Starting phenix.real_space_refine on Fri Jun 28 07:52:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy4_37915/06_2024/8wy4_37915_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy4_37915/06_2024/8wy4_37915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy4_37915/06_2024/8wy4_37915.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy4_37915/06_2024/8wy4_37915.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy4_37915/06_2024/8wy4_37915_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy4_37915/06_2024/8wy4_37915_updated.pdb" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 48 5.16 5 C 9504 2.51 5 N 2448 2.21 5 O 2852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 14864 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3685 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 8, 'TRANS': 442} Chain breaks: 1 Chain: "B" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3685 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 8, 'TRANS': 442} Chain breaks: 1 Chain: "D" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3685 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 8, 'TRANS': 442} Chain breaks: 1 Chain: "C" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3685 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 8, 'TRANS': 442} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.77, per 1000 atoms: 0.59 Number of scatterers: 14864 At special positions: 0 Unit cell: (115.08, 190.68, 68.04, 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 48 16.00 P 12 15.00 O 2852 8.00 N 2448 7.00 C 9504 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.11 Conformation dependent library (CDL) restraints added in 2.6 seconds 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3416 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 16 sheets defined 36.6% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 32 through 46 removed outlier: 3.960A pdb=" N LEU A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 removed outlier: 4.897A pdb=" N PHE A 53 " --> pdb=" O GLU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 296 through 307 Processing helix chain 'A' and resid 322 through 325 Processing helix chain 'A' and resid 359 through 371 removed outlier: 3.784A pdb=" N SER A 368 " --> pdb=" O LYS A 364 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 394 Processing helix chain 'A' and resid 398 through 401 No H-bonds generated for 'chain 'A' and resid 398 through 401' Processing helix chain 'A' and resid 414 through 422 removed outlier: 3.630A pdb=" N THR A 419 " --> pdb=" O HIS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 456 removed outlier: 4.019A pdb=" N CYS A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 492 Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'A' and resid 513 through 527 removed outlier: 3.592A pdb=" N SER A 518 " --> pdb=" O ASN A 514 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLU A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N SER A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 539 Processing helix chain 'A' and resid 541 through 550 Processing helix chain 'A' and resid 554 through 561 Processing helix chain 'A' and resid 567 through 573 Processing helix chain 'B' and resid 32 through 46 removed outlier: 3.960A pdb=" N LEU B 39 " --> pdb=" O LYS B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 53 removed outlier: 4.897A pdb=" N PHE B 53 " --> pdb=" O GLU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 90 Processing helix chain 'B' and resid 296 through 307 Processing helix chain 'B' and resid 322 through 325 Processing helix chain 'B' and resid 359 through 371 removed outlier: 3.784A pdb=" N SER B 368 " --> pdb=" O LYS B 364 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE B 371 " --> pdb=" O SER B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 394 Processing helix chain 'B' and resid 398 through 401 No H-bonds generated for 'chain 'B' and resid 398 through 401' Processing helix chain 'B' and resid 414 through 422 removed outlier: 3.630A pdb=" N THR B 419 " --> pdb=" O HIS B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 456 removed outlier: 4.019A pdb=" N CYS B 453 " --> pdb=" O GLY B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 492 Processing helix chain 'B' and resid 494 through 502 Processing helix chain 'B' and resid 513 through 527 removed outlier: 3.592A pdb=" N SER B 518 " --> pdb=" O ASN B 514 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA B 519 " --> pdb=" O ASP B 515 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLU B 522 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N SER B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 539 Processing helix chain 'B' and resid 541 through 550 Processing helix chain 'B' and resid 554 through 561 Processing helix chain 'B' and resid 567 through 573 Processing helix chain 'D' and resid 32 through 46 removed outlier: 3.960A pdb=" N LEU D 39 " --> pdb=" O LYS D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 removed outlier: 4.897A pdb=" N PHE D 53 " --> pdb=" O GLU D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 