Starting phenix.real_space_refine on Fri Mar 15 21:53:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7n_0359/03_2024/6n7n_0359_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7n_0359/03_2024/6n7n_0359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7n_0359/03_2024/6n7n_0359.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7n_0359/03_2024/6n7n_0359.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7n_0359/03_2024/6n7n_0359_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7n_0359/03_2024/6n7n_0359_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 30 5.49 5 Mg 5 5.21 5 S 78 5.16 5 C 7962 2.51 5 N 2257 2.21 5 O 2522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 274": "NH1" <-> "NH2" Residue "A GLU 306": "OE1" <-> "OE2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "C ARG 504": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 370": "NH1" <-> "NH2" Residue "D ARG 504": "NH1" <-> "NH2" Residue "D ARG 522": "NH1" <-> "NH2" Residue "E ARG 363": "NH1" <-> "NH2" Residue "E ARG 370": "NH1" <-> "NH2" Residue "F ARG 274": "NH1" <-> "NH2" Residue "F ARG 363": "NH1" <-> "NH2" Residue "F ARG 370": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12854 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2093 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 4, 'TRANS': 266} Chain breaks: 3 Chain: "B" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2111 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 4, 'TRANS': 269} Chain breaks: 3 Chain: "C" Number of atoms: 2127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2127 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 4, 'TRANS': 271} Chain breaks: 3 Chain: "D" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2086 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 266} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2003 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 254} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 1984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1984 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 252} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 300 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.30, per 1000 atoms: 0.57 Number of scatterers: 12854 At special positions: 0 Unit cell: (80.25, 127.33, 135.89, 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 78 16.00 P 30 15.00 Mg 5 11.99 O 2522 8.00 N 2257 7.00 C 7962 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.82 Conformation dependent library (CDL) restraints added in 2.3 seconds 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2866 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 7 sheets defined 30.7% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 293 through 298 removed outlier: 4.343A pdb=" N LYS A 298 " --> pdb=" O GLY A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 330 Processing helix chain 'A' and resid 346 through 357 Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 366 through 374 removed outlier: 3.562A pdb=" N ARG A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 374' Processing helix chain 'A' and resid 379 through 383 removed outlier: 3.831A pdb=" N ASP A 383 " --> pdb=" O ASP A 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 379 through 383' Processing helix chain 'A' and resid 403 through 414 removed outlier: 4.443A pdb=" N ALA A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 429 No H-bonds generated for 'chain 'A' and resid 426 through 429' Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 483 through 485 No H-bonds generated for 'chain 'A' and resid 483 through 485' Processing helix chain 'B' and resid 270 through 279 removed outlier: 4.137A pdb=" N GLU B 273 " --> pdb=" O SER B 270 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG B 274 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ILE B 275 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG B 276 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 298 removed outlier: 3.516A pdb=" N ASP B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS B 298 " --> pdb=" O GLY B 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 293 through 298' Processing helix chain 'B' and resid 318 through 331 Processing helix chain 'B' and resid 346 through 357 Processing helix chain 'B' and resid 366 through 372 Processing helix chain 'B' and resid 378 through 386 removed outlier: 3.532A pdb=" N GLU B 384 " --> pdb=" O GLN B 380 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU B 385 " --> pdb=" O TRP B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 413 Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 438 through 453 Processing helix chain 'B' and resid 483 through 485 No H-bonds generated for 'chain 'B' and resid 483 through 485' Processing helix chain 'C' and resid 272 through 276 Processing helix chain 'C' and resid 