Starting phenix.real_space_refine on Sun Sep 29 21:55:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjs_25930/09_2024/7tjs_25930.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjs_25930/09_2024/7tjs_25930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjs_25930/09_2024/7tjs_25930.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjs_25930/09_2024/7tjs_25930.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjs_25930/09_2024/7tjs_25930.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjs_25930/09_2024/7tjs_25930.cif" } resolution = 3.2 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= 0.004 sd= 0.242 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 3 5.21 5 S 35 5.16 5 C 14850 2.51 5 N 4092 2.21 5 O 4547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23539 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3631 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 459} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3657 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 462} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 3659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3659 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 463} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 3512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3512 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 442} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 3515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3515 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 444} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3520 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 444} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1917 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 8, 'TRANS': 244} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.67, per 1000 atoms: 0.54 Number of scatterers: 23539 At special positions: 0 Unit cell: (126.828, 126.828, 146.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 12 15.00 Mg 3 11.99 O 4547 8.00 N 4092 7.00 C 14850 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 Time building additional restraints: 5.81 Conformation dependent library (CDL) restraints added in 3.0 seconds 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5636 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 20 sheets defined 51.0% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.93 Creating SS restraints... Processing helix chain 'A' and resid 80 through 84 Processing helix chain 'A' and resid 102 through 106 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 176 through 188 removed outlier: 3.911A pdb=" N GLN A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 191 No H-bonds generated for 'chain 'A' and resid 189 through 191' Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 241 through 262 Proline residue: A 249 - end of helix removed outlier: 3.690A pdb=" N TRP A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 287 removed outlier: 3.518A pdb=" N GLN A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 299 through 309 removed outlier: 3.570A pdb=" N HIS A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 335 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.647A pdb=" N ALA A 379 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 403 removed outlier: 3.684A pdb=" N VAL A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.912A pdb=" N GLN A 407 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY A 409 " --> pdb=" O ALA A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 430 removed outlier: 3.552A pdb=" N ARG A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 452 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.972A pdb=" N GLY A 457 " --> pdb=" O HIS A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 478 removed outlier: 3.801A pdb=" N SER A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 489 Processing helix chain 'A' and resid 492 through 508 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 80 through 84 Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.725A pdb=" N LEU B 105 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 176 through 188 removed outlier: 3.940A pdb=" N GLN B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 241 through 262 Proline residue: B 249 - end of helix removed outlier: 4.023A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 removed outlier: 3.517A pdb=" N GLN B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 297 through 298 No H-bonds generated for 'chain 'B' and resid 297 through 298' Processing helix chain 'B' and resid 299 through 309 removed outlier: 3.688A pdb=" N ARG B 306 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 319 Processing helix chain 'B' and resid 332 through 335 Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 355 through 360 Processing helix chain 'B' and resid 376 through 380 removed outlier: 3.598A pdb=" N ALA B 379 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 389 Processing helix chain 'B' and resid 391 through 406 removed outlier: 3.687A pdb=" N ALA B 404 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE B 405 " --> pdb=" O GLU B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 431 Processing helix chain 'B' and resid 439 through 452 Proline residue: B 445 - end of helix Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 462 through 478 removed outlier: 3.747A pdb=" N SER B 468 " --> pdb=" O GLY B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 489 Processing helix chain 'B' and resid 492 through 509 Processing helix chain 'C' and resid 102 through 106 Processing helix chain 'C' and resid 152 through 159 Processing helix chain 'C' and resid 176 through 188 removed outlier: 3.921A pdb=" N GLN C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 193 Processing helix chain 'C' and resid 211 through 225 Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 241 through 262 Proline residue: C 249 - end of helix removed outlier: 3.520A pdb=" N TRP C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 287 removed