296 through 307 Processing helix chain 'D' and resid 322 through 325 Processing helix chain 'D' and resid 359 through 371 removed outlier: 3.784A pdb=" N SER D 368 " --> pdb=" O LYS D 364 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE D 371 " --> pdb=" O SER D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 394 Processing helix chain 'D' and resid 398 through 401 No H-bonds generated for 'chain 'D' and resid 398 through 401' Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.629A pdb=" N THR D 419 " --> pdb=" O HIS D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 456 removed outlier: 4.020A pdb=" N CYS D 453 " --> pdb=" O GLY D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 492 Processing helix chain 'D' and resid 494 through 502 Processing helix chain 'D' and resid 513 through 527 removed outlier: 3.592A pdb=" N SER D 518 " --> pdb=" O ASN D 514 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA D 519 " --> pdb=" O ASP D 515 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLU D 522 " --> pdb=" O SER D 518 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N SER D 523 " --> pdb=" O ALA D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 539 Processing helix chain 'D' and resid 541 through 550 Processing helix chain 'D' and resid 554 through 561 Processing helix chain 'D' and resid 567 through 573 Processing helix chain 'C' and resid 32 through 46 removed outlier: 3.959A pdb=" N LEU C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 53 removed outlier: 4.897A pdb=" N PHE C 53 " --> pdb=" O GLU C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 90 Processing helix chain 'C' and resid 296 through 307 Processing helix chain 'C' and resid 322 through 325 Processing helix chain 'C' and resid 359 through 371 removed outlier: 3.784A pdb=" N SER C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 394 Processing helix chain 'C' and resid 398 through 401 No H-bonds generated for 'chain 'C' and resid 398 through 401' Processing helix chain 'C' and resid 414 through 422 removed outlier: 3.630A pdb=" N THR C 419 " --> pdb=" O HIS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 456 removed outlier: 4.019A pdb=" N CYS C 453 " --> pdb=" O GLY C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 492 Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'C' and resid 513 through 527 removed outlier: 3.592A pdb=" N SER C 518 " --> pdb=" O ASN C 514 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA C 519 " --> pdb=" O ASP C 515 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLU C 522 " --> pdb=" O SER C 518 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N SER C 523 " --> pdb=" O ALA C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 539 Processing helix chain 'C' and resid 541 through 550 Processing helix chain 'C' and resid 554 through 561 Processing helix chain 'C' and resid 567 through 573 Processing sheet with id= A, first strand: chain 'A' and resid 17 through 20 removed outlier: 3.533A pdb=" N ILE A 8 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN A 5 " --> pdb=" O THR A 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY A 127 " --> pdb=" O TYR A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 344 through 349 removed outlier: 3.707A pdb=" N THR A 319 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLY A 29 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N PHE A 316 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR A 285 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N SER A 318 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE A 287 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 403 through 407 removed outlier: 6.723A pdb=" N ARG A 374 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU A 406 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU A 376 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR A 426 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LEU A 377 " --> pdb=" O THR A 426 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE A 428 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 435 through 437 Processing sheet with id= E, first strand: chain 'B' and resid 17 through 20 removed outlier: 3.533A pdb=" N ILE B 8 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN B 5 " --> pdb=" O THR B 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY B 127 " --> pdb=" O TYR B 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 344 through 349 removed outlier: 3.708A pdb=" N THR B 319 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLY B 29 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N PHE B 316 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR B 285 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N SER B 318 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE B 287 " --> pdb=" O SER B 318 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 403 through 407 removed outlier: 6.724A pdb=" N ARG B 374 " --> pdb=" O PHE B 404 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU B 406 " --> pdb=" O ARG B 374 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU B 376 