Starting phenix.real_space_refine on Thu Sep 26 18:02:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2s_20579/09_2024/6q2s_20579_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2s_20579/09_2024/6q2s_20579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2s_20579/09_2024/6q2s_20579.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2s_20579/09_2024/6q2s_20579.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2s_20579/09_2024/6q2s_20579_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2s_20579/09_2024/6q2s_20579_neut.cif" } resolution = 3.8 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 124 5.16 5 C 8558 2.51 5 N 2466 2.21 5 O 2570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13726 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 743 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 8, 'TRANS': 89} Chain: "C" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1527 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 12, 'TRANS': 186} Chain: "E" Number of atoms: 4491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4491 Classifications: {'peptide': 570} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 535} Chain breaks: 5 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 88 Unusual residues: {' CA': 4, 'NAG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Restraints were copied for chains: F, D, B Time building chain proxies: 10.43, per 1000 atoms: 0.76 Number of scatterers: 13726 At special positions: 0 Unit cell: (133.75, 209.72, 75.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 124 16.00 O 2570 8.00 N 2466 7.00 C 8558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 123 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 150 " - pdb=" SG CYS A 216 " distance=2.02 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 218 " distance=2.02 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 218 " distance=2.02 Simple disulfide: pdb=" SG CYS C 169 " - pdb=" SG CYS C 175 " distance=2.02 Simple disulfide: pdb=" SG CYS C 186 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 191 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 248 " - pdb=" SG CYS C 316 " distance=2.04 Simple disulfide: pdb=" SG CYS C 255 " - pdb=" SG CYS C 261 " distance=2.03 Simple disulfide: pdb=" SG CYS C 272 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 340 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 328 " distance=2.03 Simple disulfide: pdb=" SG CYS E 137 " - pdb=" SG CYS E 142 " distance=2.02 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 197 " distance=2.03 Simple disulfide: pdb=" SG CYS E 166 " - pdb=" SG CYS E 243 " distance=2.03 Simple disulfide: pdb=" SG CYS E 426 " - pdb=" SG CYS E 430 " distance=2.02 Simple disulfide: pdb=" SG CYS E 449 " - pdb=" SG CYS E 478 " distance=2.03 Simple disulfide: pdb=" SG CYS E 515 " - pdb=" SG CYS E 531 " distance=2.03 Simple disulfide: pdb=" SG CYS E 519 " - pdb=" SG CYS E 541 " distance=2.03 Simple disulfide: pdb=" SG CYS E 528 " - pdb=" SG CYS E 558 " distance=2.02 Simple disulfide: pdb=" SG CYS E 565 " - pdb=" SG CYS E 581 " distance=2.02 Simple disulfide: pdb=" SG CYS E 570 " - pdb=" SG CYS E 585 " distance=2.03 Simple disulfide: pdb=" SG CYS E 609 " - pdb=" SG CYS E 620 " distance=2.04 Simple disulfide: pdb=" SG CYS E 611 " - pdb=" SG CYS E 618 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG C1100 " - " ASN C 309 " " NAG D1100 " - " ASN D 309 " " NAG E 701 " - " ASN E 336 " " NAG E 702 " - " ASN E 377 " " NAG E 703 " - " ASN E 394 " " NAG E 704 " - " ASN E 468 " " NAG E 705 " - " ASN E 98 " " NAG E 706 " - " ASN E 361 " " NAG F 701 " - " ASN F 336 " " NAG F 702 " - " ASN F 377 " " NAG F 703 " - " ASN F 394 " " NAG F 704 " - " ASN F 468 " " NAG F 705 " - " ASN F 98 " " NAG F 706 " - " ASN F 361 " Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.6 seconds 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3256 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 36 sheets defined 23.4% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 133 through 136 removed outlier: 3.742A pdb=" N GLY A 136 " --> pdb=" O ARG A 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 133 through 136' Processing helix chain 'A' and resid 159 through 169 removed outlier: 3.521A pdb=" N LEU A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 171 removed outlier: 3.614A pdb=" N LYS C 164 " --> pdb=" O ASP C 160 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA C 166 " --> pdb=" O CYS C 162 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N CYS C 169 " --> pdb=" O PHE C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 184 removed outlier: 3.653A pdb=" N ASP C 176 " --> pdb=" O ASN C 172 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 197 through 206 removed outlier: 3.689A pdb=" N THR C 202 " --> pdb=" O ARG C 198 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 217 removed outlier: 3.600A pdb=" N GLY C 214 " --> pdb=" O PRO C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 233 removed outlier: 3.647A pdb=" N GLY C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ARG C 230 " --> pdb=" O GLY C 226 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG C 231 " --> pdb=" O CYS C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 249 through 258 removed outlier: 3.635A pdb=" N ASP C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 272 removed outlier: 3.592A pdb=" N ASP C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE C 268 " --> pdb=" O ARG C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 293 removed outlier: 3.981A pdb=" N ARG C 290 " --> pdb=" O SER C 286 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 291 " --> pdb=" O ARG C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 296 No H-bonds generated for 'chain 'C' and resid 294 through 296' Processing helix chain 'C' and resid 325 through 337 removed outlier: 3.867A pdb=" N LEU C 331 " --> pdb=" O GLU C 327 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 356 removed outlier: 3.752A pdb=" N GLN C 354 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE