Starting phenix.real_space_refine on Sat Mar 16 12:28:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ord_17120/03_2024/8ord_17120_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ord_17120/03_2024/8ord_17120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ord_17120/03_2024/8ord_17120.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ord_17120/03_2024/8ord_17120.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ord_17120/03_2024/8ord_17120_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ord_17120/03_2024/8ord_17120_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 1.102 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: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 105 5.16 5 C 9195 2.51 5 N 2460 2.21 5 O 2815 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 74": "OE1" <-> "OE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 159": "OD1" <-> "OD2" Residue "A ASP 186": "OD1" <-> "OD2" Residue "A ASP 189": "OD1" <-> "OD2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 213": "OD1" <-> "OD2" Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A ASP 246": "OD1" <-> "OD2" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 313": "OD1" <-> "OD2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "B PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 26": "OD1" <-> "OD2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B ASP 224": "OD1" <-> "OD2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B ASP 288": "OD1" <-> "OD2" Residue "B TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 313": "OD1" <-> "OD2" Residue "B TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 363": "OE1" <-> "OE2" Residue "B TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 366": "OE1" <-> "OE2" Residue "C ASP 26": "OD1" <-> "OD2" Residue "C ASP 27": "OD1" <-> "OD2" Residue "C TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 59": "OE1" <-> "OE2" Residue "C TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 74": "OE1" <-> "OE2" Residue "C ASP 82": "OD1" <-> "OD2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C GLU 95": "OE1" <-> "OE2" Residue "C GLU 102": "OE1" <-> "OE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "C ASP 189": "OD1" <-> "OD2" Residue "C PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 209": "OE1" <-> "OE2" Residue "C GLU 216": "OE1" <-> "OE2" Residue "C ASP 224": "OD1" <-> "OD2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "C GLU 336": "OE1" <-> "OE2" Residue "C GLU 366": "OE1" <-> "OE2" Residue "D ASP 27": "OD1" <-> "OD2" Residue "D PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 53": "OD1" <-> "OD2" Residue "D TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 83": "OD1" <-> "OD2" Residue "D TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D GLU 169": "OE1" <-> "OE2" Residue "D ASP 181": "OD1" <-> "OD2" Residue "D ASP 186": "OD1" <-> "OD2" Residue "D ASP 189": "OD1" <-> "OD2" Residue "D TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 213": "OD1" <-> "OD2" Residue "D GLU 216": "OE1" <-> "OE2" Residue "D ASP 224": "OD1" <-> "OD2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D GLU 239": "OE1" <-> "OE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D ASP 246": "OD1" <-> "OD2" Residue "D GLU 261": "OE1" <-> "OE2" Residue "D PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 288": "OD1" <-> "OD2" Residue "D ASP 290": "OD1" <-> "OD2" Residue "D TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 313": "OD1" <-> "OD2" Residue "D GLU 318": "OE1" <-> "OE2" Residue "D GLU 336": "OE1" <-> "OE2" Residue "D TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 366": "OE1" <-> "OE2" Residue "E PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 26": "OD1" <-> "OD2" Residue "E ASP 27": "OD1" <-> "OD2" Residue "E PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 53": "OD1" <-> "OD2" Residue "E TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 58": "OD1" <-> "OD2" Residue "E GLU 74": "OE1" <-> "OE2" Residue "E ASP 82": "OD1" <-> "OD2" Residue "E GLU 85": "OE1" <-> "OE2" Residue "E PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 101": "OE1" <-> "OE2" Residue "E GLU 102": "OE1" <-> "OE2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 186": "OD1" <-> "OD2" Residue "E ASP 189": "OD1" <-> "OD2" Residue "E TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 209": "OE1" <-> "OE2" Residue "E ASP 213": "OD1" <-> "OD2" Residue "E GLU 216": "OE1" <-> "OE2" Residue "E ASP 224": "OD1" <-> "OD2" Residue "E PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 226": "OE1" <-> "OE2" Residue "E GLU 243": "OE1" <-> "OE2" Residue "E ASP 246": "OD1" <-> "OD2" Residue "E GLU 261": "OE1" <-> "OE2" Residue "E PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 288": "OD1" <-> "OD2" Residue "E ASP 313": "OD1" <-> "OD2" Residue "E GLU 318": "OE1" <-> "OE2" Residue "E GLU 336": "OE1" <-> "OE2" Residue "E PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 362": "OD1" <-> "OD2" Residue "E TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 366": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14590 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2886 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "B" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2886 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "C" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2886 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "D" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2886 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "E" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2886 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.88, per 1000 atoms: 0.54 Number of scatterers: 14590 At special positions: 0 Unit cell: (162.44, 96.416, 137.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 105 16.00 P 15 15.00 O 2815 8.00 N 2460 7.00 C 9195 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.31 Conformation dependent library (CDL) restraints added in 2.9 seconds 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3400 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 94 helices and 20 sheets defined 44.4% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.939A pdb=" N SER A 62 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 81 through 93 Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 115 through 127 Processing helix chain 'A' and resid 139 through 146 Processing helix chain 'A' and resid 174 through 176 No H-bonds generated for 'chain 'A' and resid 174 through 176' Processing helix chain 'A' and resid 184 through 198 removed outlier: 3.668A pdb=" N THR A 196 " --> pdb=" O MET A 192 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLU A 197 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 218 Processing helix chain 'A' and resid 226 through 234 Processing helix chain 'A' and resid 254 through 263 removed outlier: 3.875A pdb=" N ARG A 258 " --> pdb=" O GLU A 255 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N CYS A 259 " --> pdb=" O ARG A 256 " (cutoff:3.500A) Proline residue: A 260 - end of helix Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 276 through 285 Processing helix chain 'A' and resid 289 through 297 removed outlier: 4.543A pdb=" N LYS A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASP A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 311 through 322 Processing helix chain 'A' and resid 337 through 350 removed outlier: 4.850A pdb=" N VAL A 341 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLY A 344 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 354 No H-bonds generated for 'chain 'A' and resid 352 through 354' Processing helix chain 'A' and resid 361 through 374 removed outlier: 3.650A pdb=" N GLU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Proline residue: A 369 - end of helix removed outlier: 5.446A pdb=" N VAL A 372 " --> pdb=" O GLY A 368 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N HIS A 373 " --> pdb=" O PRO A 369 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG A 374 " --> pdb=" O SER A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 81 through 93 Processing helix chain 'B' and resid 100 through 102 No H-bonds generated