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR B 426 " --> pdb=" O VAL B 375 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU B 377 " --> pdb=" O THR B 426 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE B 428 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 435 through 437 Processing sheet with id= I, first strand: chain 'D' and resid 17 through 20 removed outlier: 3.532A pdb=" N ILE D 8 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN D 5 " --> pdb=" O THR D 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY D 127 " --> pdb=" O TYR D 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 344 through 349 removed outlier: 3.708A pdb=" N THR D 319 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLY D 29 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N PHE D 316 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR D 285 " --> pdb=" O PHE D 316 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N SER D 318 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE D 287 " --> pdb=" O SER D 318 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 403 through 407 removed outlier: 6.723A pdb=" N ARG D 374 " --> pdb=" O PHE D 404 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU D 406 " --> pdb=" O ARG D 374 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU D 376 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR D 426 " --> pdb=" O VAL D 375 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU D 377 " --> pdb=" O THR D 426 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE D 428 " --> pdb=" O LEU D 377 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 435 through 437 Processing sheet with id= M, first strand: chain 'C' and resid 17 through 20 removed outlier: 3.534A pdb=" N ILE C 8 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN C 5 " --> pdb=" O THR C 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY C 127 " --> pdb=" O TYR C 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 344 through 349 removed outlier: 3.707A pdb=" N THR C 319 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLY C 29 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N PHE C 316 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR C 285 " --> pdb=" O PHE C 316 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N SER C 318 " --> pdb=" O TYR C 285 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE C 287 " --> pdb=" O SER C 318 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 403 through 407 removed outlier: 6.723A pdb=" N ARG C 374 " --> pdb=" O PHE C 404 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU C 406 " --> pdb=" O ARG C 374 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU C 376 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR C 426 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU C 377 " --> pdb=" O THR C 426 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE C 428 " --> pdb=" O LEU C 377 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 435 through 437 512 hydrogen bonds defined for protein. 1464 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: 4.75 Time building geometry restraints manager: 5.65 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: 4400 1.34 - 1.46: 2405 1.46 - 1.57: 8223 1.57 - 1.69: 20 1.69 - 1.81: 76 Bond restraints: 15124 Sorted by residual: bond pdb=" N GLU B 503 " pdb=" CA GLU B 503 " ideal model delta sigma weight residual 1.457 1.486 -0.029 6.40e-03 2.44e+04 2.06e+01 bond pdb=" N GLU A 503 " pdb=" CA GLU A 503 " ideal model delta sigma weight residual 1.457 1.486 -0.029 6.40e-03 2.44e+04 2.06e+01 bond pdb=" N GLU C 503 " pdb=" CA GLU C 503 " ideal model delta sigma weight residual 1.457 1.486 -0.029 6.40e-03 2.44e+04 2.06e+01 bond pdb=" N GLU D 503 " pdb=" CA GLU D 503 " ideal model delta sigma weight residual 1.457 1.485 -0.028 6.40e-03 2.44e+04 1.94e+01 bond pdb=" N VAL A 497 " pdb=" CA VAL A 497 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.19e-02 7.06e+03 8.75e+00 ... (remaining 15119 not shown) Histogram of bond angle deviations from ideal: 99.73 - 107.77: 523 107.77 - 115.81: 9122 115.81 - 123.85: 10321 123.85 - 131.88: 362 131.88 - 139.92: 16 Bond angle restraints: 20344 Sorted by residual: angle pdb=" C LYS A 116 " pdb=" N GLU A 117 " pdb=" CA GLU A 117 " ideal model delta sigma weight residual 121.54 130.91 -9.37 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C LYS D 116 " pdb=" N GLU D 117 " pdb=" CA GLU D 117 " ideal model delta sigma weight residual 121.54 130.87 -9.33 1.91e+00 2.74e-01 2.39e+01 angle pdb=" C LYS B 116 " pdb=" N GLU B 117 " pdb=" CA GLU B 117 " ideal model delta sigma weight residual 121.54 130.87 -9.33 1.91e+00 2.74e-01 2.39e+01 angle pdb=" C LYS C 116 " pdb=" N GLU C 117 " pdb=" CA GLU C 117 " ideal model delta sigma weight residual 121.54 130.85 -9.31 1.91e+00 2.74e-01 2.38e+01 angle pdb=" N ASP B 22 " pdb=" CA ASP B 22 " pdb=" C ASP B 22 " ideal model delta sigma weight residual 108.45 102.61 5.84 1.26e+00 6.30e-01 2.15e+01 ... (remaining 20339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 8132 17.18 - 34.36: 900 34.36 - 51.55: 200 51.55 - 68.73: 36 68.73 - 85.91: 20 