Starting phenix.real_space_refine on Fri Feb 16 05:56:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osf_17151/02_2024/8osf_17151_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osf_17151/02_2024/8osf_17151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osf_17151/02_2024/8osf_17151.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osf_17151/02_2024/8osf_17151.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osf_17151/02_2024/8osf_17151_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osf_17151/02_2024/8osf_17151_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 17 5.49 5 Mg 5 5.21 5 S 51 5.16 5 C 9124 2.51 5 N 2521 2.21 5 O 2811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 154": "OE1" <-> "OE2" Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 260": "OE1" <-> "OE2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B ASP 237": "OD1" <-> "OD2" Residue "B ASP 338": "OD1" <-> "OD2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 168": "OD1" <-> "OD2" Residue "D ASP 209": "OD1" <-> "OD2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "E PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 231": "OE1" <-> "OE2" Residue "E ASP 237": "OD1" <-> "OD2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "F GLU 154": "OE1" <-> "OE2" Residue "F ASP 209": "OD1" <-> "OD2" Residue "F TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14529 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2514 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 18, 'TRANS': 302} Chain breaks: 2 Chain: "B" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2514 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 18, 'TRANS': 302} Chain breaks: 2 Chain: "C" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2514 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 18, 'TRANS': 302} Chain breaks: 2 Chain: "D" Number of atoms: 2499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2499 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 18, 'TRANS': 300} Chain breaks: 2 Chain: "E" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2514 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 18, 'TRANS': 302} Chain breaks: 2 Chain: "F" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1787 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 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: {' MG': 1, 'ATP': 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: {' MG': 1, 'ATP': 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: {' MG': 1, 'ATP': 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: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.90, per 1000 atoms: 0.54 Number of scatterers: 14529 At special positions: 0 Unit cell: (130.284, 138.6, 77.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 51 16.00 P 17 15.00 Mg 5 11.99 O 2811 8.00 N 2521 7.00 C 9124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.63 Conformation dependent library (CDL) restraints added in 2.7 seconds 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3416 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 95 helices and 9 sheets defined 40.3% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'A' and resid 18 through 20 No H-bonds generated for 'chain 'A' and resid 18 through 20' Processing helix chain 'A' and resid 25 through 36 removed outlier: 4.377A pdb=" N LEU A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 62 removed outlier: 4.181A pdb=" N ALA A 61 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP A 62 " --> pdb=" O ARG A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 89 through 92 No H-bonds generated for 'chain 'A' and resid 89 through 92' Processing helix chain 'A' and resid 117 through 120 No H-bonds generated for 'chain 'A' and resid 117 through 120' Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 205 through 210 removed outlier: 4.154A pdb=" N ARG A 210 " --> pdb=" O GLN A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 238 removed outlier: 3.578A pdb=" N GLN A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG A 233 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 246 Processing helix chain 'A' and resid 248 through 264 removed outlier: 3.617A pdb=" N THR A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 285 removed outlier: 3.811A pdb=" N CYS A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 307 removed outlier: 3.587A pdb=" N VAL A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 319 No H-bonds generated for 'chain 'A' and resid 316 through 319' Processing helix chain 'A' and resid 322 through 325 No H-bonds generated for 'chain 'A' and resid 322 through 325' Processing helix chain 'A' and resid 339 through 350 removed outlier: 3.817A pdb=" N VAL A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU A 344 " --> pdb=" O GLY A 340 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 346 " --> pdb=" O LYS A 342 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 20 No H-bonds generated for 'chain 'B' and resid 18 through 20' Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 33 through 36 No H-bonds generated for 'chain 'B' and resid 33 through 36' Processing helix chain 'B' and resid 53 through 56 No H-bonds generated for 'chain 'B' and resid 53 through 56' Processing helix chain 'B' and resid 58 through 62 removed outlier: 3.702A pdb=" N ALA B 61 " --> pdb=" O ARG B 58 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP B 62 " --> pdb=" O ALA B 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 58 through 62' Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 117 through 120 No H-bonds generated for 'chain 'B' and resid 117 through 120' Processing helix chain 'B' and resid 141 through 144 No H-bonds generated for 'chain 'B' and resid 141 through 144' Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 223 through 238 removed outlier: 4.056A pdb=" N PHE B 236 " --> pdb=" O GLN B 232 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP B 237 " --> pdb=" O ARG B 233 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 263 removed outlier: 4.194A pdb=" N LEU B 244 " --> pdb=" O PRO B 240 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLU B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS B 246 " --> pdb=" O THR B 242 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR B 247 " --> pdb=" O PHE B 243 " (cutoff:3.500A) Proline residue: B 249 - end of helix removed outlier: 3.757A pdb=" N LEU B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 255 " --> pdb=" O GLN B 251 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS B 256 " --> pdb=" O THR B 252 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LYS B 257 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 285 removed outlier: 3.596A pdb=" N SER B 279 " --> pdb=" O ARG B 275 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N CYS B 282 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER B 283 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 285 " --> pdb=" O VAL B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 297 removed outlier: 4.146A pdb=" N ASN B 297 " --> pdb=" O ASP B 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 293 through 297' Processing helix chain 'B' and resid 300 through 307 removed outlier: 3.789A pdb=" N GLU B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 318 removed outlier: 3.984A pdb=" N ARG B 318 " --> pdb=" O ASP B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 324 No H-bonds generated for 'chain 'B' and resid 321 through 324' Processing helix chain 'B' and resid 341 through 350 Processing helix chain 'C' and resid 18 through 20 No H-bonds generated for 'chain 'C' and resid 18 through 20' Processing helix chain 'C' and resid 25 through 33 removed outlier: 4.075A pdb=" N LEU C 32 " --> pdb=" O LYS C 28 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 removed outlier: 4.164A pdb=" N ALA C 61 " --> pdb=" O ARG C 58 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP C 62 " --> pdb=" O ALA C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 120 No H-bonds generated for 'chain 'C' and resid 117 through 120' Processing helix chain 'C' and resid 141 through 144 No H-bonds generated for 'chain 'C' and resid 141 through 144' Processing helix chain 'C' and resid 164 through 166 No H-bonds generated for 'chain 'C' and resid 164 through 166' Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 205 through 210 Processing helix chain 'C' and resid 223 through 231 Processing helix chain 'C' and resid 234 through 237 No H-bonds generated for 'chain 'C' and resid 234 through 237' Processing helix chain 'C' and resid 240 through 263 removed outlier: 4.191A pdb=" N LEU C 244 " --> pdb=" O PRO C 240 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLU C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS C 246 " --> pdb=" O THR C 242 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR C 247 " --> pdb=" O PHE C 243 " (cutoff:3.500A) Proline residue: C 249 - end of helix removed outlier: 4.563A pdb=" N ALA C 253 " --> pdb=" O PRO C 249 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN C 255 " --> pdb=" O GLN C 251 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS C 256 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 259 " --> pdb=" O GLN C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 285 removed outlier: 3.739A pdb=" N VAL C 276 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS C 277 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 281 " --> pdb=" O LYS C 277 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N CYS C 282 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER C 283 " --> pdb=" O SER C 279 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU C 284 " --> pdb=" O GLU C 280 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 285 " --> pdb=" O VAL C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 307 removed outlier: 4.175A pdb=" N LYS C 301 " --> pdb=" O ASN C 297 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA C 302 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR C 306 " --> pdb=" O ALA C 302 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU C 307 " --> pdb=" O LEU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 318 Processing helix chain 'C' and resid 326 through 328 No H-bonds generated for 'chain 'C' and resid 326 through 328' Processing helix chain 'C' and resid 339 through 345 removed outlier: 5.051A pdb=" N GLU C 344 " --> pdb=" O GLY C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 350 No H-bonds generated for 'chain 'C' and resid 347 through 350' Processing helix chain 'D' and resid 18 through 20 No H-bonds generated for 'chain 'D' and resid 18 through 20' Processing helix chain 'D' and resid 26 through 36 Processing helix chain 'D' and resid 53 through 61 removed outlier: 4.023A pdb=" N ALA D 61 " --> pdb=" O ILE D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 120 No H-bonds generated for 'chain 'D' and resid 117 through 120' Processing helix chain 'D' and resid 155 through 157 No H-bonds generated for 'chain 'D' and resid 155 through 157' Processing helix chain 'D' and resid 163 through 171 Processing helix chain 'D' and resid 179 through 181 No H-bonds generated for 'chain 'D' and resid 179 through 181' Processing helix chain 'D' and resid 205 through 208 No H-bonds generated for 'chain 'D' and resid 205 through 208' Processing helix chain 'D' and resid 223 through 231 removed outlier: 4.294A pdb=" N GLN D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 245 removed outlier: 4.653A pdb=" N GLU D 245 " --> pdb=" O PRO D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 262 Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 272 through 277 Processing helix chain 'D' and resid 280 through 284 Processing helix chain 'D' and resid 294 through 303 removed outlier: 3.937A pdb=" N LYS D 301 " --> pdb=" O ASN D 297 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ALA D 302 " --> pdb=" O ARG D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 321 removed outlier: 3.698A pdb=" N ARG D 319 " --> pdb=" O ASP D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 350 removed outlier: 3.575A pdb=" N VAL D 346 " --> pdb=" O LYS D 342 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG D 349 " --> pdb=" O LYS D 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 36 removed outlier: 4.154A pdb=" N ILE E 36 " --> pdb=" O LEU