for 'chain 'B' and resid 100 through 102' Processing helix chain 'B' and resid 115 through 127 Processing helix chain 'B' and resid 139 through 147 Processing helix chain 'B' and resid 174 through 176 No H-bonds generated for 'chain 'B' and resid 174 through 176' Processing helix chain 'B' and resid 184 through 198 removed outlier: 3.655A pdb=" N THR B 196 " --> pdb=" O MET B 192 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLU B 197 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ARG B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 218 removed outlier: 3.804A pdb=" N GLU B 209 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 234 Processing helix chain 'B' and resid 254 through 263 removed outlier: 3.882A pdb=" N ARG B 258 " --> pdb=" O GLU B 255 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N CYS B 259 " --> pdb=" O ARG B 256 " (cutoff:3.500A) Proline residue: B 260 - end of helix Processing helix chain 'B' and resid 266 through 269 Processing helix chain 'B' and resid 276 through 285 Processing helix chain 'B' and resid 289 through 297 removed outlier: 4.560A pdb=" N LYS B 293 " --> pdb=" O ILE B 289 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ASP B 294 " --> pdb=" O ASP B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 311 through 322 Processing helix chain 'B' and resid 337 through 350 removed outlier: 5.097A pdb=" N VAL B 341 " --> pdb=" O LYS B 338 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY B 344 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA B 349 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 354 No H-bonds generated for 'chain 'B' and resid 352 through 354' Processing helix chain 'B' and resid 361 through 374 removed outlier: 3.788A pdb=" N GLU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Proline residue: B 369 - end of helix removed outlier: 5.262A pdb=" N VAL B 372 " --> pdb=" O GLY B 368 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N HIS B 373 " --> pdb=" O PRO B 369 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 81 through 93 Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 139 through 146 Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 184 through 198 removed outlier: 3.945A pdb=" N THR C 196 " --> pdb=" O MET C 192 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLU C 197 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ARG C 198 " --> pdb=" O ILE C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 218 removed outlier: 3.530A pdb=" N ILE C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 234 Processing helix chain 'C' and resid 254 through 258 removed outlier: 3.821A pdb=" N ARG C 258 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 263 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 276 through 285 Processing helix chain 'C' and resid 289 through 296 removed outlier: 4.477A pdb=" N LYS C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ASP C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 311 through 322 Processing helix chain 'C' and resid 337 through 350 removed outlier: 5.471A pdb=" N VAL C 341 " --> pdb=" O LYS C 338 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY C 344 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA C 349 " --> pdb=" O SER C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 354 No H-bonds generated for 'chain 'C' and resid 352 through 354' Processing helix chain 'C' and resid 361 through 367 removed outlier: 3.577A pdb=" N GLU C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 373 removed outlier: 3.712A pdb=" N VAL C 372 " --> pdb=" O PRO C 369 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS C 373 " --> pdb=" O SER C 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 369 through 373' Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'D' and resid 81 through 93 Processing helix chain 'D' and resid 100 through 102 No H-bonds generated for 'chain 'D' and resid 100 through 102' Processing helix chain 'D' and resid 115 through 127 Processing helix chain 'D' and resid 139 through 147 Processing helix chain 'D' and resid 174 through 176 No H-bonds generated for 'chain 'D' and resid 174 through 176' Processing helix chain 'D' and resid 184 through 198 removed outlier: 4.019A pdb=" N THR D 196 " --> pdb=" O MET D 192 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU D 197 " --> pdb=" O LYS D 193 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG D 198 " --> pdb=" O ILE D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 218 removed outlier: 3.774A pdb=" N GLU D 209 " --> pdb=" O THR D 205 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 234 Processing helix chain 'D' and resid 254 through 263 removed outlier: 3.814A pdb=" N ARG D 258 " --> pdb=" O GLU D 255 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N CYS D 259 " --> pdb=" O ARG D 256 " (cutoff:3.500A) Proline residue: D 260 - end of helix Processing helix chain 'D' and resid 266 through 269 Processing helix chain 'D' and resid 276 through 285 Processing helix chain 'D' and resid 289 through 296 removed outlier: 4.480A pdb=" N LYS D 293 " --> pdb=" O ILE D 289 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ASP D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 306 No H-bonds generated for 'chain 'D' and resid 304 through 306' Processing helix chain 'D' and resid 311 through 322 Processing helix chain 'D' and resid 337 through 348 removed outlier: 4.255A pdb=" N VAL D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N TRP D 342 " --> pdb=" O LYS D 338 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY D 345 " --> pdb=" O VAL D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 354 No H-bonds generated for 'chain 'D' and resid 352 through 354' Processing helix chain 'D' and resid 361 through 375 removed outlier: 3.606A pdb=" N GLU D 366 " --> pdb=" O ASP D 362 " (cutoff:3.500A) Proline residue: D 369 - end of helix removed outlier: 5.396A pdb=" N VAL D 372 " --> pdb=" O GLY D 368 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N HIS D 373 " --> pdb=" O PRO D 369 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG D 374 " --> pdb=" O SER D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 66 removed outlier: 5.556A pdb=" N GLY E 65 " --> pdb=" O GLN E 61 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE E 66 " --> pdb=" O SER E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 93 Processing helix chain 'E' and resid 100 through 102 No H-bonds generated for 'chain 'E' and resid 100 through 102' Processing helix chain 'E' and resid 115 through 127 Processing helix chain 'E' and resid 139 through 147 Processing helix chain 'E' and resid 174 through 176 No H-bonds generated for 'chain 'E' and resid 174 through 176' Processing helix chain 'E' and resid 184 through 197 removed outlier: 3.751A pdb=" N THR E 196 " --> pdb=" O MET E 192 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLU E 197 " --> pdb=" O LYS E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 218 Processing helix chain 'E' and resid 225 through 234 Processing helix chain 'E' and resid 254 through 263 removed outlier: 3.793A pdb=" N ARG E 258 " --> pdb=" O GLU E 255 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N CYS E 259 " --> pdb=" O ARG E 256 " (cutoff:3.500A) Proline residue: E 260 - end of helix Processing helix chain 'E' and resid 266 through 268 No H-bonds generated for 'chain 'E' and resid 266 through 268' Processing helix chain 'E' and resid 276 through 285 Processing helix chain 'E' and resid 289 through 296 removed outlier: 4.588A pdb=" N LYS E 293 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ASP E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'E' and resid 311 through 322 Processing helix chain 'E' and resid 337 through 350 removed outlier: 5.322A pdb=" N VAL E 341 " --> pdb=" O LYS E 338 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLY E 344 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA E 349 " --> pdb=" O SER E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 356 removed outlier: 3.796A pdb=" N GLN E 356 " --> pdb=" O THR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 374 removed outlier: 3.650A pdb=" N GLU E 366 " --> pdb=" O ASP E 362 " (cutoff:3.500A) Proline residue: E 369 - end of helix removed outlier: 5.414A pdb=" N VAL E 372 " --> pdb=" O GLY E 368 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N HIS E 373 " --> pdb=" O PRO E 369 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG E 374 " --> pdb=" O SER E 370 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 31 through 34 removed outlier: 7.643A pdb=" N CYS A 12 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU A 106 " --> pdb=" O CYS A 12 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN A 14 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR A 108 " --> pdb=" O ASN A 14 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 54 through 56 Processing sheet with id= C, first strand: chain 'A' and resid 299 through 302 removed outlier: 6.147A pdb=" N ILE A 153 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N SER A 302 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU A 155 " --> pdb=" O SER A 302 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 240 through 243 Processing sheet with id= E, first strand: chain 'B' and resid 134 through 138 removed outlier: 6.774A pdb=" N VAL B 105 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ALA B 137 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 107 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU B 10 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N THR B 108 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N CYS B 12 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 54 through 56 Processing sheet with id= G, first strand: chain 'B' and resid 299 through 302 removed outlier: 7.551A pdb=" N VAL B 300 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE B 153 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N SER B 302 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU B 155 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 240 through 243 Processing sheet with id= I, first strand: chain 'C' and resid 31 through 34 removed outlier: 7.684A pdb=" N CYS C 12 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU C 106 " --> pdb=" O CYS C 12 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN C 14 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR C 108 " --> pdb=" O ASN C 14 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 54 through 56 Processing sheet with id= K, first strand: chain 'C' and resid 299 through 302 removed outlier: 6.260A pdb=" N ILE C 153 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N SER C 302 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU C 155 " --> pdb=" O SER C 302 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 240 through 243 Processing sheet with id= M, first strand: chain 'D' and resid 31 through 34 removed outlier: 7.692A pdb=" N CYS D 12 " --> pdb=" O PRO D 104 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU D 106 " --> pdb=" O CYS D 12 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASN D 14 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR D 108 " --> pdb=" O ASN D 14 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 54 through 56 Processing sheet with id= O, first strand: chain 'D' and resid 299 through 302 removed outlier: 7.170A pdb=" N VAL D 300 " --> pdb=" O THR D 151 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE D 153 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N SER D 302 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU D 155 " --> pdb=" O SER D 302 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 240 through 243 Processing sheet with id= Q, first strand: chain 'E' and resid 31 through 34 removed outlier: 7.540A pdb=" N CYS E 12 " --> pdb=" O PRO E 104 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU E 106 " --> pdb=" O CYS E 12 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN E 14 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR E 108 " --> pdb=" O ASN E 14 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 54 through 56 Processing sheet with id= S, first strand: chain 'E' and resid 299 through 302 removed outlier: 7.159A pdb=" N VAL E 300 " --> pdb=" O THR E 151 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE E 153 " --> pdb=" O VAL E 300 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N SER E 302 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU E 155 " --> pdb=" O SER E 302 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 240 through 243 541 hydrogen bonds defined for protein. 1398 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: 4.54 Time building geometry restraints manager: 6.76 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: 4724 1.34 - 1.46: 3171 1.46 - 1.58: 6814 1.58 - 1.70: 16 1.70 - 1.83: 185 Bond restraints: 14910 Sorted by residual: bond pdb=" CA PRO A 334 " pdb=" C PRO A 334 " ideal model delta sigma weight residual 1.514 1.532 -0.018 5.50e-03 3.31e+04 1.06e+01 bond pdb=" O3 PO4 E 402 " pdb=" P PO4 E 402 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.64e+00 bond pdb=" O3 PO4 A 402 " pdb=" P PO4 A 402 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.34e+00 bond pdb=" O3 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.32e+00 bond pdb=" O3 PO4 D 402 " pdb=" P PO4 D 402 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.15e+00 ... (remaining 14905 not shown) Histogram of bond angle deviations from ideal: 97.07 - 104.92: 355 104.92 - 112.76: 7768 112.76 - 120.61: 6804 120.61 - 128.45: 5198 128.45 - 136.30: 105 Bond angle restraints: 20230 Sorted by residual: angle pdb=" CB MET E 46 " pdb=" CG MET E 46 " pdb=" SD MET E 46 " ideal model delta sigma weight residual 112.70 128.86 -16.16 3.00e+00 1.11e-01 2.90e+01 angle pdb=" CA PRO C 104 " pdb=" N PRO C 104 " pdb=" CD PRO C 104 " ideal model delta sigma weight residual 112.00 105.59 6.41 1.40e+00 5.10e-01 2.09e+01 angle pdb=" CB MET D 285 " pdb=" CG MET D 285 " pdb=" SD MET D 285 " ideal model delta sigma weight residual 112.70 125.54 -12.84 3.00e+00 1.11e-01 1.83e+01 angle pdb=" CA MET E 46 " pdb=" CB MET E 46 " pdb=" CG MET E 46 " ideal model delta sigma weight residual 114.10 122.14 -8.04 2.00e+00 2.50e-01 1.62e+01 angle pdb=" CB MET B 357 " pdb=" CG MET B 357 " pdb=" SD MET B 357 " ideal model delta sigma weight residual 112.70 124.46 -11.76 3.00e+00 1.11e-01 1.54e+01 ... (remaining 20225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 8656 35.40 - 70.79: 265 70.79 - 106.19: 17 106.19 - 141.58: 4 141.58 - 176.98: 3 Dihedral angle restraints: 8945 sinusoidal: 3620 harmonic: 5325 Sorted by residual: dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual 300.00 123.02 176.98 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 115.97 -175.97 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 108.92 -168.92 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 8942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1270 0.036 - 0.072: 630 0.072 - 0.108: 257 0.108 - 0.144: 65 0.144 - 0.181: 8 Chirality restraints: 2230 Sorted by residual: chirality pdb=" CA GLN E 355 " pdb=" N GLN E 355 " pdb=" C GLN E 355 " pdb=" CB GLN E 355 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.15e-01 chirality pdb=" CG LEU E 244 " pdb=" CB LEU E 244 " pdb=" CD1 LEU E 244 " pdb=" CD2 LEU E 244 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CB ILE D 194 " pdb=" CA ILE D 194 " pdb=" CG1 ILE D 194 " pdb=" CG2 ILE D 194 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.75e-01 ... (remaining 2227 not shown) Planarity restraints: 2590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 342 " 0.037 2.00e-02 2.50e+03 3.00e-02 2.25e+01 pdb=" CG TRP B 342 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP B 342 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP B 342 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 342 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 342 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 342 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 342 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 342 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP B 342 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 88 " 0.031 2.00e-02 2.50e+03 2.85e-02 2.03e+01 pdb=" CG TRP B 88 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TRP