outlier: 3.630A pdb=" N GLN C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 355 through 361 Processing helix chain 'C' and resid 376 through 381 removed outlier: 3.662A pdb=" N GLN C 381 " --> pdb=" O SER C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 390 Processing helix chain 'C' and resid 391 through 407 removed outlier: 3.731A pdb=" N GLU C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 430 Processing helix chain 'C' and resid 439 through 452 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 462 through 478 removed outlier: 3.732A pdb=" N SER C 472 " --> pdb=" O SER C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 489 removed outlier: 3.530A pdb=" N LEU C 482 " --> pdb=" O HIS C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 509 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 123 through 127 Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 162 through 178 removed outlier: 3.795A pdb=" N LYS D 176 " --> pdb=" O ASN D 172 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA D 177 " --> pdb=" O ASN D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 225 through 248 removed outlier: 4.797A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE D 239 " --> pdb=" O THR D 235 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU D 247 " --> pdb=" O PHE D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 273 removed outlier: 3.545A pdb=" N PHE D 261 " --> pdb=" O ASN D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 281 Processing helix chain 'D' and resid 284 through 294 Processing helix chain 'D' and resid 313 through 316 Processing helix chain 'D' and resid 319 through 327 removed outlier: 4.166A pdb=" N ALA D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 364 through 392 removed outlier: 3.901A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 414 Processing helix chain 'D' and resid 419 through 424 removed outlier: 3.866A pdb=" N VAL D 423 " --> pdb=" O VAL D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 446 Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 462 through 474 Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 123 through 127 Processing helix chain 'E' and resid 138 through 145 Processing helix chain 'E' and resid 162 through 179 Processing helix chain 'E' and resid 190 through 205 Processing helix chain 'E' and resid 225 through 248 removed outlier: 4.737A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE E 243 " --> pdb=" O ILE E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 272 Processing helix chain 'E' and resid 277 through 281 Processing helix chain 'E' and resid 284 through 294 removed outlier: 3.812A pdb=" N LEU E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 319 through 327 removed outlier: 3.656A pdb=" N ALA E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 342 Processing helix chain 'E' and resid 359 through 364 Processing helix chain 'E' and resid 364 through 392 removed outlier: 4.961A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 396 removed outlier: 3.776A pdb=" N LEU E 396 " --> pdb=" O MET E 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 393 through 396' Processing helix chain 'E' and resid 397 through 414 Processing helix chain 'E' and resid 421 through 426 Processing helix chain 'E' and resid 433 through 446 Processing helix chain 'E' and resid 453 through 458 Processing helix chain 'E' and resid 462 through 475 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 123 through 127 Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'F' and resid 162 through 175 Processing helix chain 'F' and resid 176 through 178 No H-bonds generated for 'chain 'F' and resid 176 through 178' Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 225 through 246 removed outlier: 3.775A pdb=" N ARG F 231 " --> pdb=" O GLY F 227 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 273 removed outlier: 3.738A pdb=" N THR F 262 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LEU F 271 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 Processing helix chain 'F' and resid 284 through 294 Processing helix chain 'F' and resid 313 through 316 Processing helix chain 'F' and resid 319 through 327 removed outlier: 4.177A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 342 removed outlier: 3.838A pdb=" N LEU F 342 " --> pdb=" O GLY F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 364 Processing helix chain 'F' and resid 364 through 391 removed outlier: 5.038A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 396 removed outlier: 3.631A pdb=" N GLU F 395 " --> pdb=" O GLY F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 415 removed outlier: 3.686A pdb=" N SER F 415 " --> pdb=" O GLN F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 426 Processing helix chain 'F' and resid 433 through 446 Processing helix chain 'F' and resid 453 through 458 Processing helix chain 'F' and resid 462 through 474 Processing helix chain 'G' and resid 2 through 56 removed outlier: 4.063A pdb=" N SER G 32 " --> pdb=" O SER G 28 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU G 48 " --> pdb=" O MET G 44 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 100 removed outlier: 3.838A pdb=" N LEU G 91 " --> pdb=" O ILE G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 120 Processing helix chain 'G' and resid 139 through 153 Processing helix chain 'G' and resid 155 through 159 Processing helix chain 'G' and resid 184 through 190 removed outlier: 3.782A pdb=" N GLN G 190 " --> pdb=" O LYS G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 276 removed outlier: 3.873A pdb=" N SER G 276 " --> pdb=" O THR G 272 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 68 removed outlier: 4.149A pdb=" N GLU A 53 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU A 54 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A 76 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ALA A 65 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE E 9 " --> pdb=" O ASP E 78 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LYS E 75 " --> pdb=" O LYS