C 356 " --> pdb=" O HIS C 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 109 Processing helix chain 'E' and resid 156 through 160 removed outlier: 3.503A pdb=" N SER E 159 " --> pdb=" O ALA E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 167 removed outlier: 3.641A pdb=" N CYS E 166 " --> pdb=" O PRO E 162 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE E 167 " --> pdb=" O ARG E 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 162 through 167' Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 309 through 314 removed outlier: 3.782A pdb=" N ARG E 313 " --> pdb=" O GLU E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 329 removed outlier: 3.873A pdb=" N GLN E 326 " --> pdb=" O ASP E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 522 removed outlier: 3.786A pdb=" N VAL E 521 " --> pdb=" O SER E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 530 removed outlier: 3.706A pdb=" N GLU E 529 " --> pdb=" O ARG E 525 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU E 530 " --> pdb=" O LEU E 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 525 through 530' Processing helix chain 'E' and resid 581 through 585 removed outlier: 3.786A pdb=" N ASP E 584 " --> pdb=" O CYS E 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 136 removed outlier: 3.742A pdb=" N GLY B 136 " --> pdb=" O ARG B 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 133 through 136' Processing helix chain 'B' and resid 159 through 169 removed outlier: 3.521A pdb=" N LEU B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 171 removed outlier: 3.613A pdb=" N LYS D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA D 166 " --> pdb=" O CYS D 162 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N CYS D 169 " --> pdb=" O PHE D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 184 removed outlier: 3.653A pdb=" N ASP D 176 " --> pdb=" O ASN D 172 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG D 177 " --> pdb=" O ASP D 173 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR D 182 " --> pdb=" O LEU D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 197 through 206 removed outlier: 3.690A pdb=" N THR D 202 " --> pdb=" O ARG D 198 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 217 removed outlier: 3.600A pdb=" N GLY D 214 " --> pdb=" O PRO D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 233 removed outlier: 3.647A pdb=" N GLY D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ARG D 230 " --> pdb=" O GLY D 226 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG D 231 " --> pdb=" O CYS D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 241 Processing helix chain 'D' and resid 249 through 258 removed outlier: 3.635A pdb=" N ASP D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 272 removed outlier: 3.592A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE D 268 " --> pdb=" O ARG D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 293 removed outlier: 3.981A pdb=" N ARG D 290 " --> pdb=" O SER D 286 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA D 291 " --> pdb=" O ARG D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 296 No H-bonds generated for 'chain 'D' and resid 294 through 296' Processing helix chain 'D' and resid 325 through 337 removed outlier: 3.866A pdb=" N LEU D 331 " --> pdb=" O GLU D 327 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 356 removed outlier: 3.752A pdb=" N GLN D 354 " --> pdb=" O ARG D 350 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE D 356 " --> pdb=" O HIS D 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 109 Processing helix chain 'F' and resid 156 through 160 removed outlier: 3.503A pdb=" N SER F 159 " --> pdb=" O ALA F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 167 removed outlier: 3.642A pdb=" N CYS F 166 " --> pdb=" O PRO F 162 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE F 167 " --> pdb=" O ARG F 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 162 through 167' Processing helix chain 'F' and resid 190 through 197 Processing helix chain 'F' and resid 309 through 314 removed outlier: 3.782A pdb=" N ARG F 313 " --> pdb=" O GLU F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 329 removed outlier: 3.873A pdb=" N GLN F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 522 removed outlier: 3.786A pdb=" N VAL F 521 " --> pdb=" O SER F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 530 removed outlier: 3.707A pdb=" N GLU F 529 " --> pdb=" O ARG F 525 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU F 530 " --> pdb=" O LEU F 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 525 through 530' Processing helix chain 'F' and resid 581 through 585 removed outlier: 3.786A pdb=" N ASP F 584 " --> pdb=" O CYS F 581 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 125 removed outlier: 3.551A pdb=" N SER A 151 " --> pdb=" O ARG A 124 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 131 Processing sheet with id=AA3, first strand: chain 'A' and resid 187 through 199 removed outlier: 6.959A pdb=" N CYS A 188 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N CYS A 218 " --> pdb=" O CYS A 188 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N CYS A 216 " --> pdb=" O PRO A 190 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG A 192 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL A 196 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG A 210 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N PHE A 198 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL A 208 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 303 through 304 Processing sheet with id=AA5, first strand: chain 'E' and resid 30 through 31 removed outlier: 3.578A pdb=" N TYR E 30 " --> pdb=" O LEU E 56 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.515A pdb=" N TYR E 36 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N SER E 148 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU E 40 " --> pdb=" O PHE E 150 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR E 152 " --> pdb=" O LEU E 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.515A pdb=" N TYR E 36 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N SER E 148 " --> pdb=" O TYR E 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 48 through 52 removed outlier: 3.924A pdb=" N THR E 48 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU E 95 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 174 through 176 removed outlier: 3.576A pdb=" N THR E 261 " --> pdb=" O PHE E 174 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL E 256 " --> pdb=" O ALA E 241 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA E 241 " --> pdb=" O VAL E 256 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 184 through 187 removed outlier: 6.665A pdb=" N THR E 184 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N THR E 225 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS E 186 " --> pdb=" O VAL E 223 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 292 through 300 removed outlier: 4.064A pdb=" N ALA E 294 " --> pdb=" O LEU E 356 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP E 353 " --> pdb=" O TRP E 334 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP E 334 " --> pdb=" O ASP E 353 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 316 through 318 removed outlier: 3.734A pdb=" N VAL E 395 " --> pdb=" O MET E 370 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 407 through 413 removed outlier: 7.220A pdb=" N TYR E 408 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N THR E 503 " --> pdb=" O TYR E 408 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU E 410 " --> pdb=" O THR E 503 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLU E 505 " --> pdb=" O LEU E 410 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N VAL E 412 " --> pdb=" O GLU E 505 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU E 500 " --> pdb=" O TYR E 483 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR E 483 " --> pdb=" O LEU E 500 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 407 through 413 removed outlier: 7.220A pdb=" N TYR E 408 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N THR E 503 " --> pdb=" O TYR E 408 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU E 410 " --> pdb=" O THR E 503 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLU E 505 " --> pdb=" O LEU E 410 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N VAL E 412 " --> pdb=" O GLU E 505 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL E 502 " --> pdb=" O LEU E 481 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU E 481 " --> pdb=" O VAL E 502 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 421 through 425 removed outlier: 7.346A pdb=" N GLN E 421 " --> pdb=" O VAL E 467 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL E 467 " --> pdb=" O GLN E 421 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY E 423 " --> pdb=" O LEU E 465 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU E 465 " --> pdb=" O GLY E 423 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER E 462 " --> pdb=" O SER E 457 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 542 through 544 Processing sheet with id=AB8, first strand: chain 'E' and resid 551 through 552 removed outlier: 4.345A pdb=" N THR E 552 " --> pdb=" O GLY E 605 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY E 605 " --> pdb=" O THR E 552 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 589 through 591 removed outlier: 6.519A pdb=" N SER E 589 " --> pdb=" O CYS E 618 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N CYS E 620 " --> pdb=" O SER E 589 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL E 591 " --> pdb=" O CYS E 620 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 124 through 125 removed outlier: 3.552A pdb=" N SER B 151 " --> pdb=" O ARG B 124 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 128 through 131 Processing sheet with id=AC3, first strand: chain 'B' and resid 187 through 199 removed outlier: 6.959A pdb=" N CYS B 188 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N CYS B 218 " --> pdb=" O CYS B 188 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N CYS B 216 " --> pdb=" O PRO B 190 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG B 192 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL B 196 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ARG B 210 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N PHE B 198 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL B 208 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 303 through 304 Processing sheet with id=AC5, first strand: chain 'F' and resid 30 through 31 removed outlier: 3.578A pdb=" N TYR F 30 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 35 through 36 removed outlier: 6.514A pdb=" N TYR F 36 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N SER F 148 " --> pdb=" O TYR F 36 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU F 40 " --> pdb=" O PHE F 150 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR F 152 " --> pdb=" O LEU F 40 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 35 through 36 removed outlier: 6.514A pdb=" N TYR F 36 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N SER F 148 " --> pdb=" O TYR F 36 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 48 through 52 removed outlier: 3.924A pdb=" N THR F 48 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU F 95 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 174 through 176 removed outlier: 3.576A pdb=" N THR F 261 " --> pdb=" O PHE F 174 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL F 256 " --> pdb=" O ALA F 241 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA F 241 " --> pdb=" O VAL F 256 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 184 through 187 removed outlier: 6.664A pdb=" N THR F 184 " --> pdb=" O THR F 225 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N THR F 225 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS F 186 " --> pdb=" O VAL F 223 