Starting phenix.real_space_refine (version: dev) on Tue Apr 5 19:44:26 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7y_9001/04_2022/6e7y_9001_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7y_9001/04_2022/6e7y_9001.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7y_9001/04_2022/6e7y_9001_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7y_9001/04_2022/6e7y_9001_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7y_9001/04_2022/6e7y_9001_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7y_9001/04_2022/6e7y_9001.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7y_9001/04_2022/6e7y_9001.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7y_9001/04_2022/6e7y_9001_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e7y_9001/04_2022/6e7y_9001_updated.pdb" } resolution = 3.57 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= -0.044 sd= 0.457 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 43": "NH1" <-> "NH2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 61": "NH1" <-> "NH2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B ARG 322": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 61": "NH1" <-> "NH2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C ARG 322": "NH1" <-> "NH2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 61": "NH1" <-> "NH2" Residue "D ARG 168": "NH1" <-> "NH2" Residue "D ARG 322": "NH1" <-> "NH2" Residue "D ARG 336": "NH1" <-> "NH2" Residue "D ARG 338": "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: 15508 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3830 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 14, 'TRANS': 460} Chain breaks: 1 Chain: "B" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3830 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 14, 'TRANS': 460} Chain breaks: 1 Chain: "C" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3830 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 14, 'TRANS': 460} Chain breaks: 1 Chain: "D" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3830 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 14, 'TRANS': 460} Chain breaks: 1 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.79, per 1000 atoms: 0.57 Number of scatterers: 15508 At special positions: 0 Unit cell: (126.26, 125.19, 114.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 12 15.00 O 2732 8.00 N 2560 7.00 C 10104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 253 " - pdb=" SG CYS A 284 " distance=2.04 Simple disulfide: pdb=" SG CYS B 166 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 253 " - pdb=" SG CYS B 284 " distance=2.04 Simple disulfide: pdb=" SG CYS C 166 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 284 " distance=2.04 Simple disulfide: pdb=" SG CYS D 166 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 253 " - pdb=" SG CYS D 284 " distance=2.04 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: 6.15 Conformation dependent library (CDL) restraints added in 2.4 seconds 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3584 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 8 sheets defined 46.5% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 45 through 48 No H-bonds generated for 'chain 'A' and resid 45 through 48' Processing helix chain 'A' and resid 52 through 58 removed outlier: 4.240A pdb=" N PHE A 56 " --> pdb=" O CYS A 53 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A 57 " --> pdb=" O ASP A 54 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A 58 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 92 removed outlier: 3.686A pdb=" N LEU A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A 77 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 105 removed outlier: 3.783A pdb=" N ILE A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.914A pdb=" N TYR A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 142 No H-bonds generated for 'chain 'A' and resid 139 through 142' Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 302 through 333 removed outlier: 3.565A pdb=" N ILE A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE A 333 " --> pdb=" O GLU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 373 removed outlier: 3.637A pdb=" N THR A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A 370 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N MET A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 406 removed outlier: 3.778A pdb=" N ILE A 388 " --> pdb=" O ASP A 384 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE A 402 " --> pdb=" O TRP A 398 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARG A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 446 removed outlier: 3.647A pdb=" N THR A 417 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 419 " --> pdb=" O ILE A 415 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Proline residue: A 423 - end of helix removed outlier: 3.582A pdb=" N CYS A 430 " --> pdb=" O MET A 426 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL A 434 " --> pdb=" O CYS A 430 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE A 435 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS A 440 " --> pdb=" O TYR A 436 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 446 " --> pdb=" O CYS A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 463 removed outlier: 3.557A pdb=" N SER A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 483 removed outlier: 3.731A pdb=" N GLN A 481 