Starting phenix.real_space_refine (version: dev) on Tue Apr 5 10:57:51 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7n_0359/04_2022/6n7n_0359_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7n_0359/04_2022/6n7n_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_0359/04_2022/6n7n_0359.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7n_0359/04_2022/6n7n_0359.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7n_0359/04_2022/6n7n_0359_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7n_0359/04_2022/6n7n_0359_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4553/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: {'TTP': 1, ' MG': 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: {'TTP': 1, ' MG': 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: {'TTP': 1, ' MG': 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: {'TTP': 1, ' MG': 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: {'TTP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.92, per 1000 atoms: 0.69 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: 4.99 Conformation dependent library (CDL) restraints added in 2.0 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: 1.27 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: 3.46 Time building geometry restraints manager: 5.36 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.650 Check model and map are aligned: 0.230 Convert atoms to be neutral: 0.100 Process input model: 35.830 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 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 % 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 *********************** 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 : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 338 average time/residue: 0.2821 time to fit residues: 131.1256 Evaluate side-chains 173 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 1.479 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1069 time to fit residues: 2.2062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 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: 2.9990 chunk 144 optimal weight: 0.0670 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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 C 468 ASN 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: 0.6724 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 13029 Z= 0.126 Angle : 0.543 13.127 17574 Z= 0.268 Chirality : 0.042 0.142 2002 Planarity : 0.003 0.034 2166 Dihedral : 15.944 177.082 1929 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 2.07 % 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: -2.28 (0.20), residues: 1556 helix: -1.13 (0.21), residues: 524 sheet: -0.40 (0.30), residues: 321 loop : -2.33 (0.21), residues: 711 *********************** 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 233 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 205 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 16 residues processed: 220 average time/residue: 0.2254 time to fit residues: 73.4055 Evaluate side-chains 170 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 154 time to evaluate : 1.382 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1195 time to fit residues: 5.4763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 HIS B 444 ASN ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 HIS E 507 GLN ** F 343 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 13029 Z= 0.283 Angle : 0.662 8.281 17574 Z= 0.326 Chirality : 0.046 0.162 2002 Planarity : 0.004 0.080 2166 Dihedral : 16.065 178.795 1929 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.20), residues: 1556 helix: -0.77 (0.22), residues: 528 sheet: -0.56 (0.30), residues: 322 loop : -2.24 (0.21), residues: 706 *********************** 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 190 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 160 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 14 residues processed: 181 average time/residue: 0.2219 time to fit residues: 60.4150 Evaluate side-chains 156 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 1.485 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1153 time to fit residues: 5.0115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 16 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 127 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 HIS B 392 HIS ** 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: 0.7081 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.056 13029 Z= 0.407 Angle : 0.793 14.398 17574 Z= 0.390 Chirality : 0.049 0.183 2002 Planarity : 0.005 0.037 2166 Dihedral : 16.532 178.404 1929 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer Outliers : 3.03 % 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: -0.95 (0.22), residues: 507 sheet: -0.80 (0.30), residues: 310 loop : -2.25 (0.20), residues: 739 *********************** 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 189 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 148 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 25 residues processed: 178 average time/residue: 0.2131 time to fit residues: 57.7259 Evaluate side-chains 163 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 1.543 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1176 time to fit residues: 7.4500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 GLN ** 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: 0.6975 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.110 13029 Z= 0.196 Angle : 0.554 7.268 17574 Z= 0.276 Chirality : 0.043 0.145 2002 Planarity : 0.003 0.087 2166 Dihedral : 15.595 177.770 1929 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.21), residues: 1556 helix: -0.31 (0.23), residues: 518 sheet: -0.62 (0.30), residues: 303 loop : -2.09 (0.21), residues: 735 *********************** 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 166 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 150 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 3 residues processed: 165 average time/residue: 0.2366 time to fit residues: 58.1503 Evaluate side-chains 135 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 132 time to evaluate : 1.701 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1520 time to fit residues: 3.0586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 37 optimal weight: 0.0970 chunk 153 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 chunk 50 optimal weight: 0.0030 chunk 80 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 