B 88 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP B 88 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 88 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 88 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 88 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 88 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 88 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP B 88 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 342 " 0.028 2.00e-02 2.50e+03 2.73e-02 1.86e+01 pdb=" CG TRP C 342 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP C 342 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP C 342 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 342 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 342 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP C 342 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 342 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 342 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP C 342 " -0.001 2.00e-02 2.50e+03 ... (remaining 2587 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 352 2.67 - 3.23: 14879 3.23 - 3.78: 24096 3.78 - 4.34: 32291 4.34 - 4.90: 51183 Nonbonded interactions: 122801 Sorted by model distance: nonbonded pdb=" OG1 THR B 151 " pdb=" OE1 GLU B 169 " model vdw 2.109 2.440 nonbonded pdb=" OE2 GLU A 272 " pdb=" OG1 THR D 68 " model vdw 2.109 2.440 nonbonded pdb=" O GLY A 158 " pdb=" OG1 THR A 305 " model vdw 2.122 2.440 nonbonded pdb=" O GLY D 158 " pdb=" OG1 THR D 305 " model vdw 2.128 2.440 nonbonded pdb=" OH TYR E 220 " pdb=" OE2 GLU E 228 " model vdw 2.132 2.440 ... (remaining 122796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 6.250 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: 26.970 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 41.880 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 : 0.005 0.111 14910 Z= 0.323 Angle : 0.921 16.158 20230 Z= 0.468 Chirality : 0.050 0.181 2230 Planarity : 0.006 0.097 2590 Dihedral : 17.818 176.981 5545 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.58 % Allowed : 32.22 % Favored : 67.20 % 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: -0.41 (0.19), residues: 1840 helix: -0.60 (0.18), residues: 740 sheet: 0.30 (0.29), residues: 345 loop : 0.06 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.006 TRP B 342 HIS 0.011 0.001 HIS A 90 PHE 0.045 0.002 PHE A 354 TYR 0.054 0.002 TYR B 168 ARG 0.009 0.001 ARG C 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 569 time to evaluate : 1.654 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: B 88 TRP cc_start: 0.9314 (m-90) cc_final: 0.8767 (m-90) REVERT: B 115 LYS cc_start: 0.8744 (mmtp) cc_final: 0.8210 (mmtp) REVERT: B 118 ARG cc_start: 0.7368 (ptt180) cc_final: 0.6894 (ptm-80) REVERT: B 208 ARG cc_start: 0.8543 (ttp80) cc_final: 0.8150 (ttm-80) REVERT: B 256 ARG cc_start: 0.8555 (mtm180) cc_final: 0.8255 (ttp-170) REVERT: B 272 GLU cc_start: 0.7294 (tt0) cc_final: 0.6992 (tt0) REVERT: B 351 LEU cc_start: 0.8969 (tp) cc_final: 0.8627 (tt) REVERT: C 71 TYR cc_start: 0.8582 (m-80) cc_final: 0.7735 (m-10) REVERT: C 197 GLU cc_start: 0.8198 (tt0) cc_final: 0.7735 (tt0) REVERT: D 134 MET cc_start: 0.8864 (tmm) cc_final: 0.8646 (tmm) REVERT: D 354 PHE cc_start: 0.8262 (t80) cc_final: 0.7850 (t80) REVERT: E 74 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7908 (mt-10) REVERT: E 193 LYS cc_start: 0.8968 (ttmt) cc_final: 0.8699 (ttmm) outliers start: 9 outliers final: 6 residues processed: 569 average time/residue: 0.2412 time to fit residues: 204.1481 Evaluate side-chains 509 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 503 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 243 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 56 optimal weight: 0.0060 chunk 88 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN ** B 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14910 Z= 0.235 Angle : 0.699 8.336 20230 Z= 0.332 Chirality : 0.046 0.169 2230 Planarity : 0.005 0.070 2590 Dihedral : 10.499 179.378 2090 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.69 % Allowed : 27.65 % Favored : 67.65 % 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: -0.08 (0.20), residues: 1840 helix: -0.22 (0.19), residues: 740 sheet: 0.16 (0.29), residues: 355 loop : 0.28 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 342 HIS 0.006 0.001 HIS B 90 PHE 0.015 0.001 PHE A 225 TYR 0.016 0.002 TYR A 296 ARG 0.005 0.001 ARG D 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 532 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.7838 (tp-100) cc_final: 0.7378 (tp-100) REVERT: A 103 HIS cc_start: 0.8325 (m90) cc_final: 0.8019 (m90) REVERT: A 142 LEU cc_start: 0.9347 (mt) cc_final: 0.8982 (mt) REVERT: A 145 TYR cc_start: 0.8152 (m-80) cc_final: 0.7295 (m-10) REVERT: A 224 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.7992 (p0) REVERT: B 80 ASN cc_start: 0.8627 (t0) cc_final: 0.8310 (t0) REVERT: B 84 MET cc_start: 0.8439 (tpp) cc_final: 0.7202 (tpp) REVERT: B 88 TRP cc_start: 0.9429 (m-90) cc_final: 0.8856 (m-90) REVERT: B 179 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.6686 (ttm170) REVERT: B 205 THR cc_start: 0.9606 (p) cc_final: 0.9219 (t) REVERT: B 272 GLU cc_start: 0.7230 (tt0) cc_final: 0.6975 (tt0) REVERT: C 64 ARG cc_start: 0.8652 (ptt90) cc_final: 0.8412 (ptt90) REVERT: C 248 GLN cc_start: 0.8758 (tt0) cc_final: 0.8063 (mt0) REVERT: C 286 LYS cc_start: 0.8979 (ttmm) cc_final: 0.8683 (mtpp) REVERT: C 342 TRP cc_start: 0.8490 (t60) cc_final: 0.7199 (t60) REVERT: D 121 MET cc_start: 0.8799 (mtm) cc_final: 0.8383 (mtp) REVERT: D 134 MET cc_start: 0.8765 (tmm) cc_final: 0.8529 (tmm) REVERT: D 292 ARG cc_start: 0.5201 (ptt-90) cc_final: 0.4778 (ptt90) REVERT: D 354 PHE cc_start: 0.8566 (t80) cc_final: 0.8330 (t80) REVERT: E 113 ASN cc_start: 0.8449 (t0) cc_final: 0.8230 (t0) REVERT: E 134 MET cc_start: 0.8514 (pmm) cc_final: 0.7999 (pmm) REVERT: E 193 LYS cc_start: 0.9011 (ttmt) cc_final: 0.8751 (ttmm) outliers start: 73 outliers final: 59 residues processed: 559 average time/residue: 0.2396 time to fit residues: 199.7427 Evaluate side-chains 556 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 495 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 305 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 4.9990 chunk 52 optimal weight: 0.4980 chunk 139 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 181 optimal weight: 0.0980 chunk 149 optimal weight: 7.9990 chunk 166 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14910 Z= 0.182 Angle : 0.661 8.030 20230 Z= 0.310 Chirality : 0.045 0.133 2230 Planarity : 0.005 0.070 2590 Dihedral : 9.989 179.062 2080 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.57 % Allowed : 27.85 % Favored : 67.59 % 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: 0.11 (0.20), residues: 1840 helix: -0.08 (0.19), residues: 740 sheet: 0.27 (0.28), residues: 350 loop : 0.41 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 342 HIS 0.007 0.001 HIS D 90 PHE 0.014 0.001 PHE B 126 TYR 0.018 0.001 TYR A 145 ARG 0.006 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 552 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.7768 (tp-100) cc_final: 0.7332 (tp-100) REVERT: A 103 HIS cc_start: 0.8373 (m90) cc_final: 0.7923 (m90) REVERT: A 142 LEU cc_start: 0.9326 (mt) cc_final: 0.9025 (mt) REVERT: A 208 ARG cc_start: 0.8419 (mtm110) cc_final: 0.8048 (ttm-80) REVERT: A 224 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.8040 (p0) REVERT: B 64 ARG cc_start: 0.9258 (ptt180) cc_final: 0.8795 (ptm160) REVERT: B 84 MET cc_start: 0.8432 (tpp) cc_final: 0.7434 (tpp) REVERT: B 88 TRP cc_start: 0.9357 (OUTLIER) cc_final: 0.8900 (m-90) REVERT: B 118 ARG cc_start: 0.7847 (ptt180) cc_final: 0.7606 (ptm-80) REVERT: B 169 GLU cc_start: 0.8871 (mp0) cc_final: 0.8455 (mp0) REVERT: B 205 THR cc_start: 0.9588 (p) cc_final: 0.8876 (t) REVERT: B 209 GLU cc_start: 0.9509 (mm-30) cc_final: 0.9224 (mp0) REVERT: B 223 LEU cc_start: 0.9029 (tt) cc_final: 0.8691 (tp) REVERT: B 272 GLU cc_start: 0.7230 (tt0) cc_final: 0.6906 (tt0) REVERT: B 294 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.8210 (t0) REVERT: B 316 GLN cc_start: 0.9185 (tm-30) cc_final: 