Dihedral angle restraints: 9288 sinusoidal: 3992 harmonic: 5296 Sorted by residual: dihedral pdb=" CA ASP B 76 " pdb=" C ASP B 76 " pdb=" N LEU B 77 " pdb=" CA LEU B 77 " ideal model delta harmonic sigma weight residual -180.00 -153.37 -26.63 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA ASP C 76 " pdb=" C ASP C 76 " pdb=" N LEU C 77 " pdb=" CA LEU C 77 " ideal model delta harmonic sigma weight residual 180.00 -153.39 -26.61 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA ASP D 76 " pdb=" C ASP D 76 " pdb=" N LEU D 77 " pdb=" CA LEU D 77 " ideal model delta harmonic sigma weight residual -180.00 -153.41 -26.59 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 9285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1641 0.057 - 0.114: 416 0.114 - 0.171: 168 0.171 - 0.228: 23 0.228 - 0.285: 8 Chirality restraints: 2256 Sorted by residual: chirality pdb=" CB ILE C 6 " pdb=" CA ILE C 6 " pdb=" CG1 ILE C 6 " pdb=" CG2 ILE C 6 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB ILE D 6 " pdb=" CA ILE D 6 " pdb=" CG1 ILE D 6 " pdb=" CG2 ILE D 6 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB ILE B 6 " pdb=" CA ILE B 6 " pdb=" CG1 ILE B 6 " pdb=" CG2 ILE B 6 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 2253 not shown) Planarity restraints: 2564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 9 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.47e+00 pdb=" C LYS B 9 " 0.037 2.00e-02 2.50e+03 pdb=" O LYS B 9 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN B 10 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 9 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C LYS C 9 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS C 9 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN C 10 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 9 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.28e+00 pdb=" C LYS A 9 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS A 9 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN A 10 " 0.012 2.00e-02 2.50e+03 ... (remaining 2561 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 4846 2.87 - 3.38: 12088 3.38 - 3.89: 24563 3.89 - 4.39: 27486 4.39 - 4.90: 47873 Nonbonded interactions: 116856 Sorted by model distance: nonbonded pdb=" OG SER D 4 " pdb=" OD2 ASP D 76 " model vdw 2.368 2.440 nonbonded pdb=" OG SER B 4 " pdb=" OD2 ASP B 76 " model vdw 2.369 2.440 nonbonded pdb=" OG SER C 4 " pdb=" OD2 ASP C 76 " model vdw 2.369 2.440 nonbonded pdb=" OG SER A 4 " pdb=" OD2 ASP A 76 " model vdw 2.370 2.440 nonbonded pdb=" OG1 THR A 339 " pdb=" O LYS A 341 " model vdw 2.378 2.440 ... (remaining 116851 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.320 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: 11.220 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 40.360 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 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 0.056 15124 Z= 0.387 Angle : 1.057 12.055 20344 Z= 0.595 Chirality : 0.061 0.285 2256 Planarity : 0.006 0.045 2564 Dihedral : 15.320 85.911 5872 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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 (0.16), residues: 1788 helix: -3.71 (0.09), residues: 732 sheet: 0.05 (0.27), residues: 392 loop : -1.83 (0.20), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.006 TRP D 126 HIS 0.006 0.002 HIS A 415 PHE 0.031 0.002 PHE A 315 TYR 0.022 0.002 TYR A 326 ARG 0.016 0.001 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.658 Fit side-chains REVERT: A 141 ASN cc_start: 0.6872 (m-40) cc_final: 0.6356 (m-40) REVERT: A 422 ASP cc_start: 0.7603 (m-30) cc_final: 0.7394 (t0) REVERT: A 474 LYS cc_start: 0.7773 (mttt) cc_final: 0.7516 (mttt) REVERT: B 141 ASN cc_start: 0.6822 (m-40) cc_final: 0.6322 (m-40) REVERT: B 422 ASP cc_start: 0.7606 (m-30) cc_final: 0.7400 (t0) REVERT: D 141 ASN cc_start: 0.6873 (m-40) cc_final: 0.6357 (m-40) REVERT: D 422 ASP cc_start: 0.7605 (m-30) cc_final: 0.7395 (t0) REVERT: D 474 LYS cc_start: 0.7753 (mttt) cc_final: 0.7523 (mttt) REVERT: C 141 ASN cc_start: 0.6874 (m-40) cc_final: 0.6357 (m-40) REVERT: C 422 ASP cc_start: 0.7604 (m-30) cc_final: 0.7387 (t0) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 1.2996 time to fit residues: 383.8776 Evaluate side-chains 167 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.8980 chunk 136 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15124 Z= 0.203 Angle : 0.606 9.034 20344 Z= 0.324 Chirality : 0.046 0.169 2256 Planarity : 0.004 0.027 2564 Dihedral : 8.443 51.711 2076 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.23 % Allowed : 8.70 % Favored : 89.07 % 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: -1.73 (0.18), residues: 1788 helix: -1.43 (0.16), residues: 736 sheet: 0.05 (0.27), residues: 404 loop : -1.36 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.002 TRP C 126 HIS 0.005 0.001 HIS D 415 PHE 0.011 0.002 PHE A 371 TYR 0.016 0.001 TYR B 314 ARG 0.008 0.001 ARG D 332 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 186 time to evaluate : 1.342 Fit side-chains REVERT: A 1 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.6609 (tmt) REVERT: A 285 TYR cc_start: 0.7823 (m-80) cc_final: 0.7536 (m-80) REVERT: A 414 ASN cc_start: 0.7087 (p0) cc_final: 0.6785 (t160) REVERT: A 422 ASP cc_start: 0.7739 (m-30) cc_final: 0.7520 (t0) REVERT: B 59 ASP cc_start: 0.7648 (OUTLIER) cc_final: 0.7355 (p0) REVERT: B 285 TYR cc_start: 0.7823 (m-80) cc_final: 0.7532 (m-80) REVERT: B 422 ASP cc_start: 0.7740 (m-30) cc_final: 0.7539 (t0) REVERT: D 1 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.6634 (tmt) REVERT: D 285 TYR cc_start: 0.7823 (m-80) cc_final: 0.7535 (m-80) REVERT: D 414 ASN cc_start: 0.7088 (p0) cc_final: 0.6784 (t160) REVERT: D 422 ASP cc_start: 0.7744 (m-30) cc_final: 0.7521 (t0) REVERT: C 1 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.6621 (tmt) REVERT: C 285 TYR cc_start: 0.7825 (m-80) cc_final: 0.7579 (m-80) REVERT: C 414 ASN cc_start: 0.7079 (p0) cc_final: 0.6774 (t160) REVERT: C 422 ASP cc_start: 0.7744 (m-30) cc_final: 0.7520 (t0) outliers start: 37 outliers final: 16 residues processed: 198 average time/residue: 1.2691 time to fit residues: 276.6891 Evaluate side-chains 182 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 348 MET Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 176 optimal weight: 0.5980 chunk 145 optimal weight: 0.7980 chunk 162 optimal weight: 0.0470 chunk 55 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS B 415 HIS D 415 HIS C 415 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15124 Z= 0.164 Angle : 0.550 10.031 20344 Z= 0.291 Chirality : 0.044 0.151 2256 Planarity : 0.003 0.029 2564 Dihedral : 7.419 51.135 2076 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.93 % Allowed : 12.26 % Favored : 85.81 % 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: -0.87 (0.19), residues: 1788 helix: -0.26 (0.18), residues: 724 sheet: 0.07 (0.28), residues: 404 loop : -1.19 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 126 HIS 0.005 0.001 HIS A 415 PHE 0.010 0.001 PHE A 315 TYR 0.015 0.001 TYR C 314 ARG 0.006 0.001 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 180 time to evaluate : 1.637 Fit side-chains REVERT: A 139 ARG cc_start: 0.6604 (mmm160) cc_final: 0.6209 (mmm160) REVERT: A 285 TYR cc_start: 0.7823 (m-80) cc_final: 0.7502 (m-80) REVERT: A 478 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7472 (ttpp) REVERT: B 59 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7276 (p0) REVERT: B 139 ARG cc_start: 0.6549 (mmm160) cc_final: 0.6096 (mmm160) REVERT: B 285 TYR cc_start: 0.7821 (m-80) cc_final: 0.7503 (m-80) REVERT: B 478 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7494 (ttpp) REVERT: D 139 ARG cc_start: 0.6608 (mmm160) cc_final: 0.6211 (mmm160) REVERT: D 285 TYR cc_start: 0.7821 (m-80) cc_final: 0.7498 (m-80) REVERT: D 478 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7466 (ttpp) REVERT: C 139 ARG cc_start: 0.6600 (mmm160) cc_final: 0.6205 (mmm160) REVERT: C 285 TYR cc_start: 0.7829 (m-80) cc_final: 0.7507 (m-80) REVERT: C 478 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7497 (ttpp) outliers start: 32 outliers final: 11 residues processed: 206 average time/residue: 1.4161 time to fit residues: 318.4056 Evaluate side-chains 177 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 478 LYS Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 46 optimal weight: 0.0970 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 ASN B 550 ASN D 550 ASN C 550 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 15124 Z= 0.366 Angle : 0.735 10.730 20344 Z= 0.383 Chirality : 0.049 0.166 2256 Planarity : 0.005 0.072 2564 Dihedral : 7.794 52.397 2076 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.74 % Allowed : 15.34 % Favored : 80.92 % 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: -0.93 (0.19), residues: 1788 helix: -0.03 (0.19), residues: 708 sheet: -0.16 (0.27), residues: 396 loop : -1.41 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 126 HIS 0.004 0.001 HIS B 427 PHE 0.018 0.002 PHE B 371 TYR 0.024 0.002 TYR C 314 ARG 0.010 0.001 ARG B 332 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 160 time to evaluate : 1.693 Fit side-chains REVERT: A 59 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7643 (p0) REVERT: A 285 TYR cc_start: 0.7994 (m-80) cc_final: 0.7566 (m-80) REVERT: A 373 GLU cc_start: 0.6589 (mm-30) cc_final: 0.6374 (pt0) REVERT: B 59 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7539 (p0) REVERT: B 285 TYR cc_start: 0.7996 (m-80) cc_final: 0.7569 (m-80) REVERT: D 285 TYR cc_start: 0.7992 (m-80) cc_final: 0.7563 (m-80) REVERT: D 373 GLU cc_start: 0.6585 (mm-30) cc_final: 0.6369 (pt0) REVERT: C 59 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7635 (p0) REVERT: C 285 TYR cc_start: 0.7993 (m-80) cc_final: 0.7564 (m-80) REVERT: C 373 GLU cc_start: 0.6566 (mm-30) cc_final: 0.6362 (pt0) outliers start: 62 outliers final: 16 residues processed: 211 average time/residue: 1.3083 time to fit residues: 302.0317 Evaluate side-chains 177 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 158 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 129 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 156 