N LYS B 318 " --> pdb=" O HIS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 358 Processing helix chain 'B' and resid 367 through 378 removed outlier: 3.504A pdb=" N ALA B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 372 " --> pdb=" O ASN B 368 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP B 378 " --> pdb=" O LEU B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 393 through 405 removed outlier: 4.133A pdb=" N GLU B 397 " --> pdb=" O SER B 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 49 removed outlier: 3.614A pdb=" N VAL C 26 " --> pdb=" O PRO C 22 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C 47 " --> pdb=" O CYS C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 120 removed outlier: 4.193A pdb=" N GLU C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU C 120 " --> pdb=" O TYR C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 removed outlier: 3.759A pdb=" N LYS C 125 " --> pdb=" O HIS C 121 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR C 126 " --> pdb=" O TRP C 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 121 through 126' Processing helix chain 'C' and resid 126 through 144 Processing helix chain 'C' and resid 152 through 168 Processing helix chain 'C' and resid 169 through 176 Processing helix chain 'C' and resid 232 through 253 Processing helix chain 'C' and resid 261 through 283 Processing helix chain 'C' and resid 284 through 287 removed outlier: 3.556A 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: 3.526A pdb=" N SER C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 359 removed outlier: 3.589A pdb=" N ARG C 355 " --> pdb=" O PHE C 351 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 379 removed outlier: 3.595A pdb=" N ALA C 371 " --> pdb=" O LYS C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 391 removed outlier: 4.129A pdb=" N PHE C 391 " --> pdb=" O ARG C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 405 Processing helix chain 'D' and resid 22 through 49 removed outlier: 3.611A pdb=" N ASP D 29 " --> pdb=" O ASP D 25 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR D 30 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 31 " --> pdb=" O PHE D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 120 removed outlier: 3.730A pdb=" N LEU D 120 " --> pdb=" O TYR D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 removed outlier: 3.639A pdb=" N LYS D 125 " --> pdb=" O HIS D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 142 removed outlier: 3.879A pdb=" N LEU D 130 " --> pdb=" O TYR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 167 removed outlier: 3.734A pdb=" N SER D 153 " --> pdb=" O PRO D 149 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LYS D 154 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 177 removed outlier: 4.316A pdb=" N THR D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 252 removed outlier: 3.667A pdb=" N LYS D 239 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE D 242 " --> pdb=" O ALA D 238 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU D 250 " --> pdb=" O LYS D 246 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL D 252 " --> pdb=" O PHE D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 282 removed outlier: 3.918A pdb=" N MET D 261 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TYR D 262 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN D 265 " --> pdb=" O MET D 261 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR D 266 " --> pdb=" O TYR D 262 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL D 267 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LEU D 268 " --> pdb=" O ARG D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 314 No H-bonds generated for 'chain 'D' and resid 312 through 314' Processing helix chain 'D' and resid 315 through 344 removed outlier: 4.332A pdb=" N ARG D 344 " --> pdb=" O TRP D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 359 removed outlier: 3.608A pdb=" N ARG D 355 " --> pdb=" O PHE D 351 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 378 Processing helix chain 'D' and resid 383 through 391 removed outlier: 4.094A pdb=" N PHE D 391 " --> pdb=" O ARG D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 405 removed outlier: 4.018A 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: 3.652A pdb=" N VAL E 26 " --> pdb=" O PRO E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 120 removed outlier: 3.843A pdb=" N TYR E 108 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER E 109 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU E 117 " --> pdb=" O GLN E 113 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG E 118 " --> pdb=" O MET E 114 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU E 120 " --> pdb=" O TYR