0.8734 (tm-30) REVERT: C 121 MET cc_start: 0.9096 (mtp) cc_final: 0.8827 (mtp) REVERT: C 286 LYS cc_start: 0.8972 (ttmm) cc_final: 0.8667 (mtpp) REVERT: C 342 TRP cc_start: 0.8449 (t60) cc_final: 0.7260 (t60) REVERT: D 123 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8361 (tt0) REVERT: D 134 MET cc_start: 0.8755 (tmm) cc_final: 0.8509 (tmm) REVERT: E 113 ASN cc_start: 0.8434 (t0) cc_final: 0.8069 (t0) REVERT: E 134 MET cc_start: 0.8551 (pmm) cc_final: 0.7960 (pmm) REVERT: E 193 LYS cc_start: 0.8988 (ttmt) cc_final: 0.8698 (ttmm) REVERT: E 209 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8621 (mm-30) REVERT: E 316 GLN cc_start: 0.8476 (tp40) cc_final: 0.8206 (tp40) outliers start: 71 outliers final: 53 residues processed: 580 average time/residue: 0.2382 time to fit residues: 207.0805 Evaluate side-chains 557 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 500 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 88 TRP Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 227 ASN Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 318 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 2.9990 chunk 126 optimal weight: 0.2980 chunk 87 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 168 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN ** B 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14910 Z= 0.235 Angle : 0.664 8.442 20230 Z= 0.312 Chirality : 0.045 0.146 2230 Planarity : 0.005 0.062 2590 Dihedral : 9.772 178.461 2078 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 6.11 % Allowed : 28.23 % Favored : 65.66 % 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: 0.19 (0.20), residues: 1840 helix: 0.02 (0.20), residues: 740 sheet: 0.13 (0.28), residues: 355 loop : 0.52 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 342 HIS 0.010 0.001 HIS B 373 PHE 0.019 0.001 PHE A 225 TYR 0.019 0.001 TYR A 308 ARG 0.006 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 529 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.7783 (tp-100) cc_final: 0.7336 (tp-100) REVERT: A 70 LYS cc_start: 0.8826 (mmmm) cc_final: 0.8392 (mmmm) REVERT: A 103 HIS cc_start: 0.8408 (m90) cc_final: 0.7885 (m90) REVERT: A 142 LEU cc_start: 0.9333 (mt) cc_final: 0.8994 (mt) REVERT: A 208 ARG cc_start: 0.8453 (mtm110) cc_final: 0.8041 (ttm-80) REVERT: A 224 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8027 (p0) REVERT: A 278 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8342 (mp0) REVERT: A 355 GLN cc_start: 0.9060 (mp10) cc_final: 0.8619 (mp10) REVERT: B 84 MET cc_start: 0.8700 (tpp) cc_final: 0.7627 (tpp) REVERT: B 88 TRP cc_start: 0.9400 (OUTLIER) cc_final: 0.8912 (m-90) REVERT: B 113 ASN cc_start: 0.9319 (t0) cc_final: 0.9106 (t0) REVERT: B 123 GLN cc_start: 0.9349 (tt0) cc_final: 0.9040 (tp40) REVERT: B 169 GLU cc_start: 0.8885 (mp0) cc_final: 0.8422 (mp0) REVERT: B 205 THR cc_start: 0.9598 (p) cc_final: 0.8931 (t) REVERT: B 208 ARG cc_start: 0.8730 (ttm-80) cc_final: 0.8410 (ttm-80) REVERT: B 209 GLU cc_start: 0.9501 (mm-30) cc_final: 0.9214 (mp0) REVERT: B 223 LEU cc_start: 0.8988 (tt) cc_final: 0.8757 (tp) REVERT: B 272 GLU cc_start: 0.7290 (tt0) cc_final: 0.7025 (tt0) REVERT: B 294 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8158 (t0) REVERT: B 331 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7295 (mtt) REVERT: B 357 MET cc_start: 0.8678 (mmm) cc_final: 0.8426 (mtp) REVERT: C 117 ASN cc_start: 0.8788 (t0) cc_final: 0.8521 (t0) REVERT: C 121 MET cc_start: 0.8981 (mtp) cc_final: 0.8667 (mtp) REVERT: C 286 LYS cc_start: 0.9010 (ttmm) cc_final: 0.8667 (mtpp) REVERT: C 316 GLN cc_start: 0.8909 (tm-30) cc_final: 0.8511 (tm-30) REVERT: C 339 TYR cc_start: 0.8715 (m-80) cc_final: 0.8227 (m-80) REVERT: C 342 TRP cc_start: 0.8508 (t60) cc_final: 0.7330 (t60) REVERT: D 30 ARG cc_start: 0.7476 (mmm-85) cc_final: 0.6965 (mtp-110) REVERT: D 118 ARG cc_start: 0.8738 (ptt-90) cc_final: 0.8495 (ptt-90) REVERT: D 121 MET cc_start: 0.8679 (mtm) cc_final: 0.8365 (mtp) REVERT: D 123 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8406 (tt0) REVERT: D 327 MET cc_start: 0.8831 (mmm) cc_final: 0.8448 (mmm) REVERT: E 30 ARG cc_start: 0.8381 (mmp80) cc_final: 0.8033 (mmm160) REVERT: E 46 MET cc_start: 0.7446 (tpp) cc_final: 0.7065 (tpp) REVERT: E 113 ASN cc_start: 0.8435 (t0) cc_final: 0.8021 (t0) REVERT: E 122 THR cc_start: 0.8776 (m) cc_final: 0.8519 (p) REVERT: E 126 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7730 (m-10) REVERT: E 134 MET cc_start: 0.8598 (pmm) cc_final: 0.8076 (pmm) REVERT: E 179 ARG cc_start: 0.8878 (ttt180) cc_final: 0.8510 (ttt180) REVERT: E 191 LEU cc_start: 0.9092 (tp) cc_final: 0.8748 (tt) REVERT: E 193 LYS cc_start: 0.8995 (ttmt) cc_final: 0.8716 (ttmm) REVERT: E 209 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8651 (mm-30) REVERT: E 228 GLU cc_start: 0.8625 (tp30) cc_final: 0.8173 (tp30) REVERT: E 316 GLN cc_start: 0.8559 (tp40) cc_final: 0.8066 (mm110) outliers start: 95 outliers final: 70 residues processed: 569 average time/residue: 0.2309 time to fit residues: 198.2294 Evaluate side-chains 568 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 492 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 88 TRP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 152 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 45 optimal weight: 0.4980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14910 Z= 0.236 Angle : 0.665 8.840 20230 Z= 0.311 Chirality : 0.045 0.146 2230 Planarity : 0.005 0.062 2590 Dihedral : 9.665 178.107 2078 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 6.75 % Allowed : 28.17 % Favored : 65.08 % 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: 0.23 (0.20), residues: 1840 helix: 0.05 (0.20), residues: 735 sheet: 0.12 (0.28), residues: 360 loop : 0.56 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 342 HIS 0.009 0.001 HIS D 175 PHE 0.017 0.001 PHE A 225 TYR 0.026 0.001 TYR A 145 ARG 0.006 0.000 ARG B 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 509 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.7887 (tp-100) cc_final: 0.7423 (tp-100) REVERT: A 70 LYS cc_start: 0.8849 (mmmm) cc_final: 0.8430 (mmmm) REVERT: A 103 HIS cc_start: 0.8323 (m90) cc_final: 0.7880 (m90) REVERT: A 118 ARG cc_start: 0.8788 (ptt180) cc_final: 0.8423 (ptt180) REVERT: A 142 LEU cc_start: 0.9318 (mt) cc_final: 0.8976 (mt) REVERT: A 208 ARG cc_start: 0.8448 (mtm110) cc_final: 0.8058 (ttm-80) REVERT: A 224 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.8100 (p0) REVERT: A 278 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8399 (mp0) REVERT: A 355 GLN cc_start: 0.9037 (mp10) cc_final: 0.8610 (mp10) REVERT: B 36 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8518 (mm) REVERT: B 84 MET cc_start: 0.8765 (tpp) cc_final: 0.7731 (tpp) REVERT: B 88 TRP cc_start: 0.9429 (OUTLIER) cc_final: 0.8922 (m-90) REVERT: B 95 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8115 (mp0) REVERT: B 119 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8685 (mt-10) REVERT: B 123 GLN cc_start: 0.9304 (tt0) cc_final: 0.9002 (tp40) REVERT: B 159 ASP cc_start: 0.7061 (t0) cc_final: 0.6843 (t0) REVERT: B 169 GLU cc_start: 0.8884 (mp0) cc_final: 0.8370 (mp0) REVERT: B 205 THR cc_start: 0.9605 (p) cc_final: 0.9016 (t) REVERT: B 209 GLU cc_start: 0.9497 (mm-30) cc_final: 0.9178 (mp0) REVERT: B 223 LEU cc_start: 0.9000 (tt) cc_final: 0.8780 (tp) REVERT: B 272 GLU cc_start: 0.7296 (tt0) cc_final: 0.7014 (tt0) REVERT: B 294 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8183 (t0) REVERT: B 307 MET cc_start: 0.8561 (mtp) cc_final: 0.8331 (mtp) REVERT: B 316 GLN cc_start: 0.8860 (tm-30) cc_final: 0.8320 (tm-30) REVERT: B 339 TYR cc_start: 0.8834 (m-80) cc_final: 0.8188 (m-80) REVERT: B 357 MET cc_start: 0.8678 (mmm) cc_final: 0.8283 (mtp) REVERT: B 358 TRP cc_start: 0.8096 (m-10) cc_final: 0.7596 (m-90) REVERT: C 117 ASN cc_start: 0.8746 (t0) cc_final: 0.8469 (t0) REVERT: C 121 MET cc_start: 0.8992 (mtp) cc_final: 0.8654 (mtp) REVERT: C 286 LYS cc_start: 0.8941 (ttmm) cc_final: 0.8604 (mtpp) REVERT: C 288 ASP cc_start: 0.8230 (m-30) cc_final: 0.7961 (m-30) REVERT: C 316 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8492 (tm-30) REVERT: C 339 TYR cc_start: 0.8709 (m-80) cc_final: 0.8394 (m-80) REVERT: D 121 MET cc_start: 0.8746 (mtm) cc_final: 0.8385 (mtp) REVERT: D 123 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8425 (tt0) REVERT: D 134 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8384 (tmm) REVERT: D 171 TYR cc_start: 0.8382 (m-80) cc_final: 0.8106 (m-80) REVERT: D 318 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8725 (mm-30) REVERT: E 30 ARG cc_start: 0.8364 (mmp80) cc_final: 0.8080 (mmm160) REVERT: E 113 ASN cc_start: 0.8439 (t0) cc_final: 0.8008 (t0) REVERT: E 122 THR cc_start: 0.8827 (m) cc_final: 0.8496 (t) REVERT: E 126 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7893 (m-10) REVERT: E 134 MET cc_start: 0.8673 (pmm) cc_final: 0.8186 (pmm) REVERT: E 179 ARG cc_start: 0.8931 (ttt180) cc_final: 0.8540 (ttt180) REVERT: E 191 LEU cc_start: 0.9095 (tp) cc_final: 0.8869 (tt) REVERT: E 193 LYS cc_start: 0.8959 (ttmt) cc_final: 0.8682 (ttmm) REVERT: E 228 GLU cc_start: 0.8628 (tp30) cc_final: 0.8168 (tp30) REVERT: E 236 SER cc_start: 0.9303 (m) cc_final: 0.8905 (t) REVERT: E 278 GLU cc_start: 0.8186 (tm-30) cc_final: 0.6982 (tm-30) REVERT: E 316 GLN cc_start: 0.8687 (tp40) cc_final: 0.8280 (tp40) REVERT: E 373 HIS cc_start: 0.7033 (m90) cc_final: 0.6792 (m90) outliers start: 105 outliers final: 75 residues processed: 554 average time/residue: 0.2302 time to fit residues: 192.2758 Evaluate side-chains 578 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 496 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 88 TRP Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 353 THR Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 318 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.7980 chunk 161 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 148 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN ** B 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN C 117 ASN C 139 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 14910 Z= 0.386 Angle : 0.756 14.721 20230 Z= 0.358 Chirality : 0.048 0.182 2230 Planarity : 0.005 0.057 2590 Dihedral : 9.923 177.308 2078 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 7.65 % Allowed : 28.36 % Favored : 63.99 % 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: -0.05 (0.20), residues: 1840 helix: -0.15 (0.19), residues: 745 sheet: 0.00 (0.29), residues: 360 loop : 0.35 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 342 HIS 0.008 0.002 HIS D 175 PHE 0.020 0.002 PHE A 354 TYR 0.021 0.002 TYR C 168 ARG 0.008 0.001 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 506 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8867 (mmmm) cc_final: 0.8520 (mmmm) REVERT: A 103 HIS cc_start: 0.8384 (m90) cc_final: 0.7860 (m90) REVERT: A 123 GLN cc_start: 0.8860 (tp-100) cc_final: 0.8637 (tp40) REVERT: A 142 LEU cc_start: 0.9462 (mt) cc_final: 0.9127 (mt) REVERT: A 278 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8458 (mp0) REVERT: A 342 TRP cc_start: 0.7583 (t60) cc_final: 0.6927 (t60) REVERT: A 355 GLN cc_start: 0.9049 (mp10) cc_final: 0.8597 (mp10) REVERT: B 88 TRP cc_start: 0.9498 (m-10) cc_final: 0.8930 (m-90) REVERT: B 95 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8055 (mp0) REVERT: B 113 ASN cc_start: 0.9289 (t0) cc_final: 0.8202 (t0) REVERT: B 115 LYS cc_start: 0.9105 (mmtt) cc_final: 0.8653 (mmmt) REVERT: B 117 ASN cc_start: 0.9002 (t0) cc_final: 0.8698 (t0) REVERT: B 119 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8709 (mt-10) REVERT: B 123 GLN cc_start: 0.9280 (tt0) cc_final: 0.9021 (tp40) REVERT: B 159 ASP cc_start: 0.7246 (t0) cc_final: 0.7046 (t0) REVERT: B 169 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8354 (mp0) REVERT: B 205 THR cc_start: 0.9552 (p) cc_final: 0.9050 (t) REVERT: B 209 GLU cc_start: 0.9487 (mm-30) cc_final: 0.9240 (mp0) REVERT: B 294 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8365 (t0) REVERT: B 307 MET cc_start: 0.8662 (mtp) cc_final: 0.8449 (mtp) REVERT: B 316 GLN cc_start: 0.9058 (tm-30) cc_final: 0.8672 (tm-30) REVERT: B 339 TYR cc_start: 0.8865 (m-80) cc_final: 0.8187 (m-80) REVERT: B 357 MET cc_start: 0.8708 (mmm) cc_final: 0.8470 (mtp) REVERT: C 129 PHE cc_start: 0.9106 (m-80) cc_final: 0.8900 (m-80) REVERT: C 248 GLN cc_start: 0.8780 (tt0) cc_final: 0.8068 (mt0) REVERT: C 286 LYS cc_start: 0.8979 (ttmm) cc_final: 0.8604 (ttmm) REVERT: C 288 ASP cc_start: 0.8370 (m-30) cc_final: 0.8101 (m-30) REVERT: C 316 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8541 (tm-30) REVERT: D 46 MET cc_start: 0.7083 (tmm) cc_final: 0.6608 (tmm) REVERT: D 115 LYS cc_start: 0.8497 (mmtt) cc_final: 0.8246 (tppt) REVERT: D 118 ARG cc_start: 0.8634 (ptt-90) cc_final: 0.7936 (ptt-90) REVERT: D 119 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8087 (mm-30) REVERT: D 121 MET cc_start: 0.8852 (mtm) cc_final: 0.8398 (mtp) REVERT: D 123 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8411 (tt0) REVERT: D 134 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8296 (tmm) REVERT: D 248 GLN cc_start: 0.8376 (mt0) cc_final: 0.8071 (mt0) REVERT: D 318 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8734 (mm-30) REVERT: D 327 MET cc_start: 0.8748 (mmm) cc_final: 0.8534 (mmm) REVERT: E 30 ARG cc_start: 0.8385 (mmp80) cc_final: 0.8099 (mmm160) REVERT: E 113 ASN cc_start: 0.8501 (t0) cc_final: 0.8087 (t0) REVERT: E 119 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8570 (tp30) REVERT: E 122 THR cc_start: 0.8935 (m) cc_final: 0.8649 (t) REVERT: E 126 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7910 (m-10) REVERT: E 134 MET cc_start: 0.8726 (pmm) cc_final: 0.8083 (pmm) REVERT: E 179 ARG cc_start: 0.8920 (ttt180) cc_final: 0.8662 (ttt180) REVERT: E 193 LYS cc_start: 0.8997 (ttmt) cc_final: 0.8707 (ttmm) REVERT: E 236 SER cc_start: 0.9296 (m) cc_final: 0.8875 (t) REVERT: E 278 GLU cc_start: 0.8459 (tm-30) cc_final: 0.7281 (tm-30) REVERT: E 316 GLN cc_start: 0.8641 (tp40) cc_final: 0.8099 (tp40) outliers start: 119 outliers final: 86 residues processed: 560 average time/residue: 0.2333 time to fit residues: 196.6351 Evaluate side-chains 571 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 480 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 353 THR Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 318 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 130 optimal weight: 0.0470 chunk 150 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 108 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 HIS ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14910 Z= 0.205 Angle : 0.680 11.169 20230 Z= 0.316 Chirality : 0.045 0.153 2230 Planarity : 0.005 0.060 2590 Dihedral : 9.712 177.547 2078 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.95 % Allowed : 31.06 % Favored : 63.99 % 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: 0.21 (0.20), residues: 1840 helix: 0.03 (0.19), residues: 740 sheet: 0.23 (0.29), residues: 350 loop : 0.47 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 342 HIS 0.009 0.001 HIS D 175 PHE 0.017 0.001 PHE B 354 TYR 0.030 0.001 TYR A 281 ARG 0.006 0.001 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 536 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8055 (tp-100) cc_final: 0.7599 (tp-100) REVERT: A 70 LYS cc_start: 0.8794 (mmmm) cc_final: 0.8478 (mmmm) REVERT: A 103 HIS cc_start: 0.8305 (m90) cc_final: 0.7826 (m90) REVERT: A 142 LEU cc_start: 0.9380 (mt) cc_final: 0.9028 (mt) REVERT: A 208 ARG cc_start: 0.8378 (mtm110) cc_final: 0.7979 (ttm-80) REVERT: A 281 TYR cc_start: 0.8391 (t80) cc_final: 0.8114 (t80) REVERT: A 342 TRP cc_start: 0.7458 (t60) cc_final: 0.6929 (t60) REVERT: A 355 GLN cc_start: 0.8994 (mp10) cc_final: 0.8630 (mp10) REVERT: B 88 TRP cc_start: 0.9394 (OUTLIER) cc_final: 0.8891 (m-90) REVERT: B 95 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8047 (mm-30) REVERT: B 113 ASN cc_start: 0.9185 (t0) cc_final: 0.8254 (t0) REVERT: B 117 ASN cc_start: 0.8935 (t0) cc_final: 0.8655 (t0) REVERT: B 119 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8693 (mt-10) REVERT: B 123 GLN cc_start: 0.9277 (tt0) cc_final: 0.9035 (tp40) REVERT: B 169 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8299 (mp0) REVERT: B 205 THR cc_start: 0.9542 (p) cc_final: 0.9030 (t) REVERT: B 208 ARG