GLN C 388 ASN ** 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: 0.6944 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.063 13029 Z= 0.155 Angle : 0.558 17.049 17574 Z= 0.278 Chirality : 0.042 0.153 2002 Planarity : 0.002 0.026 2166 Dihedral : 15.049 174.297 1929 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 1.70 % 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: -1.41 (0.21), residues: 1556 helix: 0.15 (0.24), residues: 517 sheet: -0.61 (0.30), residues: 316 loop : -1.91 (0.22), residues: 723 *********************** 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 165 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 142 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 157 average time/residue: 0.2182 time to fit residues: 52.0735 Evaluate side-chains 146 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 133 time to evaluate : 1.608 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1198 time to fit residues: 5.0418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 6.9990 chunk 87 optimal weight: 0.3980 chunk 112 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 GLN ** 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: 0.7004 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.118 13029 Z= 0.235 Angle : 0.589 9.475 17574 Z= 0.291 Chirality : 0.043 0.193 2002 Planarity : 0.003 0.084 2166 Dihedral : 15.149 175.547 1929 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer Outliers : 1.26 % 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: -1.45 (0.21), residues: 1556 helix: 0.13 (0.23), residues: 517 sheet: -0.62 (0.30), residues: 314 loop : -1.93 (0.22), residues: 725 *********************** 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 151 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 6 residues processed: 147 average time/residue: 0.2339 time to fit residues: 51.9093 Evaluate side-chains 133 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 127 time to evaluate : 1.570 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1207 time to fit residues: 3.4716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 5.9990 chunk 46 optimal weight: 0.0170 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 14 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 146 optimal weight: 7.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- 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** B 328 GLN ** B 343 GLN ** 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: 0.6978 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.081 13029 Z= 0.192 Angle : 0.553 7.071 17574 Z= 0.273 Chirality : 0.042 0.175 2002 Planarity : 0.003 0.049 2166 Dihedral : 14.950 176.959 1929 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 0.81 % 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: -1.30 (0.21), residues: 1556 helix: 0.31 (0.24), residues: 510 sheet: -0.58 (0.30), residues: 316 loop : -1.85 (0.21), residues: 730 *********************** 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 146 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 1.508 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 144 average time/residue: 0.2185 time to fit residues: 47.9292 Evaluate side-chains 134 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 1.477 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1129 time to fit residues: 3.0755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 343 GLN ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.500 13029 Z= 0.453 Angle : 0.692 33.454 17574 Z= 0.369 Chirality : 0.043 0.172 2002 Planarity : 0.004 0.132 2166 Dihedral : 15.044 179.905 1929 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.21), residues: 1556 helix: 0.31 (0.24), residues: 511 sheet: -0.62 (0.30), residues: 316 loop : -1.85 (0.22), residues: 729 *********************** 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 139 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 1.543 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 135 average time/residue: 0.2440 time to fit residues: 48.9807 Evaluate side-chains 133 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 1.496 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1232 time to fit residues: 3.2947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 104 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 134 optimal weight: 8.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** 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: 0.7098 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.284 13029 Z= 0.455 Angle : 0.779 22.497 17574 Z= 0.397 Chirality : 0.048 0.196 2002 Planarity : 0.005 0.109 2166 Dihedral : 15.641 176.795 1929 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer Outliers : 0.37 % 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: -1.91 (0.20), residues: 1556 helix: -0.31 (0.22), residues: 513 sheet: -0.85 (0.29), residues: 310 loop : -2.16 (0.21), residues: 733 ********************** 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 136 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 1.639 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 135 average time/residue: 0.2420 time to fit residues: 49.0548 Evaluate side-chains 132 residues out of total 1354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 129 time to evaluate : 1.527 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1171 time to fit residues: 2.7667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 129 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 23 optimal weight: 0.0870 chunk 110 optimal weight: 0.0670 chunk 7 optimal weight: 5.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.159949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.144159 restraints weight = 20143.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.146237 restraints weight = 12987.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.147667 restraints weight = 9358.777| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.269 13029 Z= 0.272 Angle : 0.610 17.210 17574 Z= 0.319 Chirality : 0.042 0.160 2002 Planarity : 0.004 0.119 2166 Dihedral : 14.906 175.704 1929 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.21), residues: 1556 helix: 0.45 (0.24), residues: 506 sheet: -0.68 (0.30), residues: 309 loop : -1.88 (0.22), residues: 741 =============================================================================== Job complete usr+sys time: 2209.60 seconds wall clock time: 41 minutes 23.43 seconds (2483.43 seconds total)