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA A 482 " --> pdb=" O ALA A 478 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLN A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 500 removed outlier: 3.682A pdb=" N LEU A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 519 removed outlier: 3.790A pdb=" N PHE A 513 " --> pdb=" O VAL A 509 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A 514 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 517 " --> pdb=" O PHE A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 524 No H-bonds generated for 'chain 'A' and resid 522 through 524' Processing helix chain 'B' and resid 45 through 48 No H-bonds generated for 'chain 'B' and resid 45 through 48' Processing helix chain 'B' and resid 52 through 58 removed outlier: 4.239A pdb=" N PHE B 56 " --> pdb=" O CYS B 53 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG B 57 " --> pdb=" O ASP B 54 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA B 58 " --> pdb=" O LYS B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 92 removed outlier: 3.685A pdb=" N LEU B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR B 77 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B 90 " --> pdb=" O SER B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 105 removed outlier: 3.783A pdb=" N ILE B 99 " --> pdb=" O GLU B 95 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA B 100 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 134 removed outlier: 3.914A pdb=" N TYR B 126 " --> pdb=" O ARG B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 142 No H-bonds generated for 'chain 'B' and resid 139 through 142' Processing helix chain 'B' and resid 295 through 297 No H-bonds generated for 'chain 'B' and resid 295 through 297' Processing helix chain 'B' and resid 302 through 333 removed outlier: 3.565A pdb=" N ILE B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 324 " --> pdb=" O LEU B 320 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN B 327 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN B 328 " --> pdb=" O PHE B 324 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 373 removed outlier: 3.637A pdb=" N THR B 360 " --> pdb=" O ILE B 356 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE B 370 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET B 371 " --> pdb=" O SER B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 406 removed outlier: 3.779A pdb=" N ILE B 388 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL B 401 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE B 402 " --> pdb=" O TRP B 398 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARG B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR B 404 " --> pdb=" O GLY B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 446 removed outlier: 3.648A pdb=" N THR B 417 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 419 " --> pdb=" O ILE B 415 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Proline residue: B 423 - end of helix removed outlier: 3.582A pdb=" N CYS B 430 " --> pdb=" O MET B 426 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL B 434 " --> pdb=" O CYS B 430 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE B 435 " --> pdb=" O CYS B 431 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS B 440 " --> pdb=" O TYR B 436 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B 446 " --> pdb=" O CYS B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 463 removed outlier: 3.559A pdb=" N SER B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 removed outlier: 3.731A pdb=" N GLN B 481 " --> pdb=" O PHE B 477 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA B 482 " --> pdb=" O ALA B 478 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLN B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 500 removed outlier: 3.682A pdb=" N LEU B 492 " --> pdb=" O SER B 488 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 519 removed outlier: 3.790A pdb=" N PHE B 513 " --> pdb=" O VAL B 509 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE B 514 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 515 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE B 517 " --> pdb=" O PHE B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 524 No H-bonds generated for 'chain 'B' and resid 522 through 524' Processing helix chain 'C' and resid 45 through 48 No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'C' and resid 52 through 58 removed outlier: 4.239A pdb=" N PHE C 56 " --> pdb=" O CYS C 53 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG C 57 " --> pdb=" O ASP C 54 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA C 58 " --> pdb=" O LYS C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 92 removed outlier: 3.685A pdb=" N LEU C 74 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 77 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL C 78 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C 90 " --> pdb=" O SER C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 105 removed outlier: 3.783A pdb=" N ILE C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA C 100 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 134 removed outlier: 3.914A pdb=" N TYR C 126 " --> pdb=" O ARG C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 142 No H-bonds generated for 'chain 'C' and resid 139 through 142' Processing helix chain 'C' and resid 295 through 297 No H-bonds