cc_start: 0.8754 (ttm-80) cc_final: 0.8452 (ttm-80) REVERT: B 209 GLU cc_start: 0.9453 (mm-30) cc_final: 0.9187 (mp0) REVERT: B 272 GLU cc_start: 0.7475 (tt0) cc_final: 0.7118 (tp30) REVERT: B 294 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8260 (t0) REVERT: B 307 MET cc_start: 0.8582 (mtp) cc_final: 0.8379 (mtp) REVERT: B 339 TYR cc_start: 0.8849 (m-80) cc_final: 0.8168 (m-80) REVERT: C 248 GLN cc_start: 0.8753 (tt0) cc_final: 0.8098 (mt0) REVERT: C 286 LYS cc_start: 0.8960 (ttmm) cc_final: 0.8605 (mtpp) REVERT: C 288 ASP cc_start: 0.8315 (m-30) cc_final: 0.8063 (m-30) REVERT: C 316 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8460 (tm-30) REVERT: D 123 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8446 (tt0) REVERT: D 134 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8327 (tmm) REVERT: D 171 TYR cc_start: 0.8400 (m-80) cc_final: 0.8137 (m-80) REVERT: D 248 GLN cc_start: 0.8352 (mt0) cc_final: 0.8147 (mt0) REVERT: D 318 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8702 (mm-30) REVERT: D 354 PHE cc_start: 0.8381 (t80) cc_final: 0.8026 (t80) REVERT: E 30 ARG cc_start: 0.8423 (mmp80) cc_final: 0.8061 (mmp-170) REVERT: E 49 MET cc_start: 0.7936 (ppp) cc_final: 0.7650 (ppp) REVERT: E 113 ASN cc_start: 0.8471 (t0) cc_final: 0.8070 (t0) REVERT: E 122 THR cc_start: 0.8891 (m) cc_final: 0.8580 (t) REVERT: E 126 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7788 (m-10) REVERT: E 134 MET cc_start: 0.8686 (pmm) cc_final: 0.8054 (pmm) REVERT: E 191 LEU cc_start: 0.9074 (tp) cc_final: 0.8731 (tt) REVERT: E 193 LYS cc_start: 0.8947 (ttmt) cc_final: 0.8674 (ttmm) REVERT: E 228 GLU cc_start: 0.8683 (tp30) cc_final: 0.8136 (tp30) REVERT: E 236 SER cc_start: 0.9270 (m) cc_final: 0.8898 (t) REVERT: E 278 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7112 (tm-30) REVERT: E 316 GLN cc_start: 0.8594 (tp40) cc_final: 0.8050 (tp40) outliers start: 77 outliers final: 58 residues processed: 564 average time/residue: 0.2213 time to fit residues: 190.3264 Evaluate side-chains 575 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 511 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 88 TRP Chi-restraints excluded: chain B residue 90 HIS Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 373 HIS Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 305 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 121 optimal weight: 0.0970 chunk 88 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 140 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN B 90 HIS ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14910 Z= 0.190 Angle : 0.693 10.188 20230 Z= 0.321 Chirality : 0.045 0.203 2230 Planarity : 0.005 0.057 2590 Dihedral : 9.544 178.759 2075 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.31 % Allowed : 31.77 % Favored : 63.92 % 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: 0.31 (0.20), residues: 1840 helix: 0.03 (0.19), residues: 740 sheet: 0.48 (0.29), residues: 335 loop : 0.52 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 342 HIS 0.022 0.002 HIS B 90 PHE 0.018 0.001 PHE D 257 TYR 0.028 0.001 TYR A 281 ARG 0.006 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 542 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8013 (tp-100) cc_final: 0.7572 (tp-100) REVERT: A 70 LYS cc_start: 0.8777 (mmmm) cc_final: 0.8457 (mmmm) REVERT: A 103 HIS cc_start: 0.8344 (m90) cc_final: 0.7912 (m90) REVERT: A 123 GLN cc_start: 0.8844 (tp-100) cc_final: 0.8617 (tp40) REVERT: A 142 LEU cc_start: 0.9334 (mt) cc_final: 0.9000 (mt) REVERT: A 208 ARG cc_start: 0.8314 (mtm110) cc_final: 0.7950 (ttm-80) REVERT: A 278 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8467 (mt-10) REVERT: A 281 TYR cc_start: 0.8344 (t80) cc_final: 0.8137 (t80) REVERT: A 342 TRP cc_start: 0.7415 (t60) cc_final: 0.6931 (t60) REVERT: A 355 GLN cc_start: 0.9023 (mp10) cc_final: 0.8616 (mp10) REVERT: B 88 TRP cc_start: 0.9350 (OUTLIER) cc_final: 0.8883 (m-90) REVERT: B 90 HIS cc_start: 0.8709 (OUTLIER) cc_final: 0.8253 (t70) REVERT: B 117 ASN cc_start: 0.8887 (t0) cc_final: 0.8575 (t0) REVERT: B 119 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8680 (mt-10) REVERT: B 169 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8284 (mm-30) REVERT: B 205 THR cc_start: 0.9533 (p) cc_final: 0.9005 (t) REVERT: B 209 GLU cc_start: 0.9433 (mm-30) cc_final: 0.9156 (mp0) REVERT: B 272 GLU cc_start: 0.7357 (tt0) cc_final: 0.6908 (tp30) REVERT: B 294 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.8258 (t0) REVERT: B 339 TYR cc_start: 0.8845 (m-80) cc_final: 0.8224 (m-80) REVERT: C 216 GLU cc_start: 0.8789 (tt0) cc_final: 0.8081 (mt-10) REVERT: C 248 GLN cc_start: 0.8754 (tt0) cc_final: 0.8104 (mt0) REVERT: C 286 LYS cc_start: 0.8942 (ttmm) cc_final: 0.8607 (mtpp) REVERT: C 288 ASP cc_start: 0.8296 (m-30) cc_final: 0.8045 (m-30) REVERT: C 316 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8442 (tm-30) REVERT: C 339 TYR cc_start: 0.8686 (m-80) cc_final: 0.8437 (m-80) REVERT: D 119 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8007 (mm-30) REVERT: D 123 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8479 (tt0) REVERT: D 134 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8277 (tmm) REVERT: D 171 TYR cc_start: 0.8401 (m-80) cc_final: 0.8143 (m-80) REVERT: D 248 GLN cc_start: 0.8406 (mt0) cc_final: 0.8196 (mt0) REVERT: D 318 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8658 (mm-30) REVERT: D 327 MET cc_start: 0.8798 (mmm) cc_final: 0.8489 (tpp) REVERT: D 354 PHE cc_start: 0.8236 (t80) cc_final: 0.7882 (t80) REVERT: E 30 ARG cc_start: 0.8433 (mmp80) cc_final: 0.7961 (mmp-170) REVERT: E 113 ASN cc_start: 0.8502 (t0) cc_final: 0.8091 (t0) REVERT: E 119 GLU cc_start: 0.8814 (tp30) cc_final: 0.8555 (tp30) REVERT: E 122 THR cc_start: 0.8884 (m) cc_final: 0.8558 (t) REVERT: E 126 PHE cc_start: 0.8321 (OUTLIER) cc_final: 0.7818 (m-10) REVERT: E 193 LYS cc_start: 0.8940 (ttmt) cc_final: 0.8674 (ttmm) REVERT: E 228 GLU cc_start: 0.8620 (tp30) cc_final: 0.8092 (tp30) REVERT: E 236 SER cc_start: 0.9270 (m) cc_final: 0.8900 (t) REVERT: E 316 GLN cc_start: 0.8564 (tp40) cc_final: 0.8157 (tp40) REVERT: E 373 HIS cc_start: 0.6976 (m90) cc_final: 0.6748 (m-70) outliers start: 67 outliers final: 52 residues processed: 568 average time/residue: 0.2270 time to fit residues: 196.1136 Evaluate side-chains 570 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 511 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 88 TRP Chi-restraints excluded: chain B residue 90 HIS Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 305 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 chunk 109 optimal weight: 0.4980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 HIS ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14910 Z= 0.234 Angle : 0.725 11.499 20230 Z= 0.332 Chirality : 0.046 0.204 2230 Planarity : 0.005 0.054 2590 Dihedral : 9.461 176.396 2075 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.63 % Allowed : 32.15 % Favored : 63.22 % 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: 0.26 (0.20), residues: 1840 helix: 0.03 (0.19), residues: 740 sheet: 0.45 (0.29), residues: 335 loop : 0.45 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 342 HIS 0.008 0.001 HIS D 175 PHE 0.014 0.001 PHE D 257 TYR 0.029 0.001 TYR A 281 ARG 0.006 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 517 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8021 (tp-100) cc_final: 0.7588 (tp-100) REVERT: A 51 GLN cc_start: 0.5758 (mp10) cc_final: 0.5441 (mp10) REVERT: A 70 LYS cc_start: 0.8792 (mmmm) cc_final: 0.8473 (mmmm) REVERT: A 84 MET cc_start: 0.8233 (tpt) cc_final: 0.7941 (tpt) REVERT: A 103 HIS cc_start: 0.8371 (m90) cc_final: 0.7910 (m90) REVERT: A 142 LEU cc_start: 0.9339 (mt) cc_final: 0.9025 (mt) REVERT: A 208 ARG cc_start: 0.8337 (mtm110) cc_final: 0.7940 (ttm-80) REVERT: A 212 ARG cc_start: 0.8527 (ttp80) cc_final: 0.8215 (tmm-80) REVERT: A 224 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8189 (p0) REVERT: A 278 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8511 (mt-10) REVERT: A 281 TYR cc_start: 0.8441 (t80) cc_final: 0.8146 (t80) REVERT: A 342 TRP cc_start: 0.7473 (t60) cc_final: 0.7013 (t60) REVERT: B 88 TRP