E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 Processing helix chain 'E' and resid 127 through 142 removed outlier: 3.501A pdb=" N VAL E 131 " --> pdb=" O PHE E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 167 removed outlier: 3.605A pdb=" N PHE E 158 " --> pdb=" O LYS E 154 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP E 167 " --> pdb=" O GLY E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 176 Processing helix chain 'E' and resid 232 through 253 removed outlier: 3.516A pdb=" N GLU E 236 " --> pdb=" O LYS E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 283 removed outlier: 3.937A pdb=" N LEU E 283 " --> pdb=" O TYR E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 287 removed outlier: 3.998A pdb=" N VAL E 287 " --> pdb=" O VAL E 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 284 through 287' Processing helix chain 'E' and resid 315 through 344 removed outlier: 3.798A pdb=" N PHE E 342 " --> pdb=" O LEU E 338 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG E 344 " --> pdb=" O TRP E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 359 removed outlier: 3.846A pdb=" N ARG E 355 " --> pdb=" O PHE E 351 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 381 removed outlier: 3.778A pdb=" N PHE E 372 " --> pdb=" O ASN E 368 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET E 373 " --> pdb=" O ASP E 369 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN E 379 " --> pdb=" O HIS E 375 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR E 380 " --> pdb=" O MET E 376 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP E 381 " --> pdb=" O ILE E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 391 removed outlier: 4.139A pdb=" N PHE E 391 " --> pdb=" O ARG E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 405 Processing helix chain 'F' and resid 22 through 25 Processing helix chain 'F' and resid 26 through 49 Processing helix chain 'F' and resid 106 through 120 removed outlier: 4.236A pdb=" N GLU F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU F 120 " --> pdb=" O TYR F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 126 Processing helix chain 'F' and resid 127 through 143 removed outlier: 3.693A pdb=" N ASN F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 167 removed outlier: 4.188A pdb=" N ASP F 167 " --> pdb=" O GLY F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 176 removed outlier: 3.833A pdb=" N THR F 172 " --> pdb=" O SER F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 253 removed outlier: 3.730A pdb=" N LEU F 250 " --> pdb=" O LYS F 246 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 283 removed outlier: 4.663A pdb=" N TYR F 262 " --> pdb=" O LEU F 258 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL F 263 " --> pdb=" O TYR F 259 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER F 281 " --> pdb=" O ILE F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 342 Processing helix chain 'F' and resid 351 through 359 removed outlier: 3.526A pdb=" N ARG F 355 " --> pdb=" O PHE F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 379 removed outlier: 3.593A pdb=" N PHE F 372 " --> pdb=" O ASN F 368 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP F 378 " --> pdb=" O LEU F 374 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN F 379 " --> pdb=" O HIS F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 391 removed outlier: 4.084A pdb=" N PHE F 391 " --> pdb=" O ARG F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 405 removed outlier: 3.688A pdb=" N LEU F 405 " --> pdb=" O LYS F 401 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 49 removed outlier: 3.860A pdb=" N VAL G 26 " --> pdb=" O PRO G 22 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE G 27 " --> pdb=" O TRP G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 119 removed outlier: 3.621A pdb=" N TYR G 108 " --> pdb=" O ASP G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 126 removed outlier: 3.793A pdb=" N LYS G 125 " --> pdb=" O HIS G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 143 removed outlier: 3.741A pdb=" N ASN G 143 " --> pdb=" O MET G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 148 removed outlier: 4.097A pdb=" N PHE G 148 " --> pdb=" O TRP G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 167 removed outlier: 3.557A pdb=" N ASP G 167 " --> pdb=" O GLY G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 177 removed outlier: 3.928A pdb=" N SER G 176 " --> pdb=" O THR G 172 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU G 177 " --> pdb=" O ARG G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 253 removed outlier: 3.626A pdb=" N ALA G 240 " --> pdb=" O GLU G 236 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE G 242 " --> pdb=" O ALA G 238 