293 through 299 removed outlier: 3.641A pdb=" N ASP C 297 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS C 298 " --> pdb=" O GLY C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 330 removed outlier: 3.769A pdb=" N GLN C 328 " --> pdb=" O GLN C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 357 removed outlier: 3.861A pdb=" N GLU C 351 " --> pdb=" O GLU C 347 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 353 " --> pdb=" O THR C 349 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C 355 " --> pdb=" O GLU C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 374 Processing helix chain 'C' and resid 377 through 385 removed outlier: 4.007A pdb=" N LEU C 385 " --> pdb=" O TRP C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 415 removed outlier: 4.032A pdb=" N LEU C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 438 through 456 Processing helix chain 'C' and resid 483 through 485 No H-bonds generated for 'chain 'C' and resid 483 through 485' Processing helix chain 'D' and resid 272 through 276 Processing helix chain 'D' and resid 319 through 328 removed outlier: 3.648A pdb=" N GLN D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN D 325 " --> pdb=" O PHE D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 357 Processing helix chain 'D' and resid 366 through 369 No H-bonds generated for 'chain 'D' and resid 366 through 369' Processing helix chain 'D' and resid 371 through 374 No H-bonds generated for 'chain 'D' and resid 371 through 374' Processing helix chain 'D' and resid 377 through 385 removed outlier: 3.509A pdb=" N ASP D 383 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU D 385 " --> pdb=" O TRP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 414 Processing helix chain 'D' and resid 427 through 429 No H-bonds generated for 'chain 'D' and resid 427 through 429' Processing helix chain 'D' and resid 440 through 456 removed outlier: 3.621A pdb=" N LEU D 445 " --> pdb=" O MET D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 477 No H-bonds generated for 'chain 'D' and resid 475 through 477' Processing helix chain 'E' and resid 272 through 276 Processing helix chain 'E' and resid 318 through 328 Processing helix chain 'E' and resid 348 through 357 removed outlier: 3.651A pdb=" N LEU E 353 " --> pdb=" O THR E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 371 removed outlier: 3.949A pdb=" N ARG E 370 " --> pdb=" O ASP E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 386 removed outlier: 3.970A pdb=" N LEU E 385 " --> pdb=" O TRP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 414 Processing helix chain 'E' and resid 440 through 456 removed outlier: 3.968A pdb=" N LEU E 445 " --> pdb=" O MET E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 477 No H-bonds generated for 'chain 'E' and resid 475 through 477' Processing helix chain 'E' and resid 491 through 494 No H-bonds generated for 'chain 'E' and resid 491 through 494' Processing helix chain 'F' and resid 274 through 278 Processing helix chain 'F' and resid 318 through 328 Processing helix chain 'F' and resid 348 through 357 removed outlier: 3.632A pdb=" N LEU F 353 " --> pdb=" O THR F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 371 removed outlier: 3.975A pdb=" N ARG F 370 " --> pdb=" O ASP F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 386 removed outlier: 3.677A pdb=" N GLU F 384 " --> pdb=" O GLN F 380 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU F 385 " --> pdb=" O TRP F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 414 Processing helix chain 'F' and resid 441 through 456 removed outlier: 3.619A pdb=" N LEU F 445 " --> pdb=" O MET F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 477 No H-bonds generated for 'chain 'F' and resid 475 through 477' Processing sheet with id= A, first strand: chain 'A' and resid 542 through 544 removed outlier: 7.121A pdb=" N VAL A 516 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N TYR A 532 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL A 514 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE A 499 " --> pdb=" O LEU A 519 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 542 through 544 removed outlier: 7.059A pdb=" N VAL B 516 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TYR B 532 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL B 514 " --> pdb=" O TYR B 532 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE B 499 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER B 312 " --> pdb=" O CYS B 464 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B 463 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 542 through 544 removed outlier: 6.797A pdb=" N VAL C 516 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR C 532 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL C 514 " --> pdb=" O TYR C 532 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE C 499 " --> pdb=" O LEU C 519 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 528 through 533 removed outlier: 6.951A pdb=" N VAL D 516 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYR D 532 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL D 514 " --> pdb=" O TYR D 532 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE D 499 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR D 498 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU D 460 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N VAL D 310 " --> pdb=" O LEU D 460 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL D 462 " --> pdb=" O VAL D 310 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 308 through 311 removed outlier: 6.405A pdb=" N THR E 498 " --> pdb=" O MET E 309 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N THR E 311 " --> pdb=" O THR E 498 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ILE E 500 " --> pdb=" O THR E 311 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE E 499 " --> pdb=" O LYS E 520 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS E 520 " --> pdb=" O ILE E 499 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ALA E 501 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE E 518 " --> pdb=" O ALA E 501 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLU E 503 " --> pdb=" O VAL E 516 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL E 516 " --> pdb=" O GLU E 503 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 337 through 340 removed outlier: 6.579A pdb=" N VAL E 420 " --> pdb=" O GLY E 338 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ALA E 340 " --> pdb=" O VAL E 420 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE E 422 " --> pdb=" O ALA E 340 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL E 459 " --> pdb=" O ILE E 421 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N LEU E 423 " --> pdb=" O VAL E 459 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL E 461 " --> pdb=" O LEU E 423 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'F' and resid 528 through 534 removed outlier: 6.825A pdb=" N VAL F 516 " --> pdb=" O ALA F 530 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N TYR F 532 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL F 514 " --> pdb=" O TYR F 532 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE F 499 " --> pdb=" O LEU F 519 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR F 498 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU F 460 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N VAL F 310 " --> pdb=" O LEU F 460 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL F 462 " --> pdb=" O VAL F 310 " (cutoff:3.500A) 341 hydrogen bonds defined for protein. 990 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: 2.87 Time building geometry restraints manager: 5.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2150 1.31 - 1.44: 3220 1.44 - 1.57: 7473 1.57 - 1.70: 54 1.70 - 1.83: 132 Bond restraints: 13029 Sorted by residual: bond pdb=" C6 TTP D 700 " pdb=" N1 TTP D 700 " ideal model delta sigma weight residual 1.337 1.428 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C6 TTP C 700 " pdb=" N1 TTP C 700 " ideal model delta sigma weight residual 1.337 1.427 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C6 TTP F 700 " pdb=" N1 TTP F 700 " ideal model delta sigma weight residual 1.337 1.426 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C6 TTP B 700 " pdb=" N1 TTP B 700 " ideal model delta sigma weight residual 1.337 1.425 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" C6 TTP E 700 " pdb=" N1 TTP E 700 " ideal model delta sigma weight residual 1.337 1.420 -0.083 2.00e-02 2.50e+03 1.70e+01 ... (remaining 13024 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.58: 307 106.58 - 113.42: 7216 113.42 - 120.26: 4886 120.26 - 127.09: 5045 127.09 - 133.93: 120 Bond angle restraints: 17574 Sorted by residual: angle pdb=" N ILE E 442 " pdb=" CA ILE E 442 " pdb=" C ILE E 442 " ideal model delta sigma weight residual 111.81 107.50 4.31 8.60e-01 1.35e+00 2.51e+01 angle pdb=" O3' DT T 5 " pdb=" C3' DT T 5 " pdb=" C2' DT T 5 " ideal model delta sigma weight residual 111.50 118.65 -7.15 1.50e+00 4.44e-01 2.27e+01 angle pdb=" PA TTP D 700 " pdb=" O3A TTP D 700 " pdb=" PB TTP D 700 " ideal model delta sigma weight residual 120.50 133.70 -13.20 3.00e+00 1.11e-01 1.94e+01 angle pdb=" PB TTP C 700 " pdb=" O3B TTP C 700 " pdb=" PG TTP C 700 " ideal model delta sigma weight residual 120.50 132.63 -12.13 3.00e+00 1.11e-01 1.64e+01 angle pdb=" PA TTP C 700 " pdb=" O3A TTP C 700 " pdb=" PB TTP C 700 " ideal model delta sigma weight residual 120.50 132.60 -12.10 3.00e+00 1.11e-01 1.63e+01 ... (remaining 17569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.60: 7631 35.60 - 71.20: 127 71.20 - 106.80: 11 