generated for 'chain 'C' and resid 295 through 297' Processing helix chain 'C' and resid 302 through 333 removed outlier: 3.566A pdb=" N ILE C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER C 310 " --> pdb=" O ILE C 306 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 315 " --> pdb=" O LEU C 311 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 326 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN C 327 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN C 328 " --> pdb=" O PHE C 324 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE C 333 " --> pdb=" O GLU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 373 removed outlier: 3.636A pdb=" N THR C 360 " --> pdb=" O ILE C 356 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C 368 " --> pdb=" O LEU C 364 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 370 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N MET C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 406 removed outlier: 3.778A pdb=" N ILE C 388 " --> pdb=" O ASP C 384 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 399 " --> pdb=" O LEU C 395 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY C 400 " --> pdb=" O LEU C 396 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL C 401 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE C 402 " --> pdb=" O TRP C 398 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARG C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 430 removed outlier: 3.648A pdb=" N THR C 417 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG C 419 " --> pdb=" O ILE C 415 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) Proline residue: C 423 - end of helix removed outlier: 3.582A pdb=" N CYS C 430 " --> pdb=" O MET C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 446 removed outlier: 3.587A pdb=" N LEU C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS C 440 " --> pdb=" O TYR C 436 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE C 445 " --> pdb=" O PHE C 441 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL C 446 " --> pdb=" O CYS C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 463 removed outlier: 3.558A pdb=" N SER C 461 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU C 462 " --> pdb=" O SER C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 483 removed outlier: 3.730A pdb=" N GLN C 481 " --> pdb=" O PHE C 477 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA C 482 " --> pdb=" O ALA C 478 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLN C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 500 removed outlier: 3.681A pdb=" N LEU C 492 " --> pdb=" O SER C 488 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 519 removed outlier: 3.790A pdb=" N PHE C 513 " --> pdb=" O VAL C 509 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE C 514 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA C 515 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 517 " --> pdb=" O PHE C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 524 No H-bonds generated for 'chain 'C' and resid 522 through 524' Processing helix chain 'D' and resid 45 through 48 No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'D' and resid 52 through 58 removed outlier: 4.239A pdb=" N PHE D 56 " --> pdb=" O CYS D 53 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG D 57 " --> pdb=" O ASP D 54 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA D 58 " --> pdb=" O LYS D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 92 removed outlier: 3.685A pdb=" N LEU D 74 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR D 77 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL D 78 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA D 90 " --> pdb=" O SER D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 105 removed outlier: 3.783A pdb=" N ILE D 99 " --> pdb=" O GLU D 95 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA D 100 " --> pdb=" O GLU D 96 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 104 " --> pdb=" O ALA D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 134 removed outlier: 3.913A pdb=" N TYR D 126 " --> pdb=" O ARG D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 142 No H-bonds generated for 'chain 'D' and resid 139 through 142' Processing helix chain 'D' and resid 295 through 297 No H-bonds generated for 'chain 'D' and resid 295 through 297' Processing helix chain 'D' and resid 302 through 333 removed outlier: 3.566A pdb=" N ILE D 306 " --> pdb=" O ASP D 302 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER D 310 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU D 315 " --> pdb=" O LEU D 311 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE D 324 " --> pdb=" O LEU D 320 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN D 327 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN D 328 " --> pdb=" O PHE D 324 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE D 333 " --> pdb=" O GLU D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 373 removed outlier: 3.636A pdb=" N THR D 360 " --> pdb=" O ILE D 356 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY D 368 " --> pdb=" O LEU D 364 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE D 370 " --> pdb=" O ILE D 366 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N MET D 371 " --> pdb=" O SER D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 406 removed outlier: 3.778A pdb=" N ILE D 