E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 62 removed outlier: 3.510A pdb=" N ILE E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA E 61 " --> pdb=" O ILE E 57 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASP E 62 " --> pdb=" O ARG E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 92 Processing helix chain 'E' and resid 117 through 120 No H-bonds generated for 'chain 'E' and resid 117 through 120' Processing helix chain 'E' and resid 141 through 144 No H-bonds generated for 'chain 'E' and resid 141 through 144' Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 169 through 172 No H-bonds generated for 'chain 'E' and resid 169 through 172' Processing helix chain 'E' and resid 205 through 208 No H-bonds generated for 'chain 'E' and resid 205 through 208' Processing helix chain 'E' and resid 223 through 238 Processing helix chain 'E' and resid 240 through 267 removed outlier: 4.744A pdb=" N LEU E 244 " --> pdb=" O PRO E 240 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLU E 245 " --> pdb=" O PRO E 241 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS E 246 " --> pdb=" O THR E 242 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR E 247 " --> pdb=" O PHE E 243 " (cutoff:3.500A) Proline residue: E 249 - end of helix removed outlier: 3.930A pdb=" N GLN E 255 " --> pdb=" O GLN E 251 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS E 263 " --> pdb=" O VAL E 259 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU E 264 " --> pdb=" O GLU E 260 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) Proline residue: E 266 - end of helix Processing helix chain 'E' and resid 272 through 285 removed outlier: 3.946A pdb=" N SER E 279 " --> pdb=" O ARG E 275 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU E 280 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL E 281 " --> pdb=" O LYS E 277 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER E 283 " --> pdb=" O SER E 279 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLU E 284 " --> pdb=" O GLU E 280 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU E 285 " --> pdb=" O VAL E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 303 removed outlier: 3.914A pdb=" N ASN E 297 " --> pdb=" O ASP E 293 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG E 298 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS E 301 " --> pdb=" O ASN E 297 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ALA E 302 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU E 303 " --> pdb=" O ALA E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 322 removed outlier: 3.623A pdb=" N ARG E 319 " --> pdb=" O ASP E 315 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL E 320 " --> pdb=" O ASP E 316 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR E 322 " --> pdb=" O ARG E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 351 removed outlier: 3.513A pdb=" N VAL E 343 " --> pdb=" O SER E 339 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL E 346 " --> pdb=" O LYS E 342 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG E 349 " --> pdb=" O LYS E 345 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE E 350 " --> pdb=" O VAL E 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 36 Processing helix chain 'F' and resid 53 through 60 Processing helix chain 'F' and resid 205 through 208 No H-bonds generated for 'chain 'F' and resid 205 through 208' Processing helix chain 'F' and resid 223 through 231 Processing helix chain 'F' and resid 234 through 238 Processing helix chain 'F' and resid 240 through 257 removed outlier: 4.520A pdb=" N LEU F 244 " --> pdb=" O PRO F 240 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLU F 245 " --> pdb=" O PRO F 241 " (cutoff:3.500A) Proline residue: F 249 - end of helix removed outlier: 3.538A pdb=" N LEU F 254 " --> pdb=" O GLU F 250 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN F 255 " --> pdb=" O GLN F 251 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS F 256 " --> pdb=" O THR F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 263 No H-bonds generated for 'chain 'F' and resid 261 through 263' Processing helix chain 'F' and resid 265 through 267 No H-bonds generated for 'chain 'F' and resid 265 through 267' Processing helix chain 'F' and resid 272 through 277 Processing helix chain 'F' and resid 280 through 284 Processing helix chain 'F' and resid 295 through 305 removed outlier: 3.643A pdb=" N LYS F 301 " --> pdb=" O ASN F 297 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA F 302 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR F 304 " --> pdb=" O ALA F 300 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA F 305 " --> pdb=" O LYS F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 321 removed outlier: 4.028A pdb=" N ILE F 321 " --> pdb=" O ARG F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 350 removed outlier: 3.976A pdb=" N PHE F 347 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE F 350 " --> pdb=" O VAL F 346 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 108 through 110 removed outlier: 5.873A pdb=" N ILE A 149 " --> pdb=" O VAL A 109 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.666A pdb=" N VAL A 177 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 213 through 217 removed outlier: 4.066A pdb=" N GLY B 196 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY B 47 " --> pdb=" O GLY B 196 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 150 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER B 195 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 109 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR B 151 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 111 " --> pdb=" O TYR B 151 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 66 through 69 removed outlier: 3.738A pdb=" N GLU B 102 " --> pdb=" O VAL B 69 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 175 through 179 Processing sheet with id= F, first strand: chain 'C' and resid 215 through 217 removed outlier: 3.651A pdb=" N ALA C 215 " --> pdb=" O MET C 44 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET C 46 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY C 47 " --> pdb=" O GLY C 196 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER C 195 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASP C 153 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 66 through 69 removed outlier: 3.679A pdb=" N GLU C 102 " --> pdb=" O VAL C 69 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 213 through 216 removed outlier: 3.564A pdb=" N MET D 44 " --> pdb=" O MET D 213 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 150 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER D 195 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR D 151 " --> pdb=" O VAL D 109 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 149 through 151 removed outlier: 6.902A pdb=" N VAL E 191 " --> pdb=" O LEU E 150 " (cutoff:3.500A) No H-bonds generated for sheet with id= I 290 hydrogen bonds defined for protein. 