106.80 - 142.40: 5 142.40 - 178.00: 7 Dihedral angle restraints: 7781 sinusoidal: 3305 harmonic: 4476 Sorted by residual: dihedral pdb=" O2G TTP F 700 " pdb=" O3B TTP F 700 " pdb=" PG TTP F 700 " pdb=" PB TTP F 700 " ideal model delta sinusoidal sigma weight residual -180.00 -2.00 -178.00 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2G TTP D 700 " pdb=" O3B TTP D 700 " pdb=" PG TTP D 700 " pdb=" PB TTP D 700 " ideal model delta sinusoidal sigma weight residual -180.00 -2.43 -177.57 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 TTP B 700 " pdb=" C1' TTP B 700 " pdb=" N1 TTP B 700 " pdb=" O4' TTP B 700 " ideal model delta sinusoidal sigma weight residual -58.32 114.32 -172.64 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 7778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1560 0.064 - 0.128: 377 0.128 - 0.193: 55 0.193 - 0.257: 7 0.257 - 0.321: 3 Chirality restraints: 2002 Sorted by residual: chirality pdb=" C3' DT T 5 " pdb=" C4' DT T 5 " pdb=" O3' DT T 5 " pdb=" C2' DT T 5 " both_signs ideal model delta sigma weight residual False -2.66 -2.34 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" C4' TTP B 700 " pdb=" C3' TTP B 700 " pdb=" C5' TTP B 700 " pdb=" O4' TTP B 700 " both_signs ideal model delta sigma weight residual False -2.50 -2.76 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C3' TTP F 700 " pdb=" C2' TTP F 700 " pdb=" C4' TTP F 700 " pdb=" O3' TTP F 700 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1999 not shown) Planarity restraints: 2166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 358 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.08e+00 pdb=" C ASN B 358 " -0.039 2.00e-02 2.50e+03 pdb=" O ASN B 358 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG B 359 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 342 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" C LEU C 342 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU C 342 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN C 343 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 510 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO D 511 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 511 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 511 " 0.027 5.00e-02 4.00e+02 ... (remaining 2163 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 62 2.56 - 3.15: 9242 3.15 - 3.73: 18635 3.73 - 4.32: 26691 4.32 - 4.90: 44726 Nonbonded interactions: 99356 Sorted by model distance: nonbonded pdb=" OE1 GLN D 343 " pdb="MG MG D 701 " model vdw 1.975 2.170 nonbonded pdb=" O1B TTP B 700 " pdb="MG MG B 701 " model vdw 1.985 2.170 nonbonded pdb=" NE2 GLN B 343 " pdb="MG MG B 701 " model vdw 2.041 2.250 nonbonded pdb=" O2B TTP F 700 " pdb="MG MG F 701 " model vdw 2.054 2.170 nonbonded pdb=" O1G TTP C 700 " pdb="MG MG C 701 " model vdw 2.116 2.170 ... (remaining 99351 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 264 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or (resid 440 and (name N or name CA or name C or name O or name CB )) o \ r resid 441 through 506 or resid 510 through 545)) selection = (chain 'B' and (resid 264 through 280 or resid 285 through 373 or resid 377 thro \ ugh 395 or resid 404 through 429 or (resid 440 and (name N or name CA or name C \ or name O or name CB )) or resid 441 through 506 or resid 510 through 545)) selection = (chain 'C' and (resid 264 through 280 or resid 285 through 373 or resid 377 thro \ ugh 395 or resid 404 through 429 or (resid 440 and (name N or name CA or name C \ or name O or name CB )) or resid 441 through 545)) selection = (chain 'D' and (resid 264 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or resid 440 through 506 or resid 510 through 545)) selection = (chain 'E' and (resid 264 through 429 or resid 440 through 506 or resid 510 thro \ ugh 545)) selection = (chain 'F' and (resid 264 through 506 or resid 510 through 545)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.040 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 35.690 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 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 : 0.006 0.091 13029 Z= 0.360 Angle : 0.987 13.201 17574 Z= 0.519 Chirality : 0.057 0.321 2002 Planarity : 0.004 0.048 2166 Dihedral : 14.773 177.997 4915 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.74 % Allowed : 3.48 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.18), residues: 1556 helix: -2.73 (0.17), residues: 521 sheet: -0.65 (0.30), residues: 318 loop : -2.75 (0.19), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 541 HIS 0.008 0.002 HIS A 357 PHE 0.016 0.002 PHE D 386 TYR 0.013 0.002 TYR A 535 ARG 0.006 0.001 ARG D 359 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 329 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 368 LEU cc_start: 0.7895 (tt) cc_final: 0.7687 (tt) REVERT: D 504 ARG cc_start: 