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 292 through 300 removed outlier: 4.063A pdb=" N ALA F 294 " --> pdb=" O LEU F 356 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP F 353 " --> pdb=" O TRP F 334 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP F 334 " --> pdb=" O ASP F 353 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 316 through 318 removed outlier: 3.734A pdb=" N VAL F 395 " --> pdb=" O MET F 370 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 407 through 413 removed outlier: 7.220A pdb=" N TYR F 408 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N THR F 503 " --> pdb=" O TYR F 408 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU F 410 " --> pdb=" O THR F 503 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLU F 505 " --> pdb=" O LEU F 410 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL F 412 " --> pdb=" O GLU F 505 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU F 500 " --> pdb=" O TYR F 483 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TYR F 483 " --> pdb=" O LEU F 500 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 407 through 413 removed outlier: 7.220A pdb=" N TYR F 408 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N THR F 503 " --> pdb=" O TYR F 408 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU F 410 " --> pdb=" O THR F 503 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLU F 505 " --> pdb=" O LEU F 410 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL F 412 " --> pdb=" O GLU F 505 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL F 502 " --> pdb=" O LEU F 481 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU F 481 " --> pdb=" O VAL F 502 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'F' and resid 421 through 425 removed outlier: 7.346A pdb=" N GLN F 421 " --> pdb=" O VAL F 467 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL F 467 " --> pdb=" O GLN F 421 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY F 423 " --> pdb=" O LEU F 465 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU F 465 " --> pdb=" O GLY F 423 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER F 462 " --> pdb=" O SER F 457 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 542 through 544 Processing sheet with id=AD8, first strand: chain 'F' and resid 551 through 552 removed outlier: 4.345A pdb=" N THR F 552 " --> pdb=" O GLY F 605 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY F 605 " --> pdb=" O THR F 552 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 589 through 591 removed outlier: 6.520A pdb=" N SER F 589 " --> pdb=" O CYS F 618 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N CYS F 620 " --> pdb=" O SER F 589 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL F 591 " --> pdb=" O CYS F 620 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 948 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: 3.77 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4593 1.34 - 1.47: 3334 1.47 - 1.59: 5949 1.59 - 1.72: 0 1.72 - 1.84: 142 Bond restraints: 14018 Sorted by residual: bond pdb=" C1 NAG F 706 " pdb=" O5 NAG F 706 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.47e+00 bond pdb=" C1 NAG E 706 " pdb=" O5 NAG E 706 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.43e+00 bond pdb=" C1 NAG F 702 " pdb=" O5 NAG F 702 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.16e+00 bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.09e+00 bond pdb=" C CYS F 565 " pdb=" N PRO F 566 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.09e+00 ... (remaining 14013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 18690 3.12 - 6.24: 290 6.24 - 9.37: 32 9.37 - 12.49: 4 12.49 - 15.61: 2 Bond angle restraints: 19018 Sorted by residual: angle pdb=" C VAL F 427 " pdb=" N GLU F 428 " pdb=" CA GLU F 428 " ideal model delta sigma weight residual 120.38 127.46 -7.08 1.46e+00 4.69e-01 2.35e+01 angle pdb=" C VAL E 427 " pdb=" N GLU E 428 " pdb=" CA GLU E 428 " ideal model delta sigma weight residual 120.38 127.45 -7.07 1.46e+00 4.69e-01 2.35e+01 angle pdb=" C TYR E 76 " pdb=" N ARG E 77 " pdb=" CA ARG E 77 " ideal model delta sigma weight residual 121.54 129.60 -8.06 1.91e+00 2.74e-01 1.78e+01 angle pdb=" C TYR F 76 " pdb=" N ARG F 77 " pdb=" CA ARG F 77 " ideal model delta sigma weight residual 121.54 129.57 -8.03 1.91e+00 2.74e-01 1.77e+01 angle pdb=" N VAL E 304 " pdb=" CA VAL E 304 " pdb=" C VAL E 304 " ideal model delta sigma weight residual 108.88 116.52 -7.64 2.16e+00 2.14e-01 1.25e+01 ... (remaining 19013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 8425 17.62 - 35.24: 255 35.24 - 52.86: 40 52.86 - 70.49: 12 70.49 - 88.11: 2 Dihedral angle restraints: 8734 sinusoidal: 3716 harmonic: 5018 Sorted by residual: dihedral pdb=" CB CYS E 515 " pdb=" SG CYS E 515 " pdb=" SG CYS E 531 " pdb=" CB CYS E 531 " ideal model delta sinusoidal sigma weight residual 93.00 -178.89 -88.11 1 1.00e+01 1.00e-02 9.28e+01 dihedral pdb=" CB CYS E 426 " pdb=" SG CYS E 426 " pdb=" SG CYS E 430 " pdb=" CB CYS E 430 " ideal model delta sinusoidal sigma weight residual -86.00 -168.97 82.97 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CB CYS C 272 " pdb=" SG CYS C 272 " pdb=" SG CYS C 288 " pdb=" CB CYS C 288 " ideal model delta sinusoidal sigma weight residual 93.00 137.78 -44.78 1 1.00e+01 1.00e-02 2.79e+01 ... (remaining 8731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 2118 0.132 - 0.264: 32 0.264 - 0.396: 2 0.396 - 0.528: 0 0.528 - 0.660: 4 Chirality restraints: 2156 Sorted by residual: chirality pdb=" C1 NAG E 704 " pdb=" ND2 ASN E 468 " pdb=" C2 NAG E 704 " pdb=" O5 NAG E 704 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" C1 NAG F 704 " pdb=" ND2 ASN F 468 " pdb=" C2 NAG F 704 " pdb=" O5 NAG F 704 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" C1 NAG F 702 " pdb=" ND2 ASN F 377 " pdb=" C2 NAG F 702 " pdb=" O5 NAG F 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.51e+00 ... (remaining 2153 not shown) Planarity restraints: 2492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 59 " -0.045 5.00e-02 