828 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: 3.32 Time building geometry restraints manager: 6.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3805 1.33 - 1.45: 2293 1.45 - 1.58: 8537 1.58 - 1.70: 29 1.70 - 1.82: 85 Bond restraints: 14749 Sorted by residual: bond pdb=" CB PRO E 198 " pdb=" CG PRO E 198 " ideal model delta sigma weight residual 1.492 1.611 -0.119 5.00e-02 4.00e+02 5.68e+00 bond pdb=" CG LEU E 31 " pdb=" CD2 LEU E 31 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.28e+00 bond pdb=" C PRO F 240 " pdb=" N PRO F 241 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.76e+00 bond pdb=" CB ASP A 153 " pdb=" CG ASP A 153 " ideal model delta sigma weight residual 1.516 1.548 -0.032 2.50e-02 1.60e+03 1.63e+00 bond pdb=" CG GLN F 228 " pdb=" CD GLN F 228 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.60e+00 ... (remaining 14744 not shown) Histogram of bond angle deviations from ideal: 99.59 - 107.65: 599 107.65 - 115.71: 9299 115.71 - 123.78: 9695 123.78 - 131.84: 382 131.84 - 139.90: 22 Bond angle restraints: 19997 Sorted by residual: angle pdb=" N ILE D 184 " pdb=" CA ILE D 184 " pdb=" C ILE D 184 " ideal model delta sigma weight residual 111.91 106.51 5.40 8.90e-01 1.26e+00 3.68e+01 angle pdb=" C ARG D 185 " pdb=" N HIS D 186 " pdb=" CA HIS D 186 " ideal model delta sigma weight residual 120.49 127.92 -7.43 1.42e+00 4.96e-01 2.74e+01 angle pdb=" CA PRO E 198 " pdb=" N PRO E 198 " pdb=" CD PRO E 198 " ideal model delta sigma weight residual 112.00 104.93 7.07 1.40e+00 5.10e-01 2.55e+01 angle pdb=" CB MET A 213 " pdb=" CG MET A 213 " pdb=" SD MET A 213 " ideal model delta sigma weight residual 112.70 126.42 -13.72 3.00e+00 1.11e-01 2.09e+01 angle pdb=" CB MET A 44 " pdb=" CG MET A 44 " pdb=" SD MET A 44 " ideal model delta sigma weight residual 112.70 125.60 -12.90 3.00e+00 1.11e-01 1.85e+01 ... (remaining 19992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.14: 8526 31.14 - 62.29: 614 62.29 - 93.43: 53 93.43 - 124.57: 2 124.57 - 155.72: 1 Dihedral angle restraints: 9196 sinusoidal: 3939 harmonic: 5257 Sorted by residual: dihedral pdb=" C5' ADP F 401 " pdb=" O5' ADP F 401 " pdb=" PA ADP F 401 " pdb=" O2A ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 95.72 -155.72 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" O2A ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PA ADP F 401 " pdb=" PB ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 51.15 -111.15 1 2.00e+01 2.50e-03 3.27e+01 dihedral pdb=" O1B ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PB ADP F 401 " pdb=" PA ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 49.33 -109.33 1 2.00e+01 2.50e-03 3.19e+01 ... (remaining 9193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1388 0.031 - 0.062: 603 0.062 - 0.093: 223 0.093 - 0.124: 103 0.124 - 0.155: 12 Chirality restraints: 2329 Sorted by residual: chirality pdb=" CA ILE D 184 " pdb=" N ILE D 184 " pdb=" C ILE D 184 " pdb=" CB ILE D 184 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.03e-01 chirality pdb=" CA ILE E 337 " pdb=" N ILE E 337 " pdb=" C ILE E 337 " pdb=" CB ILE E 337 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CA ASN D 156 " pdb=" N ASN D 156 " pdb=" C ASN D 156 " pdb=" CB ASN D 156 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 2326 not shown) Planarity restraints: 2585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 197 " 0.045 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO E 198 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 198 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 198 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 233 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" C ARG C 233 " -0.038 2.00e-02 2.50e+03 pdb=" O ARG C 233 " 0.014 2.00e-02 2.50e+03 pdb=" N SER C 234 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 204 " -0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO A 205 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 205 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 205 " -0.029 5.00e-02 4.00e+02 ... (remaining 2582 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 228 2.62 - 3.19: 13253 3.19 - 3.76: 22444 3.76 - 4.33: 28278 4.33 - 4.90: 43923 Nonbonded interactions: 108126 Sorted by model distance: nonbonded pdb=" O1G ATP D 401 " pdb="MG MG D 402 " model vdw 2.045 2.170 nonbonded pdb=" O1G ATP A 401 " pdb="MG MG A 402 " model vdw 2.069 2.170 nonbonded pdb=" O1G ATP B 401 " pdb="MG MG B 402 " model vdw 2.074 2.170 nonbonded pdb=" O2B ATP E 401 " pdb="MG MG E 402 " model vdw 2.076 2.170 nonbonded pdb=" O1G ATP E 401 " pdb="MG MG E 402 " model vdw 2.080 2.170 ... (remaining 108121 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 91 or resid 101 through 353 or resid 401 throug \ h 402)) selection = (chain 'B' and (resid 14 through 91 or resid 101 through 353 or resid 401 throug \ h 402)) selection = (chain 'C' and (resid 14 through 91 or resid 101 through 353 or resid 401 throug \ h 402)) selection = chain 'D' selection = (chain 'E' and (resid 14 through 91 or resid 101 through 353 or resid 401 throug \ h 402)) } 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: 1.130 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: 5.790 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 38.100 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.119 14749 Z= 0.187 Angle : 0.696 13.716 19997 Z= 0.347 Chirality : 0.042 0.155 2329 Planarity : 0.004 0.065 2585 Dihedral : 19.450 155.717 5780 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 0.44 % Allowed : 40.06 % Favored : 59.