0.6670 (OUTLIER) cc_final: 0.6289 (ptm-80) REVERT: F 309 MET cc_start: 0.7792 (mmm) cc_final: 0.7273 (mmt) outliers start: 10 outliers final: 1 residues processed: 338 average time/residue: 0.2921 time to fit residues: 134.2352 Evaluate side-chains 177 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 175 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 504 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.0980 chunk 120 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 124 optimal weight: 0.1980 chunk 48 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 ASN B 357 HIS C 325 GLN C 380 GLN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 ASN C 475 HIS D 358 ASN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 HIS E 358 ASN E 425 HIS E 506 GLN E 507 GLN F 325 GLN ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 ASN ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13029 Z= 0.138 Angle : 0.529 7.042 17574 Z= 0.263 Chirality : 0.042 0.144 2002 Planarity : 0.003 0.036 2166 Dihedral : 15.892 179.233 1934 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.37 % Allowed : 9.40 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.20), residues: 1556 helix: -1.12 (0.21), residues: 524 sheet: -0.46 (0.30), residues: 322 loop : -2.34 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 381 HIS 0.009 0.001 HIS E 278 PHE 0.021 0.001 PHE B 321 TYR 0.017 0.001 TYR A 547 ARG 0.006 0.000 ARG E 517 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 206 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 LYS cc_start: 0.4075 (ptmt) cc_final: 0.3395 (ttmt) REVERT: A 487 ARG cc_start: 0.6521 (ttp80) cc_final: 0.5337 (ttt-90) REVERT: A 542 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7452 (pp) REVERT: B 344 GLU cc_start: 0.5730 (mp0) cc_final: 0.5343 (mp0) REVERT: C 438 GLU cc_start: 0.5961 (tt0) cc_final: 0.5667 (pm20) REVERT: D 441 MET cc_start: 0.6805 (mmt) cc_final: 0.6570 (mmm) REVERT: D 482 SER cc_start: 0.7307 (m) cc_final: 0.7035 (p) REVERT: F 309 MET cc_start: 0.7812 (mmm) cc_final: 0.7251 (mmt) outliers start: 32 outliers final: 18 residues processed: 226 average time/residue: 0.2351 time to fit residues: 77.0449 Evaluate side-chains 182 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 163 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 481 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 144 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 HIS A 475 HIS ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 HIS ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13029 Z= 0.252 Angle : 0.623 7.869 17574 Z= 0.308 Chirality : 0.045 0.153 2002 Planarity : 0.004 0.045 2166 Dihedral : 15.967 177.088 1929 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.63 % Allowed : 12.88 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.20), residues: 1556 helix: -0.72 (0.22), residues: 529 sheet: -0.52 (0.30), residues: 321 loop : -2.19 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 541 HIS 0.007 0.001 HIS B 392 PHE 0.029 0.002 PHE C 321 TYR 0.015 0.001 TYR A 547 ARG 0.005 0.001 ARG D 323 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 160 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 GLN cc_start: 0.6462 (mm-40) cc_final: 0.6212 (mp10) REVERT: A 487 ARG cc_start: 0.6700 (ttp80) cc_final: 0.5401 (ttt-90) REVERT: C 438 GLU cc_start: 0.5952 (tt0) cc_final: 0.5693 (pm20) REVERT: D 441 MET cc_start: 0.6934 (mmt) cc_final: 0.6606 (mmm) REVERT: E 499 ILE cc_start: 0.7141 (OUTLIER) cc_final: 0.6913 (mt) outliers start: 49 outliers final: 25 residues processed: 192 average time/residue: 0.2258 time to fit residues: 64.5993 Evaluate side-chains 170 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 144 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain E residue 529 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Chi-restraints excluded: chain F residue 484 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 69 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 153 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 HIS B 444 ASN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 13029 Z= 0.406 Angle : 0.771 10.386 17574 Z= 0.380 Chirality : 0.049 0.184 2002 Planarity : 0.005 0.036 2166 Dihedral : 16.489 178.925 1929 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 4.22 % Allowed : 13.10 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.20), residues: 1556 helix: -0.93 (0.22), residues: 511 sheet: -0.82 (0.30), residues: 310 loop : -2.26 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 541 HIS 0.008 0.002 HIS B 392 PHE 0.027 0.003 PHE C 321 TYR 0.015 0.002 TYR A 547 ARG 0.009 0.001 ARG E 517 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 148 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 473 LYS cc_start: 0.3543 (ptmt) cc_final: 0.3022 (ttmt) REVERT: A 487 ARG cc_start: 