388 " --> pdb=" O ASP D 384 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER D 393 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL D 399 " --> pdb=" O LEU D 395 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY D 400 " --> pdb=" O LEU D 396 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL D 401 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE D 402 " --> pdb=" O TRP D 398 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ARG D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR D 404 " --> pdb=" O GLY D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 430 removed outlier: 3.648A pdb=" N THR D 417 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG D 419 " --> pdb=" O ILE D 415 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Proline residue: D 423 - end of helix removed outlier: 3.583A pdb=" N CYS D 430 " --> pdb=" O MET D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 446 removed outlier: 3.587A pdb=" N LEU D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS D 440 " --> pdb=" O TYR D 436 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL D 446 " --> pdb=" O CYS D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 463 removed outlier: 3.558A pdb=" N SER D 461 " --> pdb=" O LEU D 457 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU D 462 " --> pdb=" O SER D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 483 removed outlier: 3.730A pdb=" N GLN D 481 " --> pdb=" O PHE D 477 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA D 482 " --> pdb=" O ALA D 478 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLN D 483 " --> pdb=" O ALA D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 500 removed outlier: 3.682A pdb=" N LEU D 492 " --> pdb=" O SER D 488 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 519 removed outlier: 3.790A pdb=" N PHE D 513 " --> pdb=" O VAL D 509 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D 515 " --> pdb=" O SER D 511 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE D 517 " --> pdb=" O PHE D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 524 No H-bonds generated for 'chain 'D' and resid 522 through 524' Processing sheet with id= A, first strand: chain 'A' and resid 193 through 195 removed outlier: 3.566A pdb=" N ASN A 230 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 235 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 274 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP A 263 " --> pdb=" O PRO A 272 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 238 through 240 removed outlier: 3.962A pdb=" N CYS A 253 " --> pdb=" O GLN A 282 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN A 282 " --> pdb=" O CYS A 253 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 193 through 195 removed outlier: 3.566A pdb=" N ASN B 230 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 235 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER B 274 " --> pdb=" O THR B 261 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP B 263 " --> pdb=" O PRO B 272 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 238 through 240 removed outlier: 3.961A pdb=" N CYS B 253 " --> pdb=" O GLN B 282 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN B 282 " --> pdb=" O CYS B 253 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 193 through 195 removed outlier: 3.567A pdb=" N ASN C 230 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE C 235 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER C 274 " --> pdb=" O THR C 261 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP C 263 " --> pdb=" O PRO C 272 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 238 through 240 removed outlier: 3.962A pdb=" N CYS C 253 " --> pdb=" O GLN C 282 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN C 282 " --> pdb=" O CYS C 253 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 193 through 195 removed outlier: 3.565A pdb=" N ASN D 230 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE D 235 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER D 274 " --> pdb=" O THR D 261 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP D 263 " --> pdb=" O PRO D 272 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 238 through 240 removed outlier: 3.962A pdb=" N CYS D 253 " --> pdb=" O GLN D 282 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN D 282 " --> pdb=" O CYS D 253 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1386 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: 4.71 Time building geometry restraints manager: 6.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4718 1.34 - 1.46: 3751 1.46 - 1.58: 7243 1.58 - 1.70: 36 1.70 - 1.82: 140 Bond restraints: 15888 Sorted by residual: bond pdb=" O52 PIO A 801 " pdb=" P5 PIO A 801 " ideal model delta sigma weight residual 1.510 1.610 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" O53 PIO C 801 " pdb=" P5 PIO C 801 " ideal model delta sigma weight residual 1.510 1.610 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" O52 PIO D 801 " pdb=" P5 PIO D 801 " ideal model delta sigma weight residual 1.510 1.610 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" O41 PIO C 801 " pdb=" P4 PIO C 801 " ideal model delta sigma weight residual 1.510 1.610 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" O52 PIO C 801 " pdb=" P5 PIO C 801 " ideal model delta sigma weight residual 1.510 1.610 -0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 