cc_start: 0.9367 (m-10) cc_final: 0.8849 (m-90) REVERT: B 90 HIS cc_start: 0.8781 (OUTLIER) cc_final: 0.7732 (t70) REVERT: B 119 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8691 (mt-10) REVERT: B 123 GLN cc_start: 0.9318 (tt0) cc_final: 0.9097 (tp40) REVERT: B 149 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.6988 (mpp80) REVERT: B 169 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8481 (mm-30) REVERT: B 205 THR cc_start: 0.9569 (p) cc_final: 0.9032 (t) REVERT: B 209 GLU cc_start: 0.9442 (mm-30) cc_final: 0.9163 (mp0) REVERT: B 272 GLU cc_start: 0.7419 (tt0) cc_final: 0.6954 (tp30) REVERT: B 294 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8277 (t0) REVERT: B 339 TYR cc_start: 0.8863 (m-80) cc_final: 0.8260 (m-80) REVERT: C 123 GLN cc_start: 0.9014 (tt0) cc_final: 0.8432 (tm-30) REVERT: C 216 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8035 (mt-10) REVERT: C 248 GLN cc_start: 0.8771 (tt0) cc_final: 0.8118 (mt0) REVERT: C 286 LYS cc_start: 0.8963 (ttmm) cc_final: 0.8618 (mtpp) REVERT: C 288 ASP cc_start: 0.8312 (m-30) cc_final: 0.8078 (m-30) REVERT: C 316 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8462 (tm-30) REVERT: D 115 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7975 (tppt) REVERT: D 119 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8047 (mm-30) REVERT: D 123 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8482 (tt0) REVERT: D 134 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8313 (tmm) REVERT: D 318 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8673 (mm-30) REVERT: D 354 PHE cc_start: 0.8263 (t80) cc_final: 0.7831 (t80) REVERT: E 30 ARG cc_start: 0.8425 (mmp80) cc_final: 0.7923 (mmp-170) REVERT: E 49 MET cc_start: 0.7859 (ppp) cc_final: 0.7325 (ppp) REVERT: E 55 TYR cc_start: 0.8477 (m-80) cc_final: 0.8140 (m-10) REVERT: E 113 ASN cc_start: 0.8565 (t0) cc_final: 0.8157 (t0) REVERT: E 119 GLU cc_start: 0.8836 (tp30) cc_final: 0.8574 (tp30) REVERT: E 122 THR cc_start: 0.8869 (m) cc_final: 0.8569 (t) REVERT: E 126 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.7807 (m-10) REVERT: E 193 LYS cc_start: 0.8934 (ttmt) cc_final: 0.8664 (ttmm) REVERT: E 236 SER cc_start: 0.9286 (m) cc_final: 0.8906 (t) REVERT: E 278 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7167 (tm-30) REVERT: E 316 GLN cc_start: 0.8549 (tp40) cc_final: 0.8160 (tp40) outliers start: 72 outliers final: 56 residues processed: 549 average time/residue: 0.2298 time to fit residues: 192.1543 Evaluate side-chains 584 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 518 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 90 HIS Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 329 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN ** B 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 14910 Z= 0.432 Angle : 0.825 13.396 20230 Z= 0.390 Chirality : 0.050 0.235 2230 Planarity : 0.005 0.055 2590 Dihedral : 9.746 177.080 2075 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 22.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.63 % Allowed : 32.54 % Favored : 62.83 % 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: -0.21 (0.20), residues: 1840 helix: -0.28 (0.19), residues: 770 sheet: 0.16 (0.29), residues: 345 loop : 0.14 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 342 HIS 0.013 0.002 HIS B 90 PHE 0.022 0.002 PHE E 354 TYR 0.031 0.002 TYR A 281 ARG 0.007 0.001 ARG B 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 501 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.8130 (tp-100) cc_final: 0.7704 (tp-100) REVERT: A 51 GLN cc_start: 0.5775 (mp10) cc_final: 0.5438 (mp10) REVERT: A 70 LYS cc_start: 0.8835 (mmmm) cc_final: 0.8524 (mmmm) REVERT: A 103 HIS cc_start: 0.8402 (m90) cc_final: 0.7881 (m90) REVERT: A 142 LEU cc_start: 0.9455 (mt) cc_final: 0.9162 (mt) REVERT: A 212 ARG cc_start: 0.8557 (ttp80) cc_final: 0.8213 (tmm-80) REVERT: A 278 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8525 (mt-10) REVERT: A 281 TYR cc_start: 0.8633 (t80) cc_final: 0.8081 (t80) REVERT: A 307 MET cc_start: 0.8516 (mmm) cc_final: 0.8276 (mmt) REVERT: A 342 TRP cc_start: 0.7614 (t60) cc_final: 0.7058 (t60) REVERT: B 88 TRP cc_start: 0.9428 (m-10) cc_final: 0.9110 (m-90) REVERT: B 90 HIS cc_start: 0.8495 (OUTLIER) cc_final: 0.8229 (t-90) REVERT: B 119 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8761 (mt-10) REVERT: B 123 GLN cc_start: 0.9325 (tt0) cc_final: 0.9117 (tp40) REVERT: B 169 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8563 (mm-30) REVERT: B 205 THR cc_start: 0.9585 (p) cc_final: 0.9076 (t) REVERT: B 209 GLU cc_start: 0.9493 (mm-30) cc_final: 0.9239 (mp0) REVERT: B 272 GLU cc_start: 0.7614 (tt0) cc_final: 0.7321 (tp30) REVERT: B 294 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8399 (t0) REVERT: B 339 TYR cc_start: 0.8861 (m-80) cc_final: 0.8224 (m-80) REVERT: C 123 GLN cc_start: 0.9131 (tt0) cc_final: 0.8543 (tm-30) REVERT: C 248 GLN cc_start: 0.8809 (tt0) cc_final: 0.8247 (mt0) REVERT: C 265 GLN cc_start: 0.8646 (mp10) cc_final: 0.7904 (mp10) REVERT: C 286 LYS cc_start: 0.8987 (ttmm) cc_final: 0.8627 (mtpp) REVERT: C 288 ASP cc_start: 0.8275 (m-30) cc_final: 0.8066 (m-30) REVERT: C 316 GLN cc_start: 0.8952 (tm-30) cc_final: 0.8492 (tm-30) REVERT: C 327 MET cc_start: 0.8484 (mmm) cc_final: 0.8137 (mmm) REVERT: D 115 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8123 (tppt) REVERT: D 119 GLU cc_start: 0.8665 (mt-10) cc_final: 0.7869 (mm-30) REVERT: D 123 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8493 (tt0) REVERT: D 134 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8255 (tmm) REVERT: D 318 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8763 (mm-30) REVERT: E 30 ARG cc_start: 0.8474 (mmp80) cc_final: 0.7924 (mmp-170) REVERT: E 55 TYR cc_start: 0.8471 (m-80) cc_final: 0.8263 (m-10) REVERT: E 59 GLU cc_start: 0.8980 (pt0) cc_final: 0.8659 (tm-30) REVERT: E 84 MET cc_start: 0.8797 (tpt) cc_final: 0.8554 (tpt) REVERT: E 113 ASN cc_start: 0.8465 (t0) cc_final: 0.8243 (t0) REVERT: E 119 GLU cc_start: 0.8903 (tp30) cc_final: 0.8692 (tp30) REVERT: E 122 THR cc_start: 0.8944 (m) cc_final: 0.8699 (t) REVERT: E 126 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7845 (m-10) REVERT: E 179 ARG cc_start: 0.8960 (ttt180) cc_final: 0.8592 (ttt180) REVERT: E 193 LYS cc_start: 0.8979 (ttmt) cc_final: 0.8706 (ttmm) REVERT: E 236 SER cc_start: 0.9312 (m) cc_final: 0.8912 (t) REVERT: E 278 GLU cc_start: 0.8573 (tm-30) cc_final: 0.7421 (tm-30) REVERT: E 316 GLN cc_start: 0.8655 (tp40) cc_final: 0.8279 (mm110) REVERT: E 322 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9122 (tp) outliers start: 72 outliers final: 56 residues processed: 538 average time/residue: 0.2297 time to fit residues: 187.0766 Evaluate side-chains 559 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 495 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 90 HIS Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 126 PHE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 322 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 150 optimal weight: 0.1980 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 373 HIS ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.109473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.094381 restraints weight = 31618.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.097521 restraints weight = 15658.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.099732 restraints weight = 9384.748| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14910 Z= 0.212 Angle : 0.743 12.151 20230 Z= 0.341 Chirality : 0.046 0.194 2230 Planarity : 0.005 0.057 2590 Dihedral : 9.513 175.277 2075 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.05 % Allowed : 33.38 % Favored : 62.57 % 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: -0.00 (0.20), residues: 1840 helix: -0.18 (0.19), residues: 770 sheet: 0.40 (0.29), residues: 335 loop : 0.27 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 342 HIS 0.010 0.001 HIS B 373 PHE 0.014 0.001 PHE E 354 TYR 0.027 0.002 TYR A 281 ARG 0.007 0.000 ARG A 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4027.04 seconds wall clock time: 73 minutes 4.73 seconds (4384.73 seconds total)