E 40 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LYS E 40 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA E 36 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASN E 35 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL E 16 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASP E 22 " --> pdb=" O THR E 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 101 Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 110 removed outlier: 6.328A pdb=" N VAL A 110 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR A 270 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A 168 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LEU A 354 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE A 170 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 147 through 148 removed outlier: 4.757A pdb=" N ILE A 161 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 37 removed outlier: 6.422A pdb=" N ARG B 42 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL B 36 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 40 through 45 current: chain 'B' and resid 62 through 69 removed outlier: 5.697A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 72 through 77 current: chain 'C' and resid 40 through 45 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 40 through 45 current: chain 'C' and resid 62 through 68 removed outlier: 5.611A pdb=" N ALA C 65 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 76 " --> pdb=" O ALA C 65 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 73 through 77 current: chain 'D' and resid 20 through 24 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 20 through 24 current: chain 'D' and resid 44 through 55 removed outlier: 6.536A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 58 through 63 current: chain 'F' and resid 20 through 24 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 20 through 24 current: chain 'F' and resid 44 through 55 removed outlier: 6.613A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 101 Processing sheet with id=AA7, first strand: chain 'B' and resid 109 through 110 removed outlier: 8.661A pdb=" N ILE B 232 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS B 203 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL B 234 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N TYR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ALA B 236 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA B 207 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU B 168 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU B 354 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE B 170 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 98 through 101 Processing sheet with id=AA9, first strand: chain 'C' and resid 109 through 110 Processing sheet with id=AB1, first strand: chain 'C' and resid 328 through 330 Processing sheet with id=AB2, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB3, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.061A pdb=" N ILE D 96 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL D 183 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ASP D 256 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N THR D 185 " --> pdb=" O ASP D 256 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE D 153 " --> pdb=" O GLN D 308 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL D 310 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU D 155 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS D 152 " --> pdb=" O ALA D 331 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N THR D 333 " --> pdb=" O LYS D 152 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLY D 154 " --> pdb=" O THR D 333 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 133 through 134 removed outlier: 3.866A pdb=" N TYR D 147 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB6, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.052A pdb=" N ILE E 96 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N SER E 182 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N VAL E 218 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N PHE E 184 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N GLY E 220 " --> pdb=" O PHE E 184 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLY E 186 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL E 183 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASP E 256 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR E 185 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL E 251 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL E 307 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU E 253 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ALA E 309 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE E 255 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE E 153 " --> pdb=" O GLN E 308 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 133 through 134 removed outlier: 4.185A pdb=" N TYR E 147 " --> pdb=" O LEU E 134 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 84 through 87 removed outlier: 4.842A pdb=" N LEU F 113 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.247A pdb=" N VAL F 251 " --> pdb=" O THR F 305 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL F 307 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU F 253 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ALA F 309 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE F 255 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N TYR F 311 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE F 153 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL F 310 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU F 155 " --> pdb=" O VAL F 310 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 132 through 134 removed outlier: 4.867A pdb=" N GLU F 132 " --> pdb=" O ARG F 149 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYR F 147 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 126 through 130 removed outlier: 7.857A pdb=" N ILE G 107 " --> pdb=" O LYS G 127 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER G 129 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR G 109 " --> pdb=" O SER G 129 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE G 74 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ILE G 110 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ALA G 76 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU G 73 " --> pdb=" O SER G 163 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N PHE G 165 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL G 75 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N ASN G 167 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N ILE G 77 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N SER G 174 " --> pdb=" O VAL G 170 " (cutoff:3.500A) 1170 hydrogen bonds defined for protein. 