15883 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.78: 360 106.78 - 113.59: 8691 113.59 - 120.39: 6216 120.39 - 127.19: 6150 127.19 - 134.00: 147 Bond angle restraints: 21564 Sorted by residual: angle pdb=" C PRO A 177 " pdb=" N ALA A 178 " pdb=" CA ALA A 178 " ideal model delta sigma weight residual 121.54 129.84 -8.30 1.91e+00 2.74e-01 1.89e+01 angle pdb=" C PRO B 177 " pdb=" N ALA B 178 " pdb=" CA ALA B 178 " ideal model delta sigma weight residual 121.54 129.81 -8.27 1.91e+00 2.74e-01 1.87e+01 angle pdb=" C PRO C 177 " pdb=" N ALA C 178 " pdb=" CA ALA C 178 " ideal model delta sigma weight residual 121.54 129.80 -8.26 1.91e+00 2.74e-01 1.87e+01 angle pdb=" C PRO D 177 " pdb=" N ALA D 178 " pdb=" CA ALA D 178 " ideal model delta sigma weight residual 121.54 129.78 -8.24 1.91e+00 2.74e-01 1.86e+01 angle pdb=" CA SER C 488 " pdb=" C SER C 488 " pdb=" N LEU C 489 " ideal model delta sigma weight residual 116.84 123.16 -6.32 1.71e+00 3.42e-01 1.37e+01 ... (remaining 21559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.17: 8640 14.17 - 28.34: 440 28.34 - 42.51: 148 42.51 - 56.68: 28 56.68 - 70.85: 12 Dihedral angle restraints: 9268 sinusoidal: 3704 harmonic: 5564 Sorted by residual: dihedral pdb=" CB CYS C 253 " pdb=" SG CYS C 253 " pdb=" SG CYS C 284 " pdb=" CB CYS C 284 " ideal model delta sinusoidal sigma weight residual 93.00 39.59 53.41 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CB CYS B 253 " pdb=" SG CYS B 253 " pdb=" SG CYS B 284 " pdb=" CB CYS B 284 " ideal model delta sinusoidal sigma weight residual 93.00 39.61 53.39 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CB CYS A 253 " pdb=" SG CYS A 253 " pdb=" SG CYS A 284 " pdb=" CB CYS A 284 " ideal model delta sinusoidal sigma weight residual 93.00 39.65 53.35 1 1.00e+01 1.00e-02 3.87e+01 ... (remaining 9265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1255 0.032 - 0.065: 803 0.065 - 0.097: 295 0.097 - 0.129: 81 0.129 - 0.162: 26 Chirality restraints: 2460 Sorted by residual: chirality pdb=" CB VAL C 289 " pdb=" CA VAL C 289 " pdb=" CG1 VAL C 289 " pdb=" CG2 VAL C 289 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CA LEU C 139 " pdb=" N LEU C 139 " pdb=" C LEU C 139 " pdb=" CB LEU C 139 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CA LEU D 139 " pdb=" N LEU D 139 " pdb=" C LEU D 139 " pdb=" CB LEU D 139 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 2457 not shown) Planarity restraints: 2656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 422 " 0.037 5.00e-02 4.00e+02 5.49e-02 4.83e+00 pdb=" N PRO D 423 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 423 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 423 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 422 " -0.037 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO B 423 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 423 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 423 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 422 " -0.037 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO C 423 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 423 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 423 " -0.031 5.00e-02 4.00e+02 ... (remaining 2653 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 5284 2.87 - 3.38: 13671 3.38 - 3.89: 22968 3.89 - 4.39: 26000 4.39 - 4.90: 44969 Nonbonded interactions: 112892 Sorted by model distance: nonbonded pdb=" O TYR B 439 " pdb=" OH TYR B 497 " model vdw 2.364 2.440 nonbonded pdb=" O TYR D 439 " pdb=" OH TYR D 497 " model vdw 2.364 2.440 nonbonded pdb=" O TYR A 439 " pdb=" OH TYR A 497 " model vdw 2.365 2.440 nonbonded pdb=" O TYR C 439 " pdb=" OH TYR C 497 " model vdw 2.365 2.440 nonbonded pdb=" NE2 GLN D 69 " pdb=" OG SER D 312 " model vdw 2.376 2.520 ... (remaining 112887 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 100 5.16 5 C 10104 2.51 5 N 2560 2.21 5 O 2732 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: 1.320 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: 6.710 Check model and map are aligned: 0.220 Convert atoms to be neutral: 0.130 Process input model: 41.000 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 : 0.005 0.100 15888 Z= 0.351 Angle : 0.813 8.434 21564 Z= 0.424 Chirality : 0.048 0.162 2460 Planarity : 0.006 0.055 2656 Dihedral : 10.178 70.849 5660 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer Outliers : 0.00 % 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: -5.91 (0.13), residues: 1884 helix: -4.54 (0.06), residues: 924 sheet: -1.60 (0.37), residues: 168 loop : -3.49 (0.17), residues: 792 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 502 time to evaluate : 1.866 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 502 average time/residue: 0.2660 time to fit residues: 195.6557 Evaluate side-chains 240 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.768 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 0.9980 chunk 142 optimal weight: 0.4980 chunk 79 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 97 ASN A 103 HIS A 234 HIS ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS A 292 HIS ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 ASN A 481 GLN B 69 GLN B 97 ASN B 103 HIS B 234 HIS ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 HIS B 292 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 ASN B 481 GLN C 69 GLN C 97 ASN C 103 HIS C 234 HIS ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 