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN A 551 ASN B 414 ASN B 455 ASN B 551 ASN D 455 ASN D 551 ASN C 455 ASN C 551 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 15124 Z= 0.449 Angle : 0.813 10.448 20344 Z= 0.424 Chirality : 0.051 0.168 2256 Planarity : 0.006 0.089 2564 Dihedral : 8.262 57.668 2076 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.83 % Allowed : 16.55 % Favored : 78.62 % 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: -1.03 (0.19), residues: 1788 helix: 0.04 (0.19), residues: 700 sheet: -0.60 (0.25), residues: 396 loop : -1.36 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 126 HIS 0.004 0.002 HIS B 63 PHE 0.021 0.003 PHE B 371 TYR 0.025 0.002 TYR B 113 ARG 0.012 0.001 ARG B 332 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 170 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7756 (p0) REVERT: A 139 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.6165 (mmm160) REVERT: A 285 TYR cc_start: 0.8035 (m-80) cc_final: 0.7540 (m-80) REVERT: A 373 GLU cc_start: 0.6571 (mm-30) cc_final: 0.6333 (pt0) REVERT: B 59 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7656 (p0) REVERT: B 139 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.6163 (mmm160) REVERT: B 285 TYR cc_start: 0.8037 (m-80) cc_final: 0.7543 (m-80) REVERT: B 373 GLU cc_start: 0.6578 (mm-30) cc_final: 0.6300 (pt0) REVERT: D 110 GLU cc_start: 0.7537 (mp0) cc_final: 0.7241 (mp0) REVERT: D 139 ARG cc_start: 0.6776 (OUTLIER) cc_final: 0.6122 (mmm160) REVERT: D 285 TYR cc_start: 0.8036 (m-80) cc_final: 0.7544 (m-80) REVERT: D 373 GLU cc_start: 0.6602 (mm-30) cc_final: 0.6355 (pt0) REVERT: C 139 ARG cc_start: 0.6770 (OUTLIER) cc_final: 0.6135 (mmm160) REVERT: C 285 TYR cc_start: 0.8035 (m-80) cc_final: 0.7545 (m-80) REVERT: C 373 GLU cc_start: 0.6552 (mm-30) cc_final: 0.6331 (pt0) outliers start: 80 outliers final: 32 residues processed: 233 average time/residue: 1.3381 time to fit residues: 340.8691 Evaluate side-chains 192 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 154 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 139 ARG Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 3.9990 chunk 156 optimal weight: 0.3980 chunk 34 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN A 455 ASN B 455 ASN D 414 ASN D 455 ASN C 414 ASN C 455 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15124 Z= 0.230 Angle : 0.652 10.570 20344 Z= 0.339 Chirality : 0.046 0.152 2256 Planarity : 0.004 0.057 2564 Dihedral : 7.523 58.319 2076 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.50 % Allowed : 19.14 % Favored : 77.36 % 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: -0.51 (0.20), residues: 1788 helix: 0.62 (0.20), residues: 700 sheet: -0.43 (0.26), residues: 396 loop : -1.19 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 126 HIS 0.004 0.001 HIS A 415 PHE 0.012 0.002 PHE A 315 TYR 0.014 0.001 TYR C 314 ARG 0.005 0.001 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 156 time to evaluate : 1.646 Fit side-chains REVERT: A 285 TYR cc_start: 0.7957 (m-80) cc_final: 0.7521 (m-80) REVERT: A 334 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8112 (mt) REVERT: A 373 GLU cc_start: 0.6578 (mm-30) cc_final: 0.6319 (pt0) REVERT: B 59 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7651 (p0) REVERT: B 285 TYR cc_start: 0.7958 (m-80) cc_final: 0.7524 (m-80) REVERT: B 334 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8115 (mt) REVERT: D 110 GLU cc_start: 0.7369 (mp0) cc_final: 0.7097 (mp0) REVERT: D 285 TYR cc_start: 0.7960 (m-80) cc_final: 0.7526 (m-80) REVERT: D 334 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8111 (mt) REVERT: D 373 GLU cc_start: 0.6575 (mm-30) cc_final: 0.6325 (pt0) REVERT: C 285 TYR cc_start: 0.7957 (m-80) cc_final: 0.7523 (m-80) REVERT: C 334 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8115 (mt) outliers start: 58 outliers final: 16 residues processed: 198 average time/residue: 1.2603 time to fit residues: 274.5196 Evaluate side-chains 173 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 5.9990 chunk 19 optimal weight: 0.0770 chunk 99 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 173 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 ASN B 550 ASN D 550 ASN C 550 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15124 Z= 0.201 Angle : 0.625 11.040 20344 Z= 0.324 Chirality : 0.045 0.150 2256 Planarity : 0.003 0.052 2564 Dihedral : 7.133 58.692 2076 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.74 % Allowed : 19.38 % Favored : 76.87 % 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: -0.19 (0.20), residues: 1788 helix: 0.94 (0.20), residues: 700 sheet: -0.29 (0.26), residues: 396 loop : -1.06 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 126 HIS 0.004 0.001 HIS D 415 PHE 0.012 0.001 PHE A 315 TYR 0.014 0.001 TYR A 314 ARG 0.006 0.001 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 152 time to evaluate : 1.653 Fit side-chains revert: symmetry clash REVERT: A 285 TYR cc_start: 0.7949 (m-80) cc_final: 0.7509 (m-80) REVERT: A 317 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8610 (tp) REVERT: A 334 