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.21), residues: 1793 helix: -0.42 (0.22), residues: 604 sheet: -0.82 (0.50), residues: 131 loop : -1.77 (0.20), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 174 HIS 0.002 0.000 HIS F 214 PHE 0.020 0.001 PHE E 190 TYR 0.005 0.001 TYR D 306 ARG 0.007 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 1.933 Fit side-chains revert: symmetry clash REVERT: B 342 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8031 (mtmm) REVERT: C 229 ILE cc_start: 0.9018 (pt) cc_final: 0.8790 (tp) REVERT: E 214 HIS cc_start: 0.8473 (OUTLIER) cc_final: 0.8145 (t-90) outliers start: 7 outliers final: 3 residues processed: 152 average time/residue: 0.2442 time to fit residues: 57.4713 Evaluate side-chains 148 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 143 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain E residue 214 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 92 optimal weight: 0.0570 chunk 73 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 164 optimal weight: 7.9990 overall best weight: 2.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14749 Z= 0.208 Angle : 0.608 10.430 19997 Z= 0.295 Chirality : 0.042 0.157 2329 Planarity : 0.004 0.050 2585 Dihedral : 11.512 163.693 2162 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Rotamer: Outliers : 5.71 % Allowed : 34.73 % Favored : 59.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.21), residues: 1793 helix: -0.25 (0.22), residues: 623 sheet: -1.44 (0.44), residues: 164 loop : -1.80 (0.21), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 174 HIS 0.004 0.001 HIS D 186 PHE 0.012 0.001 PHE E 190 TYR 0.011 0.001 TYR F 306 ARG 0.003 0.000 ARG E 119 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 138 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8138 (tmm) cc_final: 0.7850 (tmm) REVERT: A 153 ASP cc_start: 0.8278 (p0) cc_final: 0.8045 (p0) REVERT: A 206 GLN cc_start: 0.9042 (tp40) cc_final: 0.8823 (tp40) REVERT: B 206 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8849 (mm-40) REVERT: C 351 PHE cc_start: 0.7587 (OUTLIER) cc_final: 0.7279 (p90) REVERT: E 213 MET cc_start: 0.7226 (pmm) cc_final: 0.6888 (pmm) REVERT: E 214 HIS cc_start: 0.8621 (OUTLIER) cc_final: 0.8148 (t-90) outliers start: 91 outliers final: 55 residues processed: 213 average time/residue: 0.2248 time to fit residues: 74.3896 Evaluate side-chains 189 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 131 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 351 PHE Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 214 HIS Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 306 TYR Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 349 ARG Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 243 PHE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 310 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 91 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 177 optimal weight: 0.3980 chunk 146 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14749 Z= 0.162 Angle : 0.594 10.838 19997 Z= 0.283 Chirality : 0.042 0.250 2329 Planarity : 0.004 0.050 2585 Dihedral : 11.097 170.991 2158 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 4.95 % Allowed : 35.99 % Favored : 59.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.21), residues: 1793 helix: -0.17 (0.22), residues: 627 sheet: -1.09 (0.46), residues: 149 loop : -1.84 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 174 HIS 0.004 0.001 HIS A 214 PHE 0.008 0.001 PHE F 18 TYR 0.008 0.001 TYR F 306 ARG 0.004 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 142 time to evaluate : 1.879 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8257 (tmm) cc_final: 0.7646 (tmm) REVERT: A 154 GLU cc_start: 0.8144 (pm20) cc_final: 0.7649 (pm20) REVERT: A 162 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7863 (mm) REVERT: A 206 GLN cc_start: 0.9089 (tp40) cc_final: 0.8861 (tp40) REVERT: D 179 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.7068 (ttp-170) REVERT: D 206 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8603 (tm-30) REVERT: E 167 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7826 (tp) REVERT: E 213 MET cc_start: 0.7492 (pmm) cc_final: 0.7257 (pmm) outliers start: 79 outliers final: 52 residues processed: 203 average time/residue: 0.2254 time to fit residues: 71.0969 Evaluate side-chains 191 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 135 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 146 ASN Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 214 HIS Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 306 TYR Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 211 PHE Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 310 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 162 optimal weight: 9.9990 chunk 123 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 chunk 165 optimal weight: 9.9990 chunk 174 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14749 Z= 0.260 Angle : 0.642 10.288 19997 Z= 0.313 Chirality : 0.044 0.196 2329 Planarity : 0.004 0.050 2585 Dihedral : 11.414 172.841 2154 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.72 % Favored : 87.28 % Rotamer: Outliers : 7.40 % Allowed : 33.48 % Favored : 59.