HIS C 292 HIS ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 ASN C 481 GLN D 69 GLN D 97 ASN D 103 HIS D 234 HIS ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 HIS D 292 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 ASN D 481 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 15888 Z= 0.260 Angle : 0.641 7.972 21564 Z= 0.321 Chirality : 0.043 0.146 2460 Planarity : 0.005 0.041 2656 Dihedral : 7.244 54.555 2156 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer Outliers : 3.13 % 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: -4.19 (0.16), residues: 1884 helix: -2.77 (0.13), residues: 912 sheet: -0.84 (0.40), residues: 188 loop : -3.18 (0.19), residues: 784 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 236 time to evaluate : 1.806 Fit side-chains outliers start: 53 outliers final: 38 residues processed: 265 average time/residue: 0.2122 time to fit residues: 90.3269 Evaluate side-chains 247 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 209 time to evaluate : 1.970 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.1384 time to fit residues: 12.4140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 142 optimal weight: 0.1980 chunk 116 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 171 optimal weight: 4.9990 chunk 184 optimal weight: 0.5980 chunk 152 optimal weight: 0.3980 chunk 169 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 137 optimal weight: 0.0050 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS A 327 GLN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 ASN ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 HIS C 327 GLN C 469 ASN D 135 GLN ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 15888 Z= 0.157 Angle : 0.569 12.039 21564 Z= 0.274 Chirality : 0.040 0.134 2460 Planarity : 0.004 0.036 2656 Dihedral : 6.665 52.386 2156 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer Outliers : 1.77 % 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: -3.09 (0.17), residues: 1884 helix: -1.60 (0.15), residues: 936 sheet: -0.60 (0.40), residues: 180 loop : -2.93 (0.20), residues: 768 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 232 time to evaluate : 1.805 Fit side-chains outliers start: 30 outliers final: 13 residues processed: 254 average time/residue: 0.2220 time to fit residues: 89.1518 Evaluate side-chains 208 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 195 time to evaluate : 1.760 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1305 time to fit residues: 5.6182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 181 optimal weight: 0.0270 chunk 89 optimal weight: 4.9990 chunk 162 optimal weight: 0.0030 chunk 48 optimal weight: 0.5980 overall best weight: 0.5250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 ASN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN D 469 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 15888 Z= 0.137 Angle : 0.545 11.464 21564 Z= 0.261 Chirality : 0.040 0.133 2460 Planarity : 0.003 0.033 2656 Dihedral : 6.222 53.053 2156 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 2.13 % 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: -2.25 (0.19), residues: 1884 helix: -0.75 (0.17), residues: 932 sheet: 0.24 (0.46), residues: 160 loop : -2.79 (0.20), residues: 792 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 213 time to evaluate : 1.871 Fit side-chains outliers start: 36 outliers final: 11 residues processed: 243 average time/residue: 0.2214 time to fit residues: 86.9357 Evaluate side-chains 195 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 184 time to evaluate : 1.889 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1327 time to fit residues: 5.3107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 0.0270 chunk 103 optimal weight: 3.9990 chunk 2 optimal weight: 0.0050 chunk 135 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.7454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 15888 Z= 0.152 Angle : 0.570 16.373 21564 Z= 0.271 Chirality : 0.041 0.231 2460 Planarity : 0.003 0.033 2656 Dihedral : 6.132 52.936 2156 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.87 (0.19), residues: 1884 helix: -0.37 (0.17), residues: 956 sheet: 0.32 (0.46), residues: 160 loop : -2.74 (0.21), residues: 768 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 196 time to evaluate : 1.901 Fit side-chains outliers start: 30 outliers final: 17 residues processed: 220 average time/residue: 0.2271 time to fit residues: 79.6076 Evaluate side-chains 202 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 185 time to evaluate : 1.801 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1346 time to fit residues: 6.8236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN C 167 GLN ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 15888 Z= 0.218 Angle : 0.613 18.840 21564 Z= 0.297 Chirality : 0.043 0.273 2460 Planarity : 0.003 0.035 2656 Dihedral : 6.226 52.495 2156 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.20), residues: 1884 helix: -0.07 (0.17), residues: 956 sheet: 0.33 (0.46), residues: 160 loop : -2.64 (0.21), residues: 768 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 196 time to evaluate : 1.688 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 209 average time/residue: 0.2345 time to fit residues: 75.6788 Evaluate side-chains 202 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 190 time to evaluate : 1.833 