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU G 243 " --> pdb=" O LYS G 239 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS G 244 " --> pdb=" O ALA G 240 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL G 245 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU G 253 " --> pdb=" O ARG G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 281 removed outlier: 3.626A pdb=" N VAL G 263 " --> pdb=" O TYR G 259 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER G 281 " --> pdb=" O ILE G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 302 Processing helix chain 'G' and resid 313 through 341 Processing helix chain 'G' and resid 352 through 357 Processing helix chain 'G' and resid 368 through 379 removed outlier: 4.019A pdb=" N PHE G 372 " --> pdb=" O ASN G 368 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN G 379 " --> pdb=" O HIS G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 389 removed outlier: 3.884A pdb=" N LYS G 386 " --> pdb=" O PRO G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 392 No H-bonds generated for 'chain 'G' and resid 390 through 392' Processing helix chain 'G' and resid 393 through 405 removed outlier: 3.715A pdb=" N GLU G 397 " --> pdb=" O SER G 393 " (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 removed outlier: 3.551A pdb=" N ILE D 53 " --> pdb=" O ASN D 309 " (cutoff:3.500A) 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 removed outlier: 3.645A pdb=" N CYS F 308 " --> pdb=" O VAL F 291 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 53 through 56 removed outlier: 3.817A pdb=" N ILE G 53 " --> pdb=" O ASN G 309 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN G 309 " --> pdb=" O ILE G 53 " (cutoff:3.500A) 1021 hydrogen bonds defined for protein. 3024 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: 4.93 Time building geometry restraints manager: 7.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5178 1.34 - 1.46: 3268 1.46 - 1.57: 9264 1.57 - 1.69: 0 1.69 - 1.81: 224 Bond restraints: 17934 Sorted by residual: bond pdb=" N ASN F 368 " pdb=" CA ASN F 368 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.58e+00 bond pdb=" C ASP C 381 " pdb=" N PRO C 382 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.50e+00 bond pdb=" N PRO D 382 " pdb=" CA PRO D 382 " ideal model delta sigma weight residual 1.469 1.484 -0.015 1.28e-02 6.10e+03 1.37e+00 bond pdb=" CB LYS C 246 " pdb=" CG LYS C 246 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.01e+00 bond pdb=" CA ASN F 368 " pdb=" CB ASN F 368 " ideal model delta sigma weight residual 1.530 1.514 0.016 1.69e-02 3.50e+03 9.09e-01 ... (remaining 17929 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.55: 360 106.55 - 113.42: 9482 113.42 - 120.29: 7213 120.29 - 127.16: 6973 127.16 - 134.03: 183 Bond angle restraints: 24211 Sorted by residual: angle pdb=" N TRP C 145 " pdb=" CA TRP C 145 " pdb=" C TRP C 145 " ideal model delta sigma weight residual 114.56 109.93 4.63 1.27e+00 6.20e-01 1.33e+01 angle pdb=" CB LYS C 246 " pdb=" CG LYS C 246 " pdb=" CD LYS C 246 " ideal model delta sigma weight residual 111.30 118.88 -7.58 2.30e+00 1.89e-01 1.09e+01 angle pdb=" N LYS F 367 " pdb=" CA LYS F 367 " pdb=" C LYS F 367 " ideal model delta sigma weight residual 108.34 112.28 -3.94 1.31e+00 5.83e-01 9.03e+00 angle pdb=" C ASN G 368 " pdb=" CA ASN G 368 " pdb=" CB ASN G 368 " ideal model delta sigma weight residual 110.42 116.08 -5.66 1.99e+00 2.53e-01 8.08e+00 angle pdb=" CA TRP B 145 " pdb=" CB TRP B 145 " pdb=" CG TRP B 145 " ideal model delta sigma weight residual 113.60 118.77 -5.17 1.90e+00 2.77e-01 7.40e+00 ... (remaining 24206 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9386 17.97 - 35.94: 983 35.94 - 53.91: 159 53.91 - 71.88: 16 71.88 - 89.85: 14 Dihedral angle restraints: 10558 sinusoidal: 4295 harmonic: 6263 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 180.00 152.21 27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA GLU B 117 " pdb=" C GLU B 117 " pdb=" N ARG B 118 " pdb=" CA ARG B 118 " ideal model delta harmonic sigma weight residual 180.00 158.51 21.49 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA GLU F 117 " pdb=" C GLU F 117 " pdb=" N ARG F 118 " pdb=" CA ARG F 118 " ideal model delta harmonic sigma weight residual 180.00 158.55 21.45 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 10555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1735 0.030 - 0.060: 667 0.060 - 0.090: 163 0.090 - 0.119: 67 0.119 - 0.149: 11 Chirality restraints: 2643 Sorted by residual: 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 2.58 -0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ILE C 53 " pdb=" N ILE C 53 " pdb=" C ILE C 53 " pdb=" CB ILE C 53 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA ILE B 363 " pdb=" N ILE B 363 " pdb=" C