3267 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: 8.81 Time building geometry restraints manager: 6.77 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: 7943 1.34 - 1.46: 2764 1.46 - 1.57: 13109 1.57 - 1.69: 14 1.69 - 1.80: 66 Bond restraints: 23896 Sorted by residual: bond pdb=" O3 PO4 F 600 " pdb=" P PO4 F 600 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.82e+00 bond pdb=" O4 PO4 F 600 " pdb=" P PO4 F 600 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.79e+00 bond pdb=" O2 PO4 F 600 " pdb=" P PO4 F 600 " ideal model delta sigma weight residual 1.567 1.510 0.057 2.00e-02 2.50e+03 8.16e+00 bond pdb=" O1 PO4 F 600 " pdb=" P PO4 F 600 " ideal model delta sigma weight residual 1.565 1.510 0.055 2.00e-02 2.50e+03 7.58e+00 bond pdb=" C LYS G 180 " pdb=" N PRO G 181 " ideal model delta sigma weight residual 1.331 1.355 -0.023 1.28e-02 6.10e+03 3.26e+00 ... (remaining 23891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 31323 1.40 - 2.80: 861 2.80 - 4.20: 166 4.20 - 5.60: 37 5.60 - 7.00: 19 Bond angle restraints: 32406 Sorted by residual: angle pdb=" C ASP F 256 " pdb=" N ASN F 257 " pdb=" CA ASN F 257 " ideal model delta sigma weight residual 121.70 128.70 -7.00 1.80e+00 3.09e-01 1.51e+01 angle pdb=" C ASP B 271 " pdb=" N ASP B 272 " pdb=" CA ASP B 272 " ideal model delta sigma weight residual 121.70 127.62 -5.92 1.80e+00 3.09e-01 1.08e+01 angle pdb=" C ASP E 256 " pdb=" N ASN E 257 " pdb=" CA ASN E 257 " ideal model delta sigma weight residual 121.70 127.44 -5.74 1.80e+00 3.09e-01 1.02e+01 angle pdb=" C TYR E 281 " pdb=" N GLN E 282 " pdb=" CA GLN E 282 " ideal model delta sigma weight residual 120.39 124.62 -4.23 1.39e+00 5.18e-01 9.26e+00 angle pdb=" CA ARG B 425 " pdb=" CB ARG B 425 " pdb=" CG ARG B 425 " ideal model delta sigma weight residual 114.10 108.06 6.04 2.00e+00 2.50e-01 9.12e+00 ... (remaining 32401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.77: 14295 33.77 - 67.54: 230 67.54 - 101.31: 34 101.31 - 135.09: 0 135.09 - 168.86: 2 Dihedral angle restraints: 14561 sinusoidal: 5754 harmonic: 8807 Sorted by residual: dihedral pdb=" O1B ADP D 600 " pdb=" O3A ADP D 600 " pdb=" PB ADP D 600 " pdb=" PA ADP D 600 " ideal model delta sinusoidal sigma weight residual 300.00 131.14 168.86 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' ADP D 600 " pdb=" O5' ADP D 600 " pdb=" PA ADP D 600 " pdb=" O2A ADP D 600 " ideal model delta sinusoidal sigma weight residual 300.00 135.30 164.70 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" CA GLU D 294 " pdb=" C GLU D 294 " pdb=" N ARG D 295 " pdb=" CA ARG D 295 " ideal model delta harmonic sigma weight residual 180.00 153.08 26.92 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 14558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3286 0.061 - 0.122: 446 0.122 - 0.183: 70 0.183 - 0.243: 2 0.243 - 0.304: 7 Chirality restraints: 3811 Sorted by residual: chirality pdb=" C2' ATP B 600 " pdb=" C1' ATP B 600 " pdb=" C3' ATP B 600 " pdb=" O2' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C2' ATP C 600 " pdb=" C1' ATP C 600 " pdb=" C3' ATP C 600 " pdb=" O2' ATP C 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" C2' ATP A 600 " pdb=" C1' ATP A 600 " pdb=" C3' ATP A 600 " pdb=" O2' ATP A 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 3808 not shown) Planarity restraints: 4200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU F 237 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C LEU F 237 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU F 237 " 0.013 2.00e-02 2.50e+03 pdb=" N THR F 238 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS G 180 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO G 181 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO G 181 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 181 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 168 " -0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO G 169 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO G 169 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 169 " -0.020 5.00e-02 4.00e+02 ... (remaining 4197 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 46 2.50 - 3.10: 18360 3.10 - 3.70: 34832 3.70 - 4.30: 54507 4.30 - 4.90: 90716 Nonbonded interactions: 198461 Sorted by model distance: nonbonded pdb=" NH1 ARG B 425 " pdb=" O ILE B 458 " model vdw 1.901 3.120 nonbonded pdb=" OG SER A 239 " pdb=" OE2 GLU D 294 " model vdw 1.972 3.040 nonbonded pdb=" O1B ATP C 600 " pdb="MG MG C 601 " model vdw 2.032 2.170 nonbonded pdb=" O2B ATP B 600 " pdb="MG MG B 601 " model vdw 2.039 2.170 nonbonded pdb=" O3G ATP C 600 " pdb="MG MG C 601 " model vdw 2.058 2.170 ... (remaining 198456 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' and (resid 30 through 315 or (resid 316 and (name N or name CA or nam \ e C or name O or name CB )) or resid 317 through 406 or (resid 407 and (name N o \ r name CA or name C or name O or name CB )) or (resid 410 through 411 and (name \ N or name CA or name C or name O or name CB )) or resid 412 through 416 or (resi \ d 417 and (name N or name CA or name C or name O or name CB )) or resid 418 thro \ ugh 474 or (resid 475 and (name N or name CA or name C or name O or name CB )) o \ r resid 476 through 509 or resid 600 through 601)) selection = (chain 