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.20), residues: 1793 helix: -0.27 (0.21), residues: 613 sheet: -1.65 (0.42), residues: 166 loop : -1.90 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 174 HIS 0.004 0.001 HIS C 214 PHE 0.015 0.002 PHE F 18 TYR 0.014 0.001 TYR F 306 ARG 0.005 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 136 time to evaluate : 1.801 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8403 (tmm) cc_final: 0.7663 (tmm) REVERT: A 153 ASP cc_start: 0.8211 (p0) cc_final: 0.8009 (p0) REVERT: A 206 GLN cc_start: 0.9133 (tp40) cc_final: 0.8813 (tp40) REVERT: A 267 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7981 (mp0) REVERT: B 206 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8843 (mm-40) REVERT: B 291 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7891 (ttt-90) REVERT: D 179 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.7224 (ttp-170) REVERT: D 206 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8966 (tp40) REVERT: D 238 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8905 (mp10) REVERT: E 44 MET cc_start: 0.8321 (tpp) cc_final: 0.8083 (tpp) REVERT: E 315 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7311 (t0) REVERT: F 286 ASP cc_start: 0.8486 (t0) cc_final: 0.8282 (t0) outliers start: 118 outliers final: 85 residues processed: 237 average time/residue: 0.2285 time to fit residues: 83.1168 Evaluate side-chains 226 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 134 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 214 HIS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 233 ARG Chi-restraints excluded: chain C residue 263 LYS Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 306 TYR Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 214 HIS Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 306 TYR Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 211 PHE Chi-restraints excluded: chain F residue 218 HIS Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 243 PHE Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 310 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 145 optimal weight: 8.9990 chunk 99 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 157 optimal weight: 0.0000 chunk 44 optimal weight: 7.9990 overall best weight: 1.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14749 Z= 0.184 Angle : 0.613 11.022 19997 Z= 0.294 Chirality : 0.043 0.163 2329 Planarity : 0.004 0.050 2585 Dihedral : 11.217 176.829 2154 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 6.58 % Allowed : 35.24 % Favored : 58.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.20), residues: 1793 helix: -0.18 (0.22), residues: 627 sheet: -1.61 (0.42), residues: 166 loop : -1.92 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 174 HIS 0.006 0.001 HIS C 214 PHE 0.011 0.001 PHE F 18 TYR 0.010 0.001 TYR F 306 ARG 0.004 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 140 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.8119 (pm20) cc_final: 0.7758 (pm20) REVERT: A 206 GLN cc_start: 0.9090 (tp-100) cc_final: 0.8760 (tp40) REVERT: A 267 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7953 (mp0) REVERT: B 206 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8864 (mm-40) REVERT: B 291 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7825 (ttt-90) REVERT: D 179 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.7179 (ttp-170) REVERT: D 206 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8946 (tp40) REVERT: D 238 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8902 (mp10) REVERT: E 315 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7214 (t0) REVERT: E 330 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6524 (tpp-160) REVERT: F 286 ASP cc_start: 0.8433 (t0) cc_final: 0.8204 (t0) outliers start: 105 outliers final: 81 residues processed: 229 average time/residue: 0.2353 time to fit residues: 82.0683 Evaluate side-chains 225 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 136 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 214 HIS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 233 ARG Chi-restraints excluded: chain C residue 263 LYS Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 306 TYR Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 214 HIS Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 306 TYR Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 330 ARG Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 211 PHE Chi-restraints excluded: chain F residue 218 HIS Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 243 PHE Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 310 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 0.6980 chunk 157 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 175 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 57 optimal weight: 0.3980 chunk 91 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14749 Z= 0.152 Angle : 0.604 11.430 19997 Z= 0.287 Chirality : 0.042 0.150 2329 Planarity : 0.004 0.050 2585 Dihedral : 10.751 176.809 2154 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 5.45 % Allowed : 36.24 % Favored : 58.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.21), residues: 1793 helix: -0.05 (0.22), residues: 640 sheet: -1.13 (0.45), residues: 156 loop : -1.92 (0.20), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 174 HIS 0.003 0.001 HIS C 327 PHE 0.007 0.001 PHE F 18 TYR 0.006 0.001 TYR D 306 ARG 0.003 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 148 time to evaluate : 1.863 Fit side-chains REVERT: A 206 GLN cc_start: 0.9095 (tp40) cc_final: 0.8741 (tp40) REVERT: B 108 MET cc_start: 0.7563 (tpt) cc_final: 0.7358 (tpt) REVERT: B 311 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7496 (pp20) REVERT: C 263 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7732 (mmmm) REVERT: D 179 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.7052 (ttp-170) REVERT: D 206 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8596 (tm-30) REVERT: D 238 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8883 (mp10) REVERT: E 31 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9065 (mm) REVERT: E 34 ASN cc_start: 0.8307 (p0) cc_final: 0.7521 (t0) REVERT: E 315 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7561 (t0) REVERT: E 330 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6451 (tpp-160) REVERT: F 34 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8801 (m-40) REVERT: F 286 ASP cc_start: 0.8451 (t0) cc_final: 0.8184 (t0) outliers start: 87 outliers final: 57 residues processed: 219 average time/residue: 0.2314 time to fit residues: 77.3875 Evaluate side-chains 206 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 140 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 214 HIS Chi-restraints excluded: chain C residue 263 LYS Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 351 PHE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 214 HIS Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 306 TYR Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 330 ARG Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 211 PHE Chi-restraints excluded: chain F residue 243 PHE Chi-restraints excluded: chain F residue 310 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 147 optimal weight: 0.6980 chunk 97 optimal weight: 0.0980 chunk 174 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 80 optimal weight: 0.1980 chunk 107 optimal weight: 0.