ILE B 363 " pdb=" CB ILE B 363 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 2640 not shown) Planarity restraints: 2948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 145 " 0.023 2.00e-02 2.50e+03 1.51e-02 5.73e+00 pdb=" CG TRP B 145 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP B 145 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP B 145 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 145 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 145 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 145 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 145 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 145 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 145 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 242 " 0.008 2.00e-02 2.50e+03 1.15e-02 2.31e+00 pdb=" CG PHE F 242 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE F 242 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE F 242 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE F 242 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE F 242 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE F 242 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 260 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C ALA C 260 " 0.024 2.00e-02 2.50e+03 pdb=" O ALA C 260 " -0.009 2.00e-02 2.50e+03 pdb=" N MET C 261 " -0.008 2.00e-02 2.50e+03 ... (remaining 2945 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4181 2.79 - 3.31: 17199 3.31 - 3.84: 27513 3.84 - 4.37: 30137 4.37 - 4.90: 52493 Nonbonded interactions: 131523 Sorted by model distance: nonbonded pdb=" NE2 HIS F 134 " pdb=" OH TYR F 279 " model vdw 2.258 2.520 nonbonded pdb=" O GLU G 352 " pdb=" OE1 GLN G 356 " model vdw 2.266 3.040 nonbonded pdb=" ND1 HIS F 314 " pdb=" OE2 GLU G 117 " model vdw 2.271 2.520 nonbonded pdb=" NH2 ARG A 58 " pdb=" OE1 GLU G 95 " model vdw 2.301 2.520 nonbonded pdb=" O ASN F 280 " pdb=" ND2 ASN F 280 " model vdw 2.303 2.520 ... (remaining 131518 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 59 or resid 96 through 175 or resid 234 through \ 405)) selection = (chain 'B' and (resid 16 through 59 or resid 96 through 175 or resid 234 through \ 405)) selection = (chain 'C' and (resid 16 through 59 or resid 96 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 59 or resid 96 through 175 or resid 177 or resi \ d 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: 5.140 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: 0.010 Extract box with map and model: 11.330 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 42.630 Find NCS groups from input model: 1.510 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: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 17934 Z= 0.175 Angle : 0.553 9.361 24211 Z= 0.312 Chirality : 0.035 0.149 2643 Planarity : 0.003 0.031 2948 Dihedral : 14.487 89.846 6462 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer Outliers : 0.00 % 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: 0.53 (0.20), residues: 2055 helix: 1.76 (0.15), residues: 1304 sheet: -0.98 (0.48), residues: 119 loop : -2.54 (0.25), residues: 632 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.3231 time to fit residues: 162.7536 Evaluate side-chains 268 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.946 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 162 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS C 251 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 HIS F 280 ASN F 398 ASN G 121 HIS G 314 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 17934 Z= 0.236 Angle : 0.571 11.403 24211 Z= 0.303 Chirality : 0.040 0.150 2643 Planarity : 0.003 0.057 2948 Dihedral : 4.122 26.514 2279 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer Outliers : 1.76 % 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: 0.57 (0.20), residues: 2055 helix: 1.64 (0.15), residues: 1347 sheet: -0.56 (0.45), residues: 137 loop : -2.59 (0.26), residues: 571 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 287 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 24 residues processed: 305 average time/residue: 0.3097 time to fit residues: 139.8033 Evaluate side-chains 285 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 261 time to evaluate : 1.961 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1577 time to fit residues: 9.8502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 chunk 203 optimal weight: 10.0000 chunk 167 optimal weight: 0.5980 chunk 186 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 151 optimal weight: 0.7980 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 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN B 398 ASN C 106 GLN ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 HIS E 398 ASN F 398 