0.7055 (ttp80) cc_final: 0.5632 (ttt-90) REVERT: B 487 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.6553 (ptp90) REVERT: C 352 ASP cc_start: 0.5688 (t0) cc_final: 0.5440 (t0) REVERT: D 341 MET cc_start: 0.8298 (mmm) cc_final: 0.8072 (mmm) REVERT: D 441 MET cc_start: 0.6863 (mmt) cc_final: 0.6551 (mmm) REVERT: E 517 ARG cc_start: 0.7264 (ttm-80) cc_final: 0.6910 (ttm110) REVERT: F 333 MET cc_start: 0.7224 (mpp) cc_final: 0.6945 (mpp) outliers start: 57 outliers final: 41 residues processed: 190 average time/residue: 0.2197 time to fit residues: 63.1652 Evaluate side-chains 181 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 139 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 419 ASP Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 529 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Chi-restraints excluded: chain F residue 484 THR Chi-restraints excluded: chain F residue 526 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 78 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 GLN ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13029 Z= 0.163 Angle : 0.529 7.688 17574 Z= 0.264 Chirality : 0.042 0.145 2002 Planarity : 0.002 0.032 2166 Dihedral : 15.364 177.995 1929 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.55 % Allowed : 14.73 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.21), residues: 1556 helix: -0.16 (0.23), residues: 517 sheet: -0.67 (0.30), residues: 306 loop : -2.01 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 541 HIS 0.003 0.001 HIS D 425 PHE 0.026 0.001 PHE B 523 TYR 0.014 0.001 TYR A 547 ARG 0.004 0.000 ARG E 517 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 153 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 473 LYS cc_start: 0.3896 (ptmt) cc_final: 0.3374 (ttmt) REVERT: A 487 ARG cc_start: 0.6920 (ttp80) cc_final: 0.5374 (ttt-90) REVERT: A 542 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7166 (pp) REVERT: D 509 ASP cc_start: 0.6563 (OUTLIER) cc_final: 0.6155 (p0) REVERT: E 285 VAL cc_start: 0.6598 (t) cc_final: 0.6362 (m) REVERT: E 517 ARG cc_start: 0.7274 (ttm-80) cc_final: 0.6961 (ttm110) REVERT: E 533 MET cc_start: 0.6610 (mtp) cc_final: 0.6274 (mtp) REVERT: F 333 MET cc_start: 0.7039 (mpp) cc_final: 0.6749 (mpp) REVERT: F 351 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6766 (mt-10) outliers start: 48 outliers final: 30 residues processed: 187 average time/residue: 0.2320 time to fit residues: 63.5070 Evaluate side-chains 173 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 141 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain E residue 412 MET Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 529 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Chi-restraints excluded: chain F residue 484 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 50 optimal weight: 0.0270 chunk 80 optimal weight: 5.9990 chunk 148 optimal weight: 0.0270 overall best weight: 2.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13029 Z= 0.275 Angle : 0.620 7.734 17574 Z= 0.307 Chirality : 0.045 0.154 2002 Planarity : 0.003 0.029 2166 Dihedral : 15.544 179.515 1929 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 4.22 % Allowed : 14.29 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.21), residues: 1556 helix: -0.22 (0.23), residues: 512 sheet: -0.75 (0.29), residues: 311 loop : -2.09 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 541 HIS 0.004 0.001 HIS A 392 PHE 0.023 0.002 PHE C 321 TYR 0.013 0.001 TYR A 547 ARG 0.004 0.001 ARG E 517 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 138 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 460 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7310 (tp) REVERT: A 473 LYS cc_start: 0.3577 (ptmt) cc_final: 0.2925 (ttmt) REVERT: A 487 ARG cc_start: 0.6904 (ttp80) cc_final: 0.5509 (ttt-90) REVERT: A 542 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7316 (pp) REVERT: B 368 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7265 (tt) REVERT: D 341 MET cc_start: 0.8042 (mmm) cc_final: 0.7827 (mmm) REVERT: D 460 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7477 (mp) REVERT: D 509 ASP cc_start: 0.6633 (OUTLIER) cc_final: 0.6213 (p0) REVERT: E 517 ARG cc_start: 0.7392 (ttm-80) cc_final: 0.7113 (ttm110) REVERT: E 522 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.7084 (mtm-85) REVERT: E 533 MET cc_start: 0.6583 (OUTLIER) cc_final: 0.6153 (mtp) REVERT: F 333 MET cc_start: 0.6969 (mpp) cc_final: 0.6687 (mpp) REVERT: F 509 ASP cc_start: 0.5465 (OUTLIER) cc_final: 0.5100 (t0) outliers start: 57 outliers final: 38 residues processed: 182 average time/residue: 0.2203 time to fit residues: 60.7235 Evaluate side-chains 178 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 132 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 522 ARG Chi-restraints excluded: chain E residue 529 ILE