'B' and (resid 30 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 410 or (resid 411 and (name N or n \ ame CA or name C or name O or name CB )) or resid 412 through 466 or (resid 467 \ and (name N or name CA or name C or name O or name CB )) or resid 468 through 47 \ 4 or (resid 475 and (name N or name CA or name C or name O or name CB )) or resi \ d 476 through 479 or (resid 480 and (name N or name CA or name C or name O or na \ me CB )) or resid 481 through 492 or (resid 493 and (name N or name CA or name C \ or name O or name CB )) or resid 494 through 509 or resid 600 through 601)) selection = (chain 'C' and (resid 30 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 315 or (resid 316 and (name N or n \ ame CA or name C or name O or name CB )) or resid 317 through 406 or (resid 407 \ and (name N or name CA or name C or name O or name CB )) or (resid 410 through 4 \ 11 and (name N or name CA or name C or name O or name CB )) or resid 412 through \ 466 or (resid 467 and (name N or name CA or name C or name O or name CB )) or r \ esid 468 through 492 or (resid 493 and (name N or name CA or name C or name O or \ name CB )) or resid 494 through 509 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 9 through 111 or (resid 112 and (name N or name CA or name \ C or name O or name CB )) or resid 113 through 168 or (resid 169 and (name N or \ name CA or name C or name O or name CB )) or resid 170 through 175 or (resid 17 \ 6 through 177 and (name N or name CA or name C or name O or name CB )) or resid \ 178 through 299 or (resid 300 and (name N or name CA or name C or name O or name \ CB )) or resid 301 through 392 or (resid 393 through 396 and (name N or name CA \ or name C or name O or name CB )) or resid 397 or (resid 398 and (name N or nam \ e CA or name C or name O or name CB )) or resid 399 through 474)) selection = (chain 'E' and (resid 9 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 28 through 111 or (resid 112 and (name N or na \ me CA or name C or name O or name CB )) or resid 113 through 168 or (resid 169 a \ nd (name N or name CA or name C or name O or name CB )) or resid 170 through 175 \ or (resid 176 through 177 and (name N or name CA or name C or name O or name CB \ )) or resid 178 through 211 or (resid 212 and (name N or name CA or name C or n \ ame O or name CB )) or resid 213 through 381 or (resid 382 and (name N or name C \ A or name C or name O or name CB )) or resid 383 through 474)) selection = (chain 'F' and (resid 9 through 211 or (resid 212 and (name N or name CA or name \ C or name O or name CB )) or resid 213 through 299 or (resid 300 and (name N or \ name CA or name C or name O or name CB )) or resid 301 through 381 or (resid 38 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 383 through \ 392 or (resid 393 through 396 and (name N or name CA or name C or name O or name \ CB )) or resid 397 or (resid 398 and (name N or name CA or name C or name O or \ name CB )) or resid 399 through 474)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 51.650 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 23896 Z= 0.188 Angle : 0.605 7.003 32406 Z= 0.327 Chirality : 0.045 0.304 3811 Planarity : 0.004 0.039 4200 Dihedral : 12.985 168.856 8925 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.15), residues: 3082 helix: 0.65 (0.14), residues: 1274 sheet: -0.00 (0.23), residues: 504 loop : 0.46 (0.18), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 258 HIS 0.004 0.001 HIS C 304 PHE 0.012 0.001 PHE B 506 TYR 0.015 0.002 TYR G 212 ARG 0.006 0.001 ARG B 425 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 475 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 ARG cc_start: 0.8186 (mtp-110) cc_final: 0.7944 (mtp180) REVERT: A 495 LEU cc_start: 0.8839 (tp) cc_final: 0.7970 (tp) REVERT: B 469 SER cc_start: 0.8936 (m) cc_final: 0.8715 (t) REVERT: C 64 MET cc_start: 0.8641 (ttt) cc_final: 0.8394 (ttp) REVERT: C 111 ASP cc_start: 0.8126 (p0) cc_final: 0.7819 (p0) REVERT: C 228 MET cc_start: 0.9067 (tpt) cc_final: 0.8825 (tpt) REVERT: C 462 ARG cc_start: 0.8196 (mtp180) cc_final: 0.7200 (ttt180) REVERT: D 277 SER cc_start: 0.8263 (t) cc_final: 0.8052 (t) REVERT: D 339 ILE cc_start: 0.9063 (mm) cc_final: 0.8841 (mt) REVERT: D 342 LEU cc_start: 0.9078 (mt) cc_final: 0.8867 (mp) REVERT: D 381 TYR cc_start: 0.9046 (t80) cc_final: 0.8649 (t80) REVERT: D 393 MET cc_start: 0.6195 (mtp) cc_final: 0.5742 (mtp) REVERT: E 64 MET cc_start: 0.8702 (mmt) cc_final: 0.8491 (mmt) REVERT: E 222 MET cc_start: 0.8506 (mtt) cc_final: 0.8175 (mtt) REVERT: E 381 TYR cc_start: 0.8525 (t80) cc_final: 0.8106 (t80) REVERT: F 386 ASP cc_start: 0.7377 (m-30) cc_final: 0.7140 (m-30) REVERT: F 391 LEU cc_start: 0.8711 (mt) cc_final: 0.8509 (mt) REVERT: F 459 MET cc_start: 0.8949 (mmt) cc_final: 0.8633 (mmt) REVERT: G 15 ASN cc_start: 0.8323 (t0) cc_final: 0.8054 (t0) REVERT: G 145 LEU cc_start: 0.7710 (mp) cc_final: 0.6977 (tp) REVERT: G 211 GLU cc_start: 0.6364 (mt-10) cc_final: 0.5576 (tt0) REVERT: G 229 GLU cc_start: 0.8339 (tt0) cc_final: 0.8123 (tt0) outliers start: 0 outliers final: 0 residues processed: 475 average time/residue: 0.4051 time to fit residues: 284.2398 Evaluate side-chains 240 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 259 optimal weight: 4.9990 chunk 232 optimal weight: 0.0170 chunk 129 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 240 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 278 optimal weight: 3.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN B 67 ASN C 220 GLN C 304 HIS D 172 ASN D 385 GLN E 263 GLN E 385 GLN E 455 HIS F 178 HIS G 49 GLN G 216 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23896 Z= 0.277 Angle : 0.605 10.998 32406 Z= 0.314 Chirality : 0.047 0.255 3811 Planarity : 0.004 0.043 4200 Dihedral : 7.612 168.094 3445 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.17 % Allowed : 6.18 % Favored : 92.