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14749 Z= 0.169 Angle : 0.612 11.696 19997 Z= 0.290 Chirality : 0.042 0.146 2329 Planarity : 0.004 0.051 2585 Dihedral : 10.730 174.168 2152 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % Rotamer: Outliers : 6.33 % Allowed : 35.99 % Favored : 57.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.21), residues: 1793 helix: -0.00 (0.22), residues: 639 sheet: -1.14 (0.45), residues: 156 loop : -1.92 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 174 HIS 0.004 0.001 HIS C 327 PHE 0.017 0.001 PHE E 190 TYR 0.009 0.001 TYR C 272 ARG 0.002 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 139 time to evaluate : 1.875 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8265 (tmm) cc_final: 0.7727 (tmm) REVERT: A 206 GLN cc_start: 0.9098 (tp40) cc_final: 0.8763 (tp40) REVERT: B 311 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7539 (pp20) REVERT: D 110 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7513 (m-30) REVERT: D 179 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.7071 (ttp-170) REVERT: D 206 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8627 (tm-30) REVERT: D 238 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8880 (mp10) REVERT: E 33 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9101 (mm) REVERT: E 315 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7476 (t0) REVERT: E 330 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6445 (tpp-160) REVERT: F 286 ASP cc_start: 0.8470 (t0) cc_final: 0.8200 (t0) outliers start: 101 outliers final: 75 residues processed: 224 average time/residue: 0.2569 time to fit residues: 88.6854 Evaluate side-chains 221 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 138 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 214 HIS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 263 LYS Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 351 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 214 HIS Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 306 TYR Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 330 ARG Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 211 PHE Chi-restraints excluded: chain F residue 243 PHE Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 310 THR Chi-restraints excluded: chain F residue 329 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 69 optimal weight: 0.0670 chunk 104 optimal weight: 7.9990 chunk 52 optimal weight: 0.2980 chunk 34 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 110 optimal weight: 0.0070 chunk 118 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 137 optimal weight: 0.2980 chunk 158 optimal weight: 0.2980 overall best weight: 0.1936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14749 Z= 0.151 Angle : 0.628 11.906 19997 Z= 0.292 Chirality : 0.042 0.307 2329 Planarity : 0.004 0.052 2585 Dihedral : 10.222 167.582 2152 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 4.95 % Allowed : 37.74 % Favored : 57.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.21), residues: 1793 helix: 0.07 (0.22), residues: 646 sheet: -0.75 (0.45), residues: 152 loop : -1.87 (0.21), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 174 HIS 0.010 0.001 HIS A 214 PHE 0.007 0.001 PHE A 190 TYR 0.008 0.001 TYR C 272 ARG 0.003 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 158 time to evaluate : 1.910 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8099 (tmm) cc_final: 0.7593 (tmm) REVERT: A 206 GLN cc_start: 0.9081 (tp40) cc_final: 0.8800 (tp40) REVERT: B 55 THR cc_start: 0.8283 (OUTLIER) cc_final: 0.7927 (t) REVERT: B 108 MET cc_start: 0.7422 (tpt) cc_final: 0.7213 (tpt) REVERT: B 311 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7322 (pp20) REVERT: C 263 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7631 (mmmm) REVERT: D 110 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7527 (m-30) REVERT: D 168 ASP cc_start: 0.8716 (m-30) cc_final: 0.8441 (m-30) REVERT: D 179 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.7025 (ttp-170) REVERT: D 206 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8582 (tm-30) REVERT: D 238 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8868 (mp10) REVERT: E 315 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7350 (t0) REVERT: E 330 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6433 (tpp-160) REVERT: F 34 ASN cc_start: 0.9053 (OUTLIER) cc_final: 0.8817 (m-40) outliers start: 79 outliers final: 56 residues processed: 223 average time/residue: 0.2354 time to fit residues: 79.8448 Evaluate side-chains 217 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 151 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 214 HIS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 263 LYS Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 214 HIS Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 306 TYR Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 330 ARG Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 211 PHE Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 310 THR Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 167 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 162 optimal weight: 0.2980 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 127 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14749 Z= 0.167 Angle : 0.638 12.818 19997 Z= 0.297 Chirality : 0.043 0.382 2329 Planarity : 0.004 0.050 2585 Dihedral : 10.306 163.804 2152 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 5.14 % Allowed : 37.99 % Favored : 56.