Chi-restraints excluded: chain E residue 533 MET Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Chi-restraints excluded: chain F residue 484 THR Chi-restraints excluded: chain F residue 509 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13029 Z= 0.224 Angle : 0.569 7.136 17574 Z= 0.283 Chirality : 0.043 0.164 2002 Planarity : 0.003 0.033 2166 Dihedral : 15.280 177.837 1929 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.07 % Allowed : 14.80 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.21), residues: 1556 helix: 0.03 (0.23), residues: 512 sheet: -0.70 (0.30), residues: 304 loop : -2.05 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 541 HIS 0.003 0.001 HIS A 392 PHE 0.020 0.002 PHE C 321 TYR 0.012 0.001 TYR A 547 ARG 0.004 0.000 ARG E 517 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 138 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 404 ARG cc_start: 0.4400 (OUTLIER) cc_final: 0.3840 (pmt100) REVERT: A 473 LYS cc_start: 0.3592 (ptmt) cc_final: 0.3081 (ttmt) REVERT: A 487 ARG cc_start: 0.7024 (ttp80) cc_final: 0.5548 (ttt-90) REVERT: A 542 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7125 (pp) REVERT: B 368 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7263 (tt) REVERT: C 370 ARG cc_start: 0.6917 (mtm180) cc_final: 0.6426 (tpm170) REVERT: D 341 MET cc_start: 0.7999 (mmm) cc_final: 0.7779 (mmm) REVERT: D 460 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7466 (mp) REVERT: D 509 ASP cc_start: 0.6600 (OUTLIER) cc_final: 0.6159 (p0) REVERT: E 517 ARG cc_start: 0.7372 (ttm-80) cc_final: 0.7102 (ttm110) REVERT: F 333 MET cc_start: 0.7047 (mpp) cc_final: 0.6756 (mpp) REVERT: F 509 ASP cc_start: 0.5472 (OUTLIER) cc_final: 0.5121 (t0) outliers start: 55 outliers final: 41 residues processed: 180 average time/residue: 0.2269 time to fit residues: 60.6731 Evaluate side-chains 184 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 137 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 404 ARG Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 529 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Chi-restraints excluded: chain F residue 484 THR Chi-restraints excluded: chain F residue 509 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 0.5980 chunk 46 optimal weight: 0.2980 chunk 30 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 120 optimal weight: 0.0060 chunk 139 optimal weight: 8.9990 chunk 146 optimal weight: 4.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13029 Z= 0.167 Angle : 0.524 6.686 17574 Z= 0.261 Chirality : 0.042 0.155 2002 Planarity : 0.002 0.039 2166 Dihedral : 14.957 176.566 1929 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.55 % Allowed : 15.32 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.21), residues: 1556 helix: 0.36 (0.24), residues: 505 sheet: -0.55 (0.30), residues: 312 loop : -1.88 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 541 HIS 0.002 0.001 HIS B 357 PHE 0.029 0.001 PHE C 321 TYR 0.012 0.001 TYR A 547 ARG 0.003 0.000 ARG E 517 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 142 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 404 ARG cc_start: 0.4408 (OUTLIER) cc_final: 0.3902 (pmt100) REVERT: A 460 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7455 (tp) REVERT: A 473 LYS cc_start: 0.3555 (ptmt) cc_final: 0.3083 (ttmt) REVERT: A 542 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6724 (pp) REVERT: C 370 ARG cc_start: 0.6884 (mtm180) cc_final: 0.6352 (tpm170) REVERT: C 446 MET cc_start: 0.7330 (ttt) cc_final: 0.7121 (tpp) REVERT: C 494 GLN cc_start: 0.6824 (mt0) cc_final: 0.6446 (mt0) REVERT: D 341 MET cc_start: 0.8007 (mmm) cc_final: 0.7770 (mmm) REVERT: D 460 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7374 (mp) REVERT: D 509 ASP cc_start: 0.6861 (OUTLIER) cc_final: 0.6467 (p0) REVERT: E 517 ARG cc_start: 0.7284 (ttm-80) cc_final: 0.7018 (ttm110) REVERT: F 333 MET cc_start: 0.7020 (mpp) cc_final: 0.6737 (mpp) outliers start: 48 outliers final: 37 residues processed: 179 average time/residue: 0.2346 time to fit residues: 61.7708 Evaluate side-chains 182 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 140 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 404 ARG Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 529 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Chi-restraints excluded: chain F residue 484 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 129 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 151 optimal weight: 0.0570 overall best weight: 1.