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 1.05 (0.15), residues: 3082 helix: 1.45 (0.15), residues: 1257 sheet: 0.01 (0.23), residues: 508 loop : 0.40 (0.18), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 191 HIS 0.005 0.001 HIS B 478 PHE 0.016 0.002 PHE C 466 TYR 0.018 0.001 TYR A 473 ARG 0.006 0.001 ARG G 9 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 264 time to evaluate : 2.682 Fit side-chains REVERT: B 82 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8071 (ttt90) REVERT: B 469 SER cc_start: 0.8891 (m) cc_final: 0.8647 (t) REVERT: C 111 ASP cc_start: 0.8157 (p0) cc_final: 0.7945 (p0) REVERT: C 462 ARG cc_start: 0.8063 (mtp180) cc_final: 0.7086 (ttt180) REVERT: E 64 MET cc_start: 0.8740 (mmt) cc_final: 0.8346 (mmt) REVERT: F 208 ASN cc_start: 0.7073 (t0) cc_final: 0.6790 (t0) REVERT: F 385 GLN cc_start: 0.7659 (mt0) cc_final: 0.7263 (mt0) REVERT: F 459 MET cc_start: 0.8778 (mmt) cc_final: 0.8515 (mmm) REVERT: G 15 ASN cc_start: 0.8189 (t0) cc_final: 0.7790 (t0) REVERT: G 145 LEU cc_start: 0.7723 (mp) cc_final: 0.6920 (tp) REVERT: G 159 TYR cc_start: 0.7695 (m-80) cc_final: 0.7093 (m-80) outliers start: 29 outliers final: 20 residues processed: 283 average time/residue: 0.3609 time to fit residues: 160.2370 Evaluate side-chains 234 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 213 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain F residue 197 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 154 optimal weight: 0.9980 chunk 86 optimal weight: 20.0000 chunk 232 optimal weight: 0.9980 chunk 189 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 279 optimal weight: 0.4980 chunk 301 optimal weight: 1.9990 chunk 248 optimal weight: 0.0970 chunk 276 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 224 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS B 452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 23896 Z= 0.188 Angle : 0.539 10.461 32406 Z= 0.275 Chirality : 0.044 0.241 3811 Planarity : 0.004 0.044 4200 Dihedral : 7.092 174.606 3445 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.01 % Allowed : 7.64 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 1.30 (0.15), residues: 3082 helix: 1.81 (0.15), residues: 1253 sheet: 0.01 (0.23), residues: 502 loop : 0.44 (0.18), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 191 HIS 0.014 0.001 HIS A 478 PHE 0.013 0.001 PHE A 506 TYR 0.018 0.001 TYR B 448 ARG 0.007 0.000 ARG G 9 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 258 time to evaluate : 2.393 Fit side-chains revert: symmetry clash REVERT: A 375 ARG cc_start: 0.7744 (mtp180) cc_final: 0.7501 (mtp180) REVERT: B 82 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8258 (ttt90) REVERT: C 371 LEU cc_start: 0.9238 (mt) cc_final: 0.8994 (mp) REVERT: C 462 ARG cc_start: 0.7894 (mtp180) cc_final: 0.7670 (mtp85) REVERT: E 64 MET cc_start: 0.8752 (mmt) cc_final: 0.8375 (mmt) REVERT: E 289 MET cc_start: 0.8782 (tpp) cc_final: 0.8455 (tpp) REVERT: G 15 ASN cc_start: 0.8150 (t0) cc_final: 0.7717 (t0) REVERT: G 145 LEU cc_start: 0.7479 (mp) cc_final: 0.6714 (tp) REVERT: G 159 TYR cc_start: 0.7574 (m-80) cc_final: 0.7217 (m-80) outliers start: 25 outliers final: 17 residues processed: 275 average time/residue: 0.3586 time to fit residues: 154.5176 Evaluate side-chains 224 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 206 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 11 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 275 optimal weight: 5.9990 chunk 209 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 133 optimal weight: 8.9990 chunk 187 optimal weight: 4.9990 chunk 280 optimal weight: 0.8980 chunk 296 optimal weight: 7.9990 chunk 146 optimal weight: 0.3980 chunk 265 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS C 145 HIS D 57 ASN F 379 GLN F 385 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 23896 Z= 0.315 Angle : 0.574 9.792 32406 Z= 0.294 Chirality : 0.046 0.267 3811 Planarity : 0.004 0.047 4200 Dihedral : 7.047 167.851 3445 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.54 % Allowed : 8.57 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 1.14 (0.15), residues: 3082 helix: 1.74 (0.15), residues: 1260 sheet: -0.22 (0.22), residues: 525 loop : 0.35 (0.18), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 191 HIS 0.007 0.001 HIS D 367 PHE 0.014 0.002 PHE A 506 TYR 0.013 0.002 TYR D 311 ARG 0.009 0.000 ARG D 412 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 227 time to evaluate : 2.684 Fit side-chains revert: symmetry clash REVERT: B 82 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8220 (ttt90) REVERT: B 89 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8256 (tp) REVERT: C 462 ARG cc_start: 0.7919 (mtp180) cc_final: 0.7678 (mtp85) REVERT: C 466 PHE cc_start: 0.8777 (t80) cc_final: 0.8544 (t80) REVERT: E 64 MET cc_start: 0.8760 (mmt) cc_final: 0.8387 (mmt) REVERT: G 15 ASN cc_start: 0.8153 (t0) cc_final: 0.7702 (t0) REVERT: G 145 LEU cc_start: 0.7599 (mp) cc_final: 0.6825 (tp) REVERT: G 159 TYR cc_start: 0.7607 (m-80) cc_final: 0.7132 (m-80) outliers start: 38 outliers final: 22 residues processed: 251 average time/residue: 0.3665 time to fit residues: 144.3853 Evaluate side-chains 225 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 201 time to evaluate : 2.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain E residue 40 LYS Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 422 GLU Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 11 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 247 optimal weight: 0.0270 chunk 168 optimal weight: 2.9990 chunk 4 optimal weight: 0.0470 chunk 220 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 253 optimal weight: 4.9990 chunk 205 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 151 optimal weight: 0.0060 chunk 266 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.2952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 328 HIS D 379 GLN F 385 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 23896 Z= 0.133 Angle : 0.504 12.252 32406 Z= 0.256 Chirality : 0.042 0.212 3811 Planarity : 0.004 0.049 4200 Dihedral : 6.476 160.208 3445 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.13 % Allowed : 9.09 