4.00e+02 6.86e-02 7.52e+00 pdb=" N PRO E 60 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 60 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 60 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 59 " -0.045 5.00e-02 4.00e+02 6.85e-02 7.50e+00 pdb=" N PRO F 60 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO F 60 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 60 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 258 " 0.040 5.00e-02 4.00e+02 6.08e-02 5.92e+00 pdb=" N PRO D 259 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 259 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 259 " 0.033 5.00e-02 4.00e+02 ... (remaining 2489 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.07: 37 2.07 - 2.78: 2967 2.78 - 3.49: 16403 3.49 - 4.19: 30175 4.19 - 4.90: 51736 Nonbonded interactions: 101318 Sorted by model distance: nonbonded pdb=" OD2 ASP F 300 " pdb=" OH TYR F 314 " model vdw 1.366 3.040 nonbonded pdb=" OD2 ASP E 300 " pdb=" OH TYR E 314 " model vdw 1.367 3.040 nonbonded pdb=" OD1 ASP E 266 " pdb=" OD2 ASP E 302 " model vdw 1.613 3.040 nonbonded pdb=" OD1 ASP F 266 " pdb=" OD2 ASP F 302 " model vdw 1.613 3.040 nonbonded pdb=" O THR F 564 " pdb=" OD2 ASP F 567 " model vdw 1.692 3.040 ... (remaining 101313 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.650 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.820 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5127 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 : 0.008 0.061 14018 Z= 0.508 Angle : 1.064 15.609 19018 Z= 0.580 Chirality : 0.062 0.660 2156 Planarity : 0.007 0.069 2478 Dihedral : 9.187 57.568 5406 Min Nonbonded Distance : 1.366 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.13 % Allowed : 1.72 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -4.58 (0.15), residues: 1702 helix: -4.22 (0.13), residues: 320 sheet: -2.35 (0.23), residues: 434 loop : -3.01 (0.15), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.005 TRP F 139 HIS 0.015 0.002 HIS E 352 PHE 0.026 0.003 PHE F 433 TYR 0.037 0.004 TYR F 122 ARG 0.015 0.001 ARG E 544 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 417 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.5898 (p90) cc_final: 0.5193 (p90) REVERT: C 249 LEU cc_start: 0.7440 (mt) cc_final: 0.6798 (mm) REVERT: C 296 ILE cc_start: 0.7425 (mt) cc_final: 0.7206 (mt) REVERT: E 324 TRP cc_start: 0.5509 (t60) cc_final: 0.4488 (t-100) REVERT: D 199 GLN cc_start: 0.7314 (mm-40) cc_final: 0.7079 (mm-40) REVERT: D 283 THR cc_start: 0.4763 (p) cc_final: 0.4547 (m) REVERT: F 471 LYS cc_start: 0.7210 (mmtt) cc_final: 0.6799 (pptt) outliers start: 2 outliers final: 0 residues processed: 419 average time/residue: 0.3274 time to fit residues: 181.9366 Evaluate side-chains 171 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 30.0000 chunk 128 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 133 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS C 194 HIS C 247 ASN C 338 ASN E 44 GLN E 103 HIS E 187 GLN E 333 HIS E 403 HIS E 443 HIS D 247 ASN F 81 HIS F 103 HIS F 187 GLN F 333 HIS F 403 HIS F 437 ASN F 443 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5782 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 14018 Z= 0.250 Angle : 0.763 13.616 19018 Z= 0.386 Chirality : 0.048 0.319 2156 Planarity : 0.006 0.053 2478 Dihedral : 6.981 50.916 2202 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.51 % Allowed : 10.34 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -3.66 (0.17), residues: 1702 helix: -2.70 (0.23), residues: 330 sheet: -1.68 (0.24), residues: 422 loop : -2.75 (0.16), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 205 HIS 0.006 0.001 HIS C 273 PHE 0.026 0.002 PHE D 203 TYR 0.028 0.002 TYR E 122 ARG 0.007 0.001 ARG F 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 215 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 296 ILE cc_start: 0.8640 (mt) cc_final: 0.8428 (mm) REVERT: E 56 LEU cc_start: 0.5196 (OUTLIER) cc_final: 0.4808 (mm) REVERT: E 161 LYS cc_start: 0.7046 (mtmm) cc_final: 0.6696 (ptpt) REVERT: F 102 ASP cc_start: 0.6879 (p0) cc_final: 0.6677 (p0) REVERT: F 353 ASP cc_start: 0.2266 (OUTLIER) cc_final: 0.2006 (t0) outliers start: 53 outliers final: 33 residues processed: 250 average time/residue: 0.2433 time to fit residues: 89.3701 Evaluate side-chains 194 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 159 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 439 GLN Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 578 ILE Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 356 PHE Chi-restraints excluded: chain F residue 227 TRP Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 353 ASP Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 406 SER Chi-restraints excluded: chain F residue 467 VAL Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 575 THR Chi-restraints excluded: chain F residue 579 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 128 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 167 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN C 192 GLN C 247 ASN C 303 ASN E 392 HIS E 403 HIS ** E 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 HIS F 84 ASN F 371 GLN ** F 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.8776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 14018 Z= 0.479 Angle : 0.998 11.054 19018 Z= 0.510 Chirality : 0.056 0.484 2156 Planarity : 0.008 0.060 2478 Dihedral : 7.792 52.372 2202 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.40 % Favored : 91.54 % Rotamer: Outliers : 5.77 % Allowed : 11.80 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.74 (0.17), residues: 1702 helix: -2.75 (0.22), residues: 346 sheet: -1.88 (0.24), residues: 412 loop : -2.70 (0.17), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP E 37 HIS 0.015 0.002 HIS F 443 PHE 0.037 0.003 PHE B 198 TYR 0.022 0.003 TYR C 292 ARG 0.017 0.001 ARG F 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 175 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 330 MET cc_start: 0.7040 (OUTLIER) cc_final: 