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.21), residues: 1793 helix: 0.15 (0.22), residues: 652 sheet: -0.82 (0.42), residues: 176 loop : -1.94 (0.21), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 174 HIS 0.007 0.001 HIS A 214 PHE 0.017 0.001 PHE E 190 TYR 0.021 0.001 TYR B 341 ARG 0.002 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 142 time to evaluate : 1.994 Fit side-chains REVERT: A 44 MET cc_start: 0.8227 (tmm) cc_final: 0.7733 (tmm) REVERT: A 206 GLN cc_start: 0.9051 (tp-100) cc_final: 0.8785 (tp40) REVERT: B 311 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7344 (pp20) REVERT: C 107 GLN cc_start: 0.8525 (tp40) cc_final: 0.8281 (mm110) REVERT: C 263 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7731 (mmmm) REVERT: D 110 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7488 (m-30) REVERT: D 179 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.7039 (ttp-170) REVERT: D 206 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8618 (tm-30) REVERT: D 238 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8863 (mp10) REVERT: E 330 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6531 (tpp-160) REVERT: F 34 ASN cc_start: 0.9091 (OUTLIER) cc_final: 0.8855 (m-40) REVERT: F 286 ASP cc_start: 0.8480 (t0) cc_final: 0.8201 (t0) outliers start: 82 outliers final: 66 residues processed: 209 average time/residue: 0.2153 time to fit residues: 70.1044 Evaluate side-chains 216 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 142 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 214 HIS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 263 LYS Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 214 HIS Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 306 TYR Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 330 ARG Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 211 PHE Chi-restraints excluded: chain F residue 243 PHE Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 310 THR Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 104 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 180 optimal weight: 7.9990 chunk 165 optimal weight: 8.9990 chunk 143 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 110 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 152 optimal weight: 10.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 ASN E 232 GLN ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14749 Z= 0.275 Angle : 0.714 13.189 19997 Z= 0.340 Chirality : 0.045 0.371 2329 Planarity : 0.004 0.049 2585 Dihedral : 11.233 173.351 2152 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.22 % Favored : 86.78 % Rotamer: Outliers : 5.64 % Allowed : 37.62 % Favored : 56.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.20), residues: 1793 helix: -0.13 (0.22), residues: 629 sheet: -1.19 (0.41), residues: 174 loop : -1.99 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 174 HIS 0.007 0.001 HIS A 214 PHE 0.017 0.002 PHE F 18 TYR 0.014 0.001 TYR E 306 ARG 0.004 0.000 ARG B 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 129 time to evaluate : 1.922 Fit side-chains REVERT: A 44 MET cc_start: 0.8370 (tmm) cc_final: 0.7917 (tmm) REVERT: A 49 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8096 (mtm-85) REVERT: A 206 GLN cc_start: 0.9127 (tp-100) cc_final: 0.8690 (tp40) REVERT: B 206 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8872 (mm-40) REVERT: B 311 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7546 (pp20) REVERT: B 330 ARG cc_start: 0.7250 (ptp-170) cc_final: 0.6965 (ptp-170) REVERT: C 75 PHE cc_start: 0.6767 (OUTLIER) cc_final: 0.6495 (t80) REVERT: D 110 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7584 (m-30) REVERT: D 179 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.7202 (ttp-170) REVERT: D 206 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.8476 (tm-30) REVERT: D 238 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8845 (mp10) REVERT: E 315 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7278 (t0) REVERT: E 330 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6452 (tpp-160) REVERT: F 286 ASP cc_start: 0.8482 (t0) cc_final: 0.8214 (t0) outliers start: 90 outliers final: 70 residues processed: 207 average time/residue: 0.2355 time to fit residues: 74.9361 Evaluate side-chains 208 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 128 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 342 LYS Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 214 HIS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 263 LYS Chi-restraints excluded: chain C residue 267 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 351 PHE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 214 HIS Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 286 ASP Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 306 TYR Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 330 ARG Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 211 PHE Chi-restraints excluded: chain F residue 243 PHE Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 310 THR Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 43 optimal weight: 0.0470 chunk 132 optimal weight: 0.6980 chunk 21 optimal weight: 0.0170 chunk 39 optimal weight: 8.9990 chunk 143 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 ASN E 232 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.101129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.083535 restraints weight = 57175.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.085491 restraints weight = 35003.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.086836 restraints weight = 25243.912| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14749 Z= 0.161 Angle : 0.671 13.112 19997 Z= 0.309 Chirality : 0.044 0.411 2329 Planarity : 0.004 0.050 2585 Dihedral : 10.654 171.551 2152 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 4.01 % Allowed : 39.50 % Favored : 56.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.21), residues: 1793 helix: 0.10 (0.22), residues: 638 sheet: -0.56 (0.45), residues: 157 loop : -1.88 (0.21), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 174 HIS 0.007 0.001 HIS A 214 PHE 0.009 0.001 PHE C 75 TYR 0.008 0.001 TYR C 272 ARG 0.003 0.000 ARG A 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2701.72 seconds wall clock time: 50 minutes 0.27 seconds (3000.27 seconds total)