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 1.49 (0.16), residues: 3082 helix: 2.08 (0.15), residues: 1268 sheet: 0.13 (0.23), residues: 492 loop : 0.36 (0.18), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 191 HIS 0.007 0.001 HIS A 478 PHE 0.011 0.001 PHE A 506 TYR 0.016 0.001 TYR B 399 ARG 0.010 0.000 ARG D 412 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 262 time to evaluate : 2.832 Fit side-chains revert: symmetry clash REVERT: A 446 LEU cc_start: 0.8321 (mp) cc_final: 0.8090 (mp) REVERT: A 494 GLU cc_start: 0.7022 (tm-30) cc_final: 0.6625 (tp30) REVERT: C 462 ARG cc_start: 0.7813 (mtp180) cc_final: 0.7568 (mtp85) REVERT: C 466 PHE cc_start: 0.8676 (t80) cc_final: 0.8334 (t80) REVERT: E 64 MET cc_start: 0.8703 (mmt) cc_final: 0.8347 (mmt) REVERT: E 289 MET cc_start: 0.8793 (tpp) cc_final: 0.8510 (tpp) REVERT: E 356 ARG cc_start: 0.8051 (mmm-85) cc_final: 0.7511 (mtp85) REVERT: G 15 ASN cc_start: 0.8104 (t0) cc_final: 0.7661 (t0) REVERT: G 145 LEU cc_start: 0.7486 (mp) cc_final: 0.6700 (tp) outliers start: 28 outliers final: 9 residues processed: 279 average time/residue: 0.3503 time to fit residues: 154.6815 Evaluate side-chains 217 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 208 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 140 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 99 optimal weight: 0.5980 chunk 267 optimal weight: 0.4980 chunk 58 optimal weight: 7.9990 chunk 174 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 297 optimal weight: 5.9990 chunk 246 optimal weight: 0.9990 chunk 137 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 478 HIS C 428 GLN D 208 ASN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 385 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 23896 Z= 0.161 Angle : 0.502 11.000 32406 Z= 0.255 Chirality : 0.043 0.304 3811 Planarity : 0.004 0.043 4200 Dihedral : 6.373 160.121 3445 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.85 % Allowed : 10.51 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 1.55 (0.16), residues: 3082 helix: 2.14 (0.15), residues: 1264 sheet: 0.05 (0.23), residues: 504 loop : 0.45 (0.18), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 191 HIS 0.005 0.001 HIS A 478 PHE 0.011 0.001 PHE A 506 TYR 0.017 0.001 TYR B 399 ARG 0.009 0.000 ARG D 412 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 232 time to evaluate : 2.589 Fit side-chains REVERT: A 64 MET cc_start: 0.8144 (ptm) cc_final: 0.7805 (ttp) REVERT: A 446 LEU cc_start: 0.8359 (mp) cc_final: 0.8080 (mp) REVERT: A 494 GLU cc_start: 0.6908 (tm-30) cc_final: 0.6527 (tp30) REVERT: C 462 ARG cc_start: 0.7757 (mtp180) cc_final: 0.6911 (ttt-90) REVERT: C 466 PHE cc_start: 0.8636 (t80) cc_final: 0.8341 (t80) REVERT: E 64 MET cc_start: 0.8780 (mmt) cc_final: 0.8467 (mmt) REVERT: E 356 ARG cc_start: 0.8028 (mmm-85) cc_final: 0.7577 (mtp85) REVERT: G 15 ASN cc_start: 0.8101 (t0) cc_final: 0.7653 (t0) REVERT: G 145 LEU cc_start: 0.7304 (mp) cc_final: 0.6475 (tp) outliers start: 21 outliers final: 16 residues processed: 248 average time/residue: 0.3436 time to fit residues: 136.7114 Evaluate side-chains 223 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 207 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 422 GLU Chi-restraints excluded: chain F residue 133 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 286 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 216 optimal weight: 0.8980 chunk 168 optimal weight: 0.7980 chunk 250 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 295 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 477 ASN C 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23896 Z= 0.197 Angle : 0.509 10.222 32406 Z= 0.259 Chirality : 0.043 0.262 3811 Planarity : 0.004 0.042 4200 Dihedral : 6.340 158.603 3445 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.97 % Allowed : 10.95 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.16), residues: 3082 helix: 2.14 (0.15), residues: 1265 sheet: 0.00 (0.23), residues: 515 loop : 0.41 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 191 HIS 0.004 0.001 HIS A 478 PHE 0.011 0.001 PHE F 261 TYR 0.028 0.001 TYR B 448 ARG 0.010 0.000 ARG D 412 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 210 time to evaluate : 2.447 Fit side-chains revert: symmetry clash REVERT: C 462 ARG cc_start: 0.7777 (mtp180) cc_final: 0.7548 (mtp85) REVERT: E 64 MET cc_start: 0.8749 (mmt) cc_final: 0.8455 (mmt) REVERT: E 289 MET cc_start: 0.8751 (tpp) cc_final: 0.8532 (tpt) REVERT: E 356 ARG cc_start: 0.8089 (mmm-85) cc_final: 0.7640 (mtp85) REVERT: G 15 ASN cc_start: 0.8106 (t0) cc_final: 0.7655 (t0) REVERT: G 102 GLN cc_start: 0.6826 (mp10) cc_final: 0.6250 (pp30) REVERT: G 145 LEU cc_start: 0.7310 (mp) cc_final: 0.6504 (tp) outliers start: 24 outliers final: 19 residues processed: 226 average time/residue: 0.3415 time to fit residues: 122.2492 Evaluate side-chains 219 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 200 time to evaluate : 2.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 422 GLU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain G residue 11 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 183 optimal weight: 4.9990 chunk 118 optimal weight: 0.5980 chunk 176 optimal weight: 0.6980 chunk 89 optimal weight: 0.0870 chunk 58 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 chunk 201 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 232 optimal weight: 6.9990 overall best weight: 1.