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1420 time to fit residues: 5.7277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 132 optimal weight: 0.0980 chunk 102 optimal weight: 0.8980 chunk 153 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 181 optimal weight: 0.0870 chunk 113 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 83 optimal weight: 0.3980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 327 GLN B 69 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 15888 Z= 0.123 Angle : 0.560 12.224 21564 Z= 0.265 Chirality : 0.040 0.233 2460 Planarity : 0.003 0.035 2656 Dihedral : 5.925 56.417 2156 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer Outliers : 0.47 % 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: -1.16 (0.20), residues: 1884 helix: 0.33 (0.17), residues: 952 sheet: 0.52 (0.47), residues: 160 loop : -2.52 (0.21), residues: 772 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 195 time to evaluate : 2.071 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 201 average time/residue: 0.2370 time to fit residues: 74.2012 Evaluate side-chains 189 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 186 time to evaluate : 1.753 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1302 time to fit residues: 3.1348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 123 optimal weight: 10.0000 chunk 89 optimal weight: 0.2980 chunk 16 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 15888 Z= 0.179 Angle : 0.611 16.767 21564 Z= 0.294 Chirality : 0.042 0.296 2460 Planarity : 0.003 0.033 2656 Dihedral : 6.027 55.970 2156 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.20), residues: 1884 helix: 0.65 (0.18), residues: 932 sheet: 0.44 (0.47), residues: 160 loop : -2.35 (0.21), residues: 792 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 191 time to evaluate : 1.677 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 198 average time/residue: 0.2598 time to fit residues: 79.4483 Evaluate side-chains 192 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 185 time to evaluate : 1.850 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1399 time to fit residues: 4.3615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 152 optimal weight: 0.0980 chunk 159 optimal weight: 1.9990 chunk 110 optimal weight: 0.0050 chunk 178 optimal weight: 0.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 15888 Z= 0.136 Angle : 0.573 12.706 21564 Z= 0.275 Chirality : 0.041 0.252 2460 Planarity : 0.003 0.033 2656 Dihedral : 5.861 58.394 2156 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 0.41 % 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: -0.69 (0.20), residues: 1884 helix: 0.78 (0.18), residues: 940 sheet: 0.37 (0.47), residues: 160 loop : -2.26 (0.21), residues: 784 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 194 time to evaluate : 1.621 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 199 average time/residue: 0.2386 time to fit residues: 74.4426 Evaluate side-chains 189 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 186 time to evaluate : 1.772 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1280 time to fit residues: 3.1405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 0.8980 chunk 84 optimal weight: 0.1980 chunk 124 optimal weight: 0.9980 chunk 187 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 118 optimal weight: 0.3980 chunk 158 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 469 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 15888 Z= 0.139 Angle : 0.572 12.737 21564 Z= 0.274 Chirality : 0.041 0.232 2460 Planarity : 0.003 0.034 2656 Dihedral : 5.783 59.533 2156 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.20), residues: 1884 helix: 0.92 (0.18), residues: 940 sheet: 0.48 (0.48), residues: 160 loop : -2.22 (0.21), residues: 784 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 194 time to evaluate : 1.954 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 195 average time/residue: 0.2438 time to fit residues: 75.2553 Evaluate side-chains 192 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 189 time to evaluate : 1.905 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1377 time to fit residues: 3.3633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 0.9990 chunk 137 optimal weight: 0.3980 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 149 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 153 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 469 ASN D 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.143763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.111491 restraints weight = 25894.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.113980 restraints weight = 15801.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.115623 restraints weight = 11810.457| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 15888 Z= 0.138 Angle : 0.562 12.809 21564 Z= 0.270 Chirality : 0.041 0.225 2460 Planarity : 0.003 0.033 2656 Dihedral : 5.731 58.936 2156 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer Outliers : 0.41 % 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: -0.54 (0.20), residues: 1884 helix: 0.93 (0.18), residues: 952 sheet: 0.47 (0.48), residues: 160 loop : -2.28 (0.21), residues: 772 =============================================================================== Job complete usr+sys time: 2733.11 seconds wall clock time: 50 minutes 56.49 seconds (3056.49 seconds total)