0.6811 (ttm) REVERT: E 370 MET cc_start: 0.4521 (pmm) cc_final: 0.4224 (pmm) REVERT: D 270 THR cc_start: 0.8190 (OUTLIER) cc_final: 0.7957 (p) REVERT: D 324 LEU cc_start: 0.8658 (mt) cc_final: 0.8398 (mt) REVERT: F 102 ASP cc_start: 0.7470 (p0) cc_final: 0.7058 (p0) REVERT: F 187 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6425 (tm-30) REVERT: F 580 ILE cc_start: 0.6012 (OUTLIER) cc_final: 0.5448 (mt) outliers start: 87 outliers final: 45 residues processed: 244 average time/residue: 0.2524 time to fit residues: 90.0837 Evaluate side-chains 177 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 128 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain E residue 30 TYR Chi-restraints excluded: chain E residue 122 TYR Chi-restraints excluded: chain E residue 185 PHE Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 356 LEU Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 578 ILE Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 326 GLU Chi-restraints excluded: chain D residue 356 PHE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 227 TRP Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 265 GLU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 353 ASP Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 406 SER Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 575 THR Chi-restraints excluded: chain F residue 579 ASN Chi-restraints excluded: chain F residue 580 ILE Chi-restraints excluded: chain F residue 602 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 9.9990 chunk 116 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 17 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 164 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 chunk 147 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** E 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 HIS F 84 ASN F 371 GLN ** F 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.9115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14018 Z= 0.224 Angle : 0.713 9.625 19018 Z= 0.355 Chirality : 0.046 0.314 2156 Planarity : 0.005 0.055 2478 Dihedral : 6.087 42.021 2202 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.65 % Allowed : 15.25 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -3.09 (0.18), residues: 1702 helix: -2.13 (0.25), residues: 342 sheet: -1.26 (0.25), residues: 422 loop : -2.45 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 205 HIS 0.007 0.001 HIS F 333 PHE 0.022 0.002 PHE B 198 TYR 0.031 0.002 TYR F 76 ARG 0.014 0.001 ARG C 230 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 169 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.3498 (ptp) cc_final: 0.3230 (ptp) REVERT: C 213 GLN cc_start: 0.6800 (mp10) cc_final: 0.6530 (mt0) REVERT: E 370 MET cc_start: 0.4383 (pmm) cc_final: 0.4177 (pmm) REVERT: F 102 ASP cc_start: 0.7289 (p0) cc_final: 0.6888 (p0) REVERT: F 616 GLU cc_start: 0.6212 (tp30) cc_final: 0.5938 (tt0) outliers start: 55 outliers final: 37 residues processed: 210 average time/residue: 0.2412 time to fit residues: 74.9073 Evaluate side-chains 171 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 134 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain E residue 185 PHE Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 356 PHE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 227 TRP Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 406 SER Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 580 ILE Chi-restraints excluded: chain F residue 602 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 67 optimal weight: 20.0000 chunk 140 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 0 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN E 246 HIS ** E 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN ** F 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.9417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14018 Z= 0.179 Angle : 0.663 10.176 19018 Z= 0.325 Chirality : 0.045 0.280 2156 Planarity : 0.005 0.048 2478 Dihedral : 5.388 39.700 2202 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.72 % Allowed : 17.71 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -2.56 (0.19), residues: 1702 helix: -1.46 (0.27), residues: 332 sheet: -0.87 (0.25), residues: 424 loop : -2.24 (0.18), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 106 HIS 0.007 0.001 HIS F 333 PHE 0.017 0.001 PHE C 268 TYR 0.033 0.001 TYR E 122 ARG 0.007 0.000 ARG E 600 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 165 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 300 MET cc_start: 0.7627 (tpp) cc_final: 0.7314 (tpp) REVERT: E 34 ASP cc_start: 0.6861 (t0) cc_final: 0.6602 (t0) REVERT: E 370 MET cc_start: 0.4471 (pmm) cc_final: 0.4261 (pmm) REVERT: B 203 SER cc_start: 0.8104 (m) cc_final: 0.7643 (p) REVERT: D 169 CYS cc_start: 0.6848 (OUTLIER) cc_final: 0.6396 (t) REVERT: F 102 ASP cc_start: 0.7135 (p0) cc_final: 0.6730 (p0) REVERT: F 187 GLN cc_start: 0.7105 (OUTLIER) cc_final: 0.6759 (tm-30) REVERT: F 470 THR cc_start: 0.6359 (m) cc_final: 0.6115 (m) outliers start: 41 outliers final: 34 residues processed: 200 average time/residue: 0.2356 time to fit residues: 72.2135 Evaluate side-chains 180 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 144 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain E residue 185 PHE Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 525 ARG Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain D residue 169 CYS Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 356 PHE Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 227 TRP Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 406 SER Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 602 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 164 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 chunk 76 optimal weight: 30.0000 chunk 13 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.9693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14018 Z= 0.185 Angle : 0.658 9.355 19018 Z= 0.322 Chirality : 0.045 0.285 2156 Planarity : 0.005 0.045 2478 Dihedral : 