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8146 (mt) REVERT: A 373 GLU cc_start: 0.6572 (mm-30) cc_final: 0.6328 (pt0) REVERT: B 59 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7547 (p0) REVERT: B 285 TYR cc_start: 0.7946 (m-80) cc_final: 0.7507 (m-80) REVERT: B 317 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8611 (tp) REVERT: B 334 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8122 (mt) REVERT: B 478 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7736 (ttpp) REVERT: B 496 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.5748 (mm-30) REVERT: D 110 GLU cc_start: 0.7302 (mp0) cc_final: 0.7020 (mp0) REVERT: D 285 TYR cc_start: 0.7960 (m-80) cc_final: 0.7519 (m-80) REVERT: D 317 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8603 (tp) REVERT: D 334 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8145 (mt) REVERT: C 285 TYR cc_start: 0.7959 (m-80) cc_final: 0.7517 (m-80) REVERT: C 317 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8612 (tp) REVERT: C 334 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8146 (mt) REVERT: C 496 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.5753 (mm-30) outliers start: 62 outliers final: 21 residues processed: 199 average time/residue: 1.2766 time to fit residues: 279.7970 Evaluate side-chains 185 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 152 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 496 GLU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7663 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15124 Z= 0.198 Angle : 0.619 11.364 20344 Z= 0.318 Chirality : 0.045 0.150 2256 Planarity : 0.003 0.052 2564 Dihedral : 7.135 59.747 2076 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.08 % Allowed : 20.59 % Favored : 76.33 % 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: 0.02 (0.20), residues: 1788 helix: 1.22 (0.21), residues: 680 sheet: -0.28 (0.27), residues: 396 loop : -0.93 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 126 HIS 0.004 0.001 HIS D 415 PHE 0.012 0.001 PHE C 315 TYR 0.014 0.001 TYR C 314 ARG 0.006 0.001 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 154 time to evaluate : 1.593 Fit side-chains revert: symmetry clash REVERT: A 285 TYR cc_start: 0.7958 (m-80) cc_final: 0.7541 (m-80) REVERT: A 317 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8624 (tp) REVERT: A 334 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8142 (mt) REVERT: B 59 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7532 (p0) REVERT: B 139 ARG cc_start: 0.6716 (mmm160) cc_final: 0.6149 (mmm160) REVERT: B 285 TYR cc_start: 0.7957 (m-80) cc_final: 0.7543 (m-80) REVERT: B 317 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8624 (tp) REVERT: B 334 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8141 (mt) REVERT: B 478 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7754 (ttpp) REVERT: B 496 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.5756 (mm-30) REVERT: D 110 GLU cc_start: 0.7317 (mp0) cc_final: 0.7098 (mp0) REVERT: D 285 TYR cc_start: 0.7970 (m-80) cc_final: 0.7561 (m-80) REVERT: D 317 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8625 (tp) REVERT: D 334 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8138 (mt) REVERT: C 139 ARG cc_start: 0.6694 (mmm160) cc_final: 0.6133 (mmm160) REVERT: C 285 TYR cc_start: 0.7967 (m-80) cc_final: 0.7562 (m-80) REVERT: C 317 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8625 (tp) REVERT: C 334 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8144 (mt) REVERT: C 496 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.5757 (mm-30) outliers start: 51 outliers final: 19 residues processed: 190 average time/residue: 1.2264 time to fit residues: 258.6101 Evaluate side-chains 184 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 153 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 496 GLU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 4.9990 chunk 166 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 49 optimal weight: 0.0570 chunk 146 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- 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: 0.7650 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15124 Z= 0.185 Angle : 0.609 11.659 20344 Z= 0.311 Chirality : 0.045 0.147 2256 Planarity : 0.003 0.047 2564 Dihedral : 7.057 59.930 2076 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.66 % Allowed : 21.26 % Favored : 76.09 % 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: 0.18 (0.20), residues: 1788 helix: 1.32 (0.21), residues: 680 sheet: 0.16 (0.27), residues: 380 loop : -1.02 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 126 HIS 0.004 0.001 HIS D 415 PHE 0.012 0.001 PHE D 315 TYR 0.013 0.001 TYR B 314 ARG 0.009 0.001 ARG D 481 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 163 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.6695 (mmm160) cc_final: 0.6108 (mmm160) REVERT: A 285 TYR cc_start: 0.7967 (m-80) cc_final: 0.7573 (m-80) REVERT: A 317 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8650 (tp) REVERT: A 334 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8164 (mt) REVERT: B 59 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7529 (p0) REVERT: B 139 ARG cc_start: 0.6686 (mmm160) cc_final: 0.6102 (mmm160) REVERT: B 285 TYR cc_start: 0.7959 (m-80) cc_final: 0.7566 (m-80) REVERT: B 317 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8648 (tp) REVERT: B 334 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8142 (mt) REVERT: B 478 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7515 (tttt) REVERT: B 496 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.5765 (mm-30) REVERT: D 110 GLU cc_start: 0.7315 (mp0) cc_final: 0.7097 (mp0) REVERT: D 139 ARG cc_start: 0.6694 (mmm160) cc_final: 0.6111 (mmm160) REVERT: D 285 TYR cc_start: 0.7982 (m-80) cc_final: 0.7592 (m-80) REVERT: D 317 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8650 (tp) REVERT: D 334 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8140 (mt) REVERT: C 110 GLU cc_start: 0.7323 (mp0) cc_final: 0.7050 (mp0) REVERT: C 139 ARG cc_start: 0.6707 (mmm160) cc_final: 0.6124 (mmm160) REVERT: C 285 TYR cc_start: 0.7982 (m-80) cc_final: 0.7593 (m-80) REVERT: C 317 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8623 (tp) REVERT: C 334 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8167 (mt) REVERT: C 496 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.5763 (mm-30) outliers start: 44 outliers final: 22 residues processed: 191 average time/residue: 1.1682 time to fit residues: 247.7222 Evaluate side-chains 197 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 163 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 496 GLU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 455 ASN Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 496 GLU Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 179 optimal weight: 0.0020 chunk 165 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- 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: 0.7730 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 15124 Z= 0.352 Angle : 0.752 11.693 20344 Z= 0.385 Chirality : 0.048 0.160 2256 Planarity : 0.005 0.071 2564 Dihedral : 7.544 59.739 2076 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.08 % Allowed : 20.83 % Favored : 76.09 % 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: -0.17 (0.20), residues: 1788 helix: 0.96 (0.20), residues: 680 sheet: -0.16 (0.25), residues: 380 loop : -1.06 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 126 HIS 0.004 0.001 HIS B 415 PHE 0.015 0.002 PHE A 315 TYR 0.021 0.002 TYR D 314 ARG 0.009 0.001 ARG C 481 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 157 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 285 TYR cc_start: 0.8010 (m-80) cc_final: 0.7611 (m-80) REVERT: A 317 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8613 (tp) REVERT: A 334 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8115 (mt) REVERT: B 285 TYR cc_start: 0.8009 (m-80) cc_final: 0.7613 (m-80) REVERT: B 317 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8612 (tp) REVERT: B 334 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8116 (mt) REVERT: B 478 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7654 (tttt) REVERT: D 110 GLU cc_start: 0.7439 (mp0) cc_final: 0.7210 (mp0) REVERT: D 285 TYR cc_start: 0.8016 (m-80) cc_final: 0.7615 (m-80) REVERT: D 317 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8617 (tp) REVERT: D 334 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8112 (mt) REVERT: D 373 GLU cc_start: 0.6549 (mm-30) cc_final: 0.6346 (pt0) REVERT: C 110 GLU cc_start: 0.7546 (mp0) cc_final: 0.7234 (mp0) REVERT: C 285 TYR cc_start: 0.8010 (m-80) cc_final: 0.7611 (m-80) REVERT: C 317 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8616 (tp) REVERT: C 334 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8118 (mt) outliers start: 51 outliers final: 25 residues processed: 197 average time/residue: 1.1612 time to fit residues: 253.7864 Evaluate side-chains 189 residues out of total 1656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 155 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 chunk 143 optimal weight: 0.0980 chunk 59 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.221584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.190862 restraints weight = 17059.273| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 1.66 r_work: 0.4038 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3934 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15124 Z= 0.178 Angle : 0.620 12.026 20344 Z= 0.316 Chirality : 0.045 0.147 2256 Planarity : 0.003 0.043 2564 Dihedral : 7.162 59.128 2076 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.39 % Allowed : 22.52 % Favored : 76.09 % 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: 0.02 (0.20), residues: 1788 helix: 1.11 (0.20), residues: 700 sheet: 0.09 (0.27), residues: 380 loop : -1.10 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 126 HIS 0.004 0.001 HIS B 415 PHE 0.013 0.001 PHE A 315 TYR 0.011 0.001 TYR D 314 ARG 0.007 0.001 ARG B 481 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5366.74 seconds wall clock time: 94 minutes 47.89 seconds (5687.89 seconds total)