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 17934 Z= 0.212 Angle : 0.533 10.279 24211 Z= 0.284 Chirality : 0.039 0.150 2643 Planarity : 0.003 0.031 2948 Dihedral : 4.042 26.697 2279 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer Outliers : 1.03 % 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: 0.58 (0.20), residues: 2055 helix: 1.61 (0.15), residues: 1353 sheet: -0.49 (0.45), residues: 137 loop : -2.52 (0.27), residues: 565 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 285 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 294 average time/residue: 0.3188 time to fit residues: 139.7853 Evaluate side-chains 271 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 257 time to evaluate : 2.146 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2257 time to fit residues: 8.2770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 126 optimal weight: 0.7980 chunk 188 optimal weight: 5.9990 chunk 200 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 179 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 HIS ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 HIS F 398 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 17934 Z= 0.185 Angle : 0.519 11.432 24211 Z= 0.273 Chirality : 0.038 0.148 2643 Planarity : 0.003 0.028 2948 Dihedral : 3.944 26.335 2279 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer Outliers : 1.65 % 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: 0.61 (0.20), residues: 2055 helix: 1.63 (0.15), residues: 1348 sheet: -0.48 (0.46), residues: 139 loop : -2.47 (0.26), residues: 568 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 278 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 17 residues processed: 296 average time/residue: 0.2998 time to fit residues: 134.3519 Evaluate side-chains 280 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 263 time to evaluate : 1.923 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1657 time to fit residues: 7.8551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 0.9980 chunk 113 optimal weight: 0.0970 chunk 2 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 170 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 ASN E 157 HIS F 375 HIS F 398 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 17934 Z= 0.173 Angle : 0.500 12.213 24211 Z= 0.266 Chirality : 0.038 0.147 2643 Planarity : 0.003 0.033 2948 Dihedral : 3.910 26.334 2279 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer Outliers : 1.60 % 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: 0.69 (0.20), residues: 2055 helix: 1.70 (0.15), residues: 1349 sheet: -0.40 (0.46), residues: 138 loop : -2.49 (0.26), residues: 568 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 282 time to evaluate : 2.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 19 residues processed: 300 average time/residue: 0.3057 time to fit residues: 138.4691 Evaluate side-chains 281 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 262 time to evaluate : 2.289 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1758 time to fit residues: 8.8777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 0.0040 chunk 180 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 200 optimal weight: 0.9980 chunk 166 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 HIS F 398 ASN G 106 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 17934 Z= 0.168 Angle : 0.519 12.533 24211 Z= 0.271 Chirality : 0.037 0.153 2643 Planarity : 0.003 0.030 2948 Dihedral : 3.848 25.772 2279 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer Outliers : 1.19 % 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: 0.67 (0.20), residues: 2055 helix: 1.66 (0.15), residues: 1356 sheet: -0.39 (0.46), residues: 138 loop : -2.49 (0.26), residues: 561 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 286 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 298 average time/residue: 0.3085 time to fit residues: 137.5864 Evaluate side-chains 282 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 269 time to evaluate : 2.043 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1700 time to fit residues: 6.8092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 168 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 199 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 121 optimal weight: 0.0000 chunk 92 optimal weight: 0.7980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS C 143 ASN E 157 HIS G 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 17934 Z= 0.158 Angle : 0.529 14.945 24211 Z= 0.273 Chirality : 0.037 0.151 2643 Planarity : 0.003 0.027 2948 Dihedral : 3.815 25.810 2279 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer Outliers : 1.03 % 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: 0.70 (0.20), residues: 2055 helix: 1.69 (0.15), residues: 1358 sheet: -0.40 (0.45), residues: 138 loop : -2.50 (0.26), residues: 559 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 284 time to evaluate : 2.