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 385 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23896 Z= 0.242 Angle : 0.526 9.809 32406 Z= 0.268 Chirality : 0.044 0.239 3811 Planarity : 0.004 0.043 4200 Dihedral : 6.385 156.794 3445 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.09 % Allowed : 11.15 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 1.44 (0.16), residues: 3082 helix: 2.11 (0.15), residues: 1260 sheet: -0.06 (0.23), residues: 528 loop : 0.37 (0.18), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 191 HIS 0.004 0.001 HIS E 367 PHE 0.011 0.001 PHE F 261 TYR 0.026 0.001 TYR B 448 ARG 0.010 0.000 ARG D 412 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 210 time to evaluate : 2.734 Fit side-chains REVERT: C 462 ARG cc_start: 0.7836 (mtp180) cc_final: 0.7593 (mtp85) REVERT: E 64 MET cc_start: 0.8781 (mmt) cc_final: 0.8459 (mmt) REVERT: E 356 ARG cc_start: 0.8092 (mmm-85) cc_final: 0.7654 (mtp85) REVERT: G 15 ASN cc_start: 0.8145 (t0) cc_final: 0.7649 (t0) REVERT: G 102 GLN cc_start: 0.6735 (mp10) cc_final: 0.6131 (pp30) REVERT: G 145 LEU cc_start: 0.7326 (mp) cc_final: 0.6517 (tp) outliers start: 27 outliers final: 21 residues processed: 228 average time/residue: 0.3478 time to fit residues: 126.0755 Evaluate side-chains 209 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 188 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 422 GLU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain G residue 11 LYS Chi-restraints excluded: chain G residue 237 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 269 optimal weight: 0.9980 chunk 283 optimal weight: 4.9990 chunk 258 optimal weight: 0.7980 chunk 275 optimal weight: 4.9990 chunk 165 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 216 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 249 optimal weight: 4.9990 chunk 260 optimal weight: 0.9990 chunk 274 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23896 Z= 0.181 Angle : 0.511 9.953 32406 Z= 0.259 Chirality : 0.043 0.231 3811 Planarity : 0.004 0.043 4200 Dihedral : 6.255 154.541 3445 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.93 % Allowed : 11.47 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.16), residues: 3082 helix: 2.17 (0.15), residues: 1268 sheet: -0.01 (0.23), residues: 519 loop : 0.38 (0.18), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 191 HIS 0.004 0.001 HIS A 478 PHE 0.011 0.001 PHE F 261 TYR 0.024 0.001 TYR B 448 ARG 0.009 0.000 ARG D 412 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 210 time to evaluate : 2.633 Fit side-chains revert: symmetry clash REVERT: A 441 GLU cc_start: 0.8512 (pm20) cc_final: 0.8298 (pt0) REVERT: B 447 ILE cc_start: 0.8687 (mm) cc_final: 0.8365 (tp) REVERT: C 462 ARG cc_start: 0.7824 (mtp180) cc_final: 0.6991 (ttt-90) REVERT: E 64 MET cc_start: 0.8766 (mmt) cc_final: 0.8443 (mmt) REVERT: E 289 MET cc_start: 0.8745 (tpp) cc_final: 0.8433 (tpp) REVERT: E 356 ARG cc_start: 0.8064 (mmm-85) cc_final: 0.7652 (mtp85) REVERT: G 15 ASN cc_start: 0.8102 (t0) cc_final: 0.7644 (t0) REVERT: G 102 GLN cc_start: 0.6793 (mp10) cc_final: 0.6233 (pp30) REVERT: G 145 LEU cc_start: 0.7329 (mp) cc_final: 0.6514 (tp) outliers start: 23 outliers final: 15 residues processed: 225 average time/residue: 0.3640 time to fit residues: 130.4502 Evaluate side-chains 208 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 193 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 422 GLU Chi-restraints excluded: chain F residue 133 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 181 optimal weight: 0.9990 chunk 291 optimal weight: 7.9990 chunk 177 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 305 optimal weight: 5.9990 chunk 281 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 407 GLN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 399 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 23896 Z= 0.463 Angle : 0.635 9.173 32406 Z= 0.324 Chirality : 0.049 0.236 3811 Planarity : 0.005 0.045 4200 Dihedral : 6.741 156.006 3445 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.81 % Allowed : 11.68 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.15), residues: 3082 helix: 1.73 (0.15), residues: 1260 sheet: -0.41 (0.22), residues: 538 loop : 0.16 (0.18), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 191 HIS 0.008 0.001 HIS D 367 PHE 0.050 0.002 PHE C 466 TYR 0.021 0.002 TYR B 399 ARG 0.011 0.001 ARG D 412 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 196 time to evaluate : 2.819 Fit side-chains REVERT: C 462 ARG cc_start: 0.7795 (mtp180) cc_final: 0.7502 (mtp85) REVERT: E 64 MET cc_start: 0.8719 (mmt) cc_final: 0.8387 (mmt) REVERT: E 356 ARG cc_start: 0.8160 (mmm-85) cc_final: 0.7857 (mtp85) REVERT: G 15 ASN cc_start: 0.8209 (t0) cc_final: 0.7754 (t0) REVERT: G 102 GLN cc_start: 0.6734 (mp10) cc_final: 0.6176 (pp30) REVERT: G 145 LEU cc_start: 0.7126 (mp) cc_final: 0.6329 (tp) outliers start: 20 outliers final: 17 residues processed: 212 average time/residue: 0.3772 time to fit residues: 125.8350 Evaluate side-chains 198 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 181 time to evaluate : 2.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 246 TYR Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 422 GLU Chi-restraints excluded: chain F residue 133 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 193 optimal weight: 0.8980 chunk 259 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 224 optimal weight: 0.0010 chunk 35 optimal weight: 1.9990 chunk 67 optimal weight: 0.0870 chunk 243 optimal weight: 2.9990 chunk 102 optimal weight: 0.0010 chunk 250 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 overall best weight: 0.2170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 385 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.126228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.098883 restraints weight = 29761.001| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.77 r_work: 0.2960 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 23896 Z= 0.143 Angle : 0.521 9.774 32406 Z= 0.264 Chirality : 0.043 0.222 3811 Planarity : 0.004 0.046 4200 Dihedral : 6.200 151.145 3445 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.44 % Allowed : 12.36 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 1.38 (0.16), residues: 3082 helix: 2.08 (0.15), residues: 1270 sheet: 0.06 (0.24), residues: 472 loop : 0.19 (0.18), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 191 HIS 0.003 0.001 HIS A 478 PHE 0.042 0.001 PHE C 466 TYR 0.021 0.001 TYR B 399 ARG 0.009 0.001 ARG D 412 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4701.70 seconds wall clock time: 84 minutes 44.72 seconds (5084.72 seconds total)