5.165 39.031 2202 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.45 % Allowed : 17.44 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -2.34 (0.19), residues: 1702 helix: -1.26 (0.28), residues: 344 sheet: -0.63 (0.25), residues: 420 loop : -2.15 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP E 543 HIS 0.006 0.001 HIS F 333 PHE 0.025 0.002 PHE D 165 TYR 0.031 0.001 TYR E 122 ARG 0.008 0.000 ARG E 600 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 146 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 ASP cc_start: 0.6932 (t0) cc_final: 0.6658 (t0) REVERT: E 567 ASP cc_start: 0.6260 (p0) cc_final: 0.5957 (p0) REVERT: D 169 CYS cc_start: 0.6815 (OUTLIER) cc_final: 0.6440 (t) REVERT: F 102 ASP cc_start: 0.7108 (p0) cc_final: 0.6729 (p0) REVERT: F 187 GLN cc_start: 0.7181 (OUTLIER) cc_final: 0.6790 (tm-30) REVERT: F 470 THR cc_start: 0.6435 (m) cc_final: 0.6197 (m) outliers start: 52 outliers final: 43 residues processed: 189 average time/residue: 0.2119 time to fit residues: 62.6065 Evaluate side-chains 174 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 129 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain E residue 185 PHE Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain D residue 169 CYS Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 356 PHE Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 227 TRP Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 406 SER Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 609 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 138 optimal weight: 0.9990 chunk 91 optimal weight: 0.0040 chunk 163 optimal weight: 20.0000 chunk 102 optimal weight: 7.9990 chunk 99 optimal weight: 0.1980 chunk 75 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN C 190 HIS ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN F 84 ASN ** F 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.9870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14018 Z= 0.155 Angle : 0.626 9.933 19018 Z= 0.306 Chirality : 0.043 0.251 2156 Planarity : 0.004 0.042 2478 Dihedral : 4.891 37.488 2202 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.45 % Allowed : 17.64 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -2.06 (0.19), residues: 1702 helix: -0.83 (0.29), residues: 330 sheet: -0.57 (0.26), residues: 408 loop : -1.98 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 205 HIS 0.028 0.001 HIS C 190 PHE 0.020 0.001 PHE B 147 TYR 0.032 0.001 TYR E 122 ARG 0.005 0.000 ARG E 600 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 151 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 ASP cc_start: 0.6847 (t0) cc_final: 0.6571 (t0) REVERT: E 255 MET cc_start: 0.7165 (tmm) cc_final: 0.6669 (tmm) REVERT: E 567 ASP cc_start: 0.6177 (p0) cc_final: 0.5874 (p0) REVERT: D 169 CYS cc_start: 0.6758 (OUTLIER) cc_final: 0.6273 (t) REVERT: D 323 ASN cc_start: 0.6422 (t0) cc_final: 0.5547 (p0) REVERT: F 102 ASP cc_start: 0.7168 (p0) cc_final: 0.6756 (p0) REVERT: F 187 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6739 (tm-30) REVERT: F 296 LEU cc_start: 0.6106 (tt) cc_final: 0.5826 (tt) REVERT: F 470 THR cc_start: 0.6558 (m) cc_final: 0.6325 (m) outliers start: 52 outliers final: 39 residues processed: 188 average time/residue: 0.2136 time to fit residues: 62.7261 Evaluate side-chains 180 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 139 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 316 CYS Chi-restraints excluded: chain E residue 185 PHE Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain E residue 578 ILE Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain D residue 169 CYS Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 356 PHE Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 227 TRP Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 578 ILE Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 609 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 9.9990 chunk 97 optimal weight: 0.0370 chunk 49 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 chunk 149 optimal weight: 0.5980 overall best weight: 3.1264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 HIS C 303 ASN C 352 HIS ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN B 202 ASN F 71 HIS F 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 1.0329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14018 Z= 0.231 Angle : 0.689 10.455 19018 Z= 0.340 Chirality : 0.046 0.313 2156 Planarity : 0.005 0.041 2478 Dihedral : 5.226 39.193 2202 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.98 % Allowed : 17.90 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -2.16 (0.19), residues: 1702 helix: -1.00 (0.28), residues: 346 sheet: -0.44 (0.26), residues: 418 loop : -2.14 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 205 HIS 0.037 0.002 HIS C 190 PHE 0.029 0.002 PHE D 165 TYR 0.032 0.002 TYR E 122 ARG 0.008 0.001 ARG E 600 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 134 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.5254 (mm) cc_final: 0.5042 (mm) REVERT: E 148 SER cc_start: 0.6366 (m) cc_final: 0.5924 (p) REVERT: E 392 HIS cc_start: 0.6089 (m90) cc_final: 0.5799 (m-70) REVERT: D 169 CYS cc_start: 0.7015 (OUTLIER) cc_final: 0.6562 (t) REVERT: F 102 ASP cc_start: 0.7262 (p0) cc_final: 0.6870 (p0) REVERT: F 187 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.7012 (tm-30) REVERT: F 296 LEU cc_start: 0.6129 (tt) cc_final: 0.5867 (tt) REVERT: F 470 THR cc_start: 0.6531 (m) cc_final: 0.6315 (m) outliers start: 60 outliers final: 52 residues processed: 179 average time/residue: 0.2015 time to fit residues: 57.7211 Evaluate side-chains 169 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 115 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 316 CYS Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 185 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 525 ARG Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain E residue 578 ILE Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 600 ARG Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain D residue 169 CYS Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 356 PHE Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 227 TRP Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 578 ILE Chi-restraints excluded: chain F residue 580 ILE Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 609 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 30.0000 chunk 143 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 137 optimal weight: 0.9980 chunk 144 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 161 optimal weight: 0.0870 overall best weight: 4.