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 293 average time/residue: 0.3092 time to fit residues: 135.4143 Evaluate side-chains 283 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 272 time to evaluate : 2.018 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1735 time to fit residues: 6.2535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS C 143 ASN D 113 GLN F 398 ASN G 106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 17934 Z= 0.184 Angle : 0.543 13.488 24211 Z= 0.281 Chirality : 0.038 0.157 2643 Planarity : 0.003 0.049 2948 Dihedral : 3.849 25.748 2279 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer Outliers : 0.93 % 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: 0.66 (0.20), residues: 2055 helix: 1.66 (0.15), residues: 1355 sheet: -0.39 (0.45), residues: 138 loop : -2.49 (0.26), residues: 562 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 279 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 290 average time/residue: 0.3035 time to fit residues: 131.7299 Evaluate side-chains 276 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 266 time to evaluate : 2.033 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1718 time to fit residues: 6.0662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 1.9990 chunk 191 optimal weight: 7.9990 chunk 174 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 145 optimal weight: 0.0570 chunk 57 optimal weight: 8.9990 chunk 168 optimal weight: 0.8980 chunk 175 optimal weight: 0.9980 chunk 122 optimal weight: 0.0270 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS C 143 ASN F 398 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 17934 Z= 0.155 Angle : 0.536 13.137 24211 Z= 0.275 Chirality : 0.037 0.156 2643 Planarity : 0.003 0.046 2948 Dihedral : 3.822 25.195 2279 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer Outliers : 0.83 % 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: 0.73 (0.20), residues: 2055 helix: 1.70 (0.15), residues: 1357 sheet: -0.20 (0.46), residues: 136 loop : -2.51 (0.26), residues: 562 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 279 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 284 average time/residue: 0.3167 time to fit residues: 134.3643 Evaluate side-chains 280 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 268 time to evaluate : 2.108 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1895 time to fit residues: 6.9384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 0.3980 chunk 119 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 206 optimal weight: 0.7980 chunk 189 optimal weight: 7.9990 chunk 164 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 chunk 100 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 HIS F 398 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 17934 Z= 0.175 Angle : 0.558 12.817 24211 Z= 0.290 Chirality : 0.038 0.168 2643 Planarity : 0.003 0.043 2948 Dihedral : 3.844 26.386 2279 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.08 % Favored : 93.87 % Rotamer Outliers : 0.46 % 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: 0.65 (0.20), residues: 2055 helix: 1.63 (0.15), residues: 1355 sheet: -0.16 (0.46), residues: 136 loop : -2.48 (0.26), residues: 564 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 272 time to evaluate : 2.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 276 average time/residue: 0.3138 time to fit residues: 129.9206 Evaluate side-chains 268 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 264 time to evaluate : 2.148 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1892 time to fit residues: 4.2910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.194014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.151717 restraints weight = 29870.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.152855 restraints weight = 18863.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.153940 restraints weight = 12694.363| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 17934 Z= 0.196 Angle : 0.554 12.766 24211 Z= 0.290 Chirality : 0.038 0.164 2643 Planarity : 0.003 0.041 2948 Dihedral : 3.893 28.461 2279 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.13 % Favored : 93.82 % Rotamer Outliers : 0.41 % 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: 0.66 (0.20), residues: 2055 helix: 1.62 (0.15), residues: 1357 sheet: -0.22 (0.46), residues: 138 loop : -2.46 (0.26), residues: 560 =============================================================================== Job complete usr+sys time: 3277.23 seconds wall clock time: 60 minutes 57.15 seconds (3657.15 seconds total)