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13029 Z= 0.224 Angle : 0.572 6.726 17574 Z= 0.284 Chirality : 0.043 0.164 2002 Planarity : 0.003 0.045 2166 Dihedral : 15.120 176.100 1929 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.55 % Allowed : 15.25 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.21), residues: 1556 helix: 0.21 (0.24), residues: 518 sheet: -0.65 (0.30), residues: 312 loop : -1.94 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 541 HIS 0.003 0.001 HIS A 392 PHE 0.028 0.002 PHE C 321 TYR 0.012 0.001 TYR A 547 ARG 0.003 0.000 ARG E 517 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 142 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 328 GLN cc_start: 0.6507 (mm-40) cc_final: 0.6252 (mp10) REVERT: A 404 ARG cc_start: 0.4429 (OUTLIER) cc_final: 0.3882 (pmt100) REVERT: A 460 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7358 (tp) REVERT: A 473 LYS cc_start: 0.3562 (ptmt) cc_final: 0.2764 (ttmt) REVERT: A 542 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6829 (pp) REVERT: C 370 ARG cc_start: 0.6862 (mtm180) cc_final: 0.6381 (tpm170) REVERT: C 494 GLN cc_start: 0.6825 (mt0) cc_final: 0.6507 (mt0) REVERT: D 341 MET cc_start: 0.8045 (mmm) cc_final: 0.7824 (mmm) REVERT: D 460 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7429 (mp) REVERT: D 509 ASP cc_start: 0.6860 (OUTLIER) cc_final: 0.6440 (p0) REVERT: E 517 ARG cc_start: 0.7331 (ttm-80) cc_final: 0.7062 (ttm110) REVERT: F 333 MET cc_start: 0.7037 (mpp) cc_final: 0.6799 (mpp) outliers start: 48 outliers final: 37 residues processed: 180 average time/residue: 0.2280 time to fit residues: 61.1348 Evaluate side-chains 180 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 138 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 ARG Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 529 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Chi-restraints excluded: chain F residue 484 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 126 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 ASN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13029 Z= 0.179 Angle : 0.535 6.981 17574 Z= 0.266 Chirality : 0.042 0.156 2002 Planarity : 0.003 0.095 2166 Dihedral : 14.921 175.527 1929 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.48 % Allowed : 15.69 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.21), residues: 1556 helix: 0.49 (0.24), residues: 505 sheet: -0.57 (0.30), residues: 314 loop : -1.82 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 541 HIS 0.003 0.001 HIS B 357 PHE 0.027 0.001 PHE B 523 TYR 0.011 0.001 TYR A 547 ARG 0.004 0.000 ARG B 370 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 140 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 328 GLN cc_start: 0.6551 (mm-40) cc_final: 0.6301 (mp10) REVERT: A 341 MET cc_start: 0.6016 (tpp) cc_final: 0.5741 (mmt) REVERT: A 404 ARG cc_start: 0.4376 (OUTLIER) cc_final: 0.3819 (pmt100) REVERT: A 460 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7511 (tp) REVERT: A 473 LYS cc_start: 0.3542 (ptmt) cc_final: 0.2943 (ttmt) REVERT: A 542 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6724 (pp) REVERT: B 368 LEU cc_start: 0.7825 (tp) cc_final: 0.7501 (tt) REVERT: C 370 ARG cc_start: 0.6825 (mtm180) cc_final: 0.6359 (tpm170) REVERT: C 494 GLN cc_start: 0.6823 (mt0) cc_final: 0.6455 (mt0) REVERT: D 341 MET cc_start: 0.7973 (mmm) cc_final: 0.7759 (mmm) REVERT: D 460 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7377 (mp) REVERT: D 509 ASP cc_start: 0.6811 (OUTLIER) cc_final: 0.6393 (p0) REVERT: E 517 ARG cc_start: 0.7304 (ttm-80) cc_final: 0.7051 (ttm110) outliers start: 47 outliers final: 38 residues processed: 177 average time/residue: 0.2342 time to fit residues: 61.3999 Evaluate side-chains 182 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 139 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 ARG Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 510 MET Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 529 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 458 VAL Chi-restraints excluded: chain F residue 481 VAL Chi-restraints excluded: chain F residue 484 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.154708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.139642 restraints weight = 20481.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.140560 restraints weight = 14122.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.141664 restraints weight = 11374.215| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13029 Z= 0.321 Angle : 0.661 7.692 17574 Z= 0.328 Chirality : 0.046 0.173 2002 Planarity : 0.004 0.085 2166 Dihedral : 15.467 177.573 1929 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 3.33 % Allowed : 15.91 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.21), residues: 1556 helix: -0.10 (0.23), residues: 524 sheet: -0.75 (0.30), residues: 310 loop : -2.08 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 541 HIS 0.005 0.001 HIS A 392 PHE 0.030 0.002 PHE C 321 TYR 0.013 0.002 TYR E 411 ARG 0.005 0.001 ARG B 370 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2387.03 seconds wall clock time: 44 minutes 16.43 seconds (2656.43 seconds total)