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN ** F 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 1.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14018 Z= 0.271 Angle : 0.735 10.757 19018 Z= 0.362 Chirality : 0.047 0.343 2156 Planarity : 0.005 0.047 2478 Dihedral : 5.591 42.458 2202 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 3.78 % Allowed : 18.83 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -2.28 (0.19), residues: 1702 helix: -1.08 (0.28), residues: 348 sheet: -0.44 (0.26), residues: 396 loop : -2.23 (0.18), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 205 HIS 0.007 0.001 HIS F 594 PHE 0.023 0.002 PHE B 147 TYR 0.034 0.002 TYR E 122 ARG 0.011 0.001 ARG B 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 135 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 240 VAL cc_start: 0.7791 (t) cc_final: 0.7557 (t) REVERT: D 169 CYS cc_start: 0.7024 (OUTLIER) cc_final: 0.6613 (t) REVERT: F 34 ASP cc_start: 0.5955 (p0) cc_final: 0.5643 (p0) REVERT: F 39 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7165 (ptpp) REVERT: F 102 ASP cc_start: 0.7265 (p0) cc_final: 0.6838 (p0) REVERT: F 187 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.6895 (tm-30) outliers start: 57 outliers final: 49 residues processed: 180 average time/residue: 0.2163 time to fit residues: 60.6359 Evaluate side-chains 168 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 116 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 316 CYS Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 185 PHE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 525 ARG Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain E residue 578 ILE Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain D residue 169 CYS Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 356 PHE Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 227 TRP Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 580 ILE Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 609 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 104 optimal weight: 0.3980 chunk 82 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 143 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN C 190 HIS ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 1.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14018 Z= 0.168 Angle : 0.692 12.390 19018 Z= 0.335 Chirality : 0.044 0.264 2156 Planarity : 0.005 0.054 2478 Dihedral : 4.955 38.706 2202 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.79 % Allowed : 19.96 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -1.99 (0.20), residues: 1702 helix: -0.70 (0.29), residues: 334 sheet: -0.50 (0.26), residues: 398 loop : -1.96 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 205 HIS 0.028 0.001 HIS C 190 PHE 0.022 0.001 PHE B 147 TYR 0.031 0.001 TYR E 122 ARG 0.007 0.000 ARG E 600 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 148 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 169 CYS cc_start: 0.6835 (OUTLIER) cc_final: 0.6319 (t) REVERT: D 323 ASN cc_start: 0.6642 (t0) cc_final: 0.5982 (p0) REVERT: D 324 LEU cc_start: 0.7726 (tp) cc_final: 0.7398 (tp) REVERT: F 102 ASP cc_start: 0.7136 (p0) cc_final: 0.6702 (p0) REVERT: F 187 GLN cc_start: 0.7157 (OUTLIER) cc_final: 0.6745 (tm-30) REVERT: F 470 THR cc_start: 0.6288 (m) cc_final: 0.6056 (m) REVERT: F 484 MET cc_start: 0.6116 (ppp) cc_final: 0.5361 (ppp) REVERT: F 558 CYS cc_start: 0.6927 (OUTLIER) cc_final: 0.6070 (m) outliers start: 42 outliers final: 37 residues processed: 179 average time/residue: 0.2124 time to fit residues: 59.3066 Evaluate side-chains 170 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 130 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 316 CYS Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 551 ILE Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain D residue 169 CYS Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 356 PHE Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 227 TRP Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 558 CYS Chi-restraints excluded: chain F residue 608 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 chunk 135 optimal weight: 40.0000 chunk 56 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN C 190 HIS ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN ** F 499 GLN ** 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 = 0.4192 r_free = 0.4192 target = 0.111263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.091178 restraints weight = 56901.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.093877 restraints weight = 36430.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.096104 restraints weight = 20670.123| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 1.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14018 Z= 0.266 Angle : 0.763 12.175 19018 Z= 0.373 Chirality : 0.046 0.326 2156 Planarity : 0.005 0.063 2478 Dihedral : 5.416 41.252 2202 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.18 % Allowed : 19.83 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -2.13 (0.20), residues: 1702 helix: -0.95 (0.28), residues: 346 sheet: -0.27 (0.27), residues: 396 loop : -2.17 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP F 543 HIS 0.024 0.002 HIS C 190 PHE 0.025 0.002 PHE B 198 TYR 0.033 0.002 TYR E 122 ARG 0.005 0.001 ARG F 525 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2614.47 seconds wall clock time: 47 minutes 35.14 seconds (2855.14 seconds total)