Starting phenix.real_space_refine on Thu Mar 5 09:07:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f5v_31468/03_2026/7f5v_31468.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f5v_31468/03_2026/7f5v_31468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f5v_31468/03_2026/7f5v_31468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f5v_31468/03_2026/7f5v_31468.map" model { file = "/net/cci-nas-00/data/ceres_data/7f5v_31468/03_2026/7f5v_31468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f5v_31468/03_2026/7f5v_31468.cif" } resolution = 3.6 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 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= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 13116 2.51 5 N 3688 2.21 5 O 3988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20912 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5228 Classifications: {'peptide': 690} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 665} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Restraints were copied for chains: B, C, D Time building chain proxies: 5.03, per 1000 atoms: 0.24 Number of scatterers: 20912 At special positions: 0 Unit cell: (193.98, 98.58, 94.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 3988 8.00 N 3688 7.00 C 13116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 910.8 milliseconds 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5144 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 20 sheets defined 47.1% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 51 through 56 removed outlier: 4.140A pdb=" N LYS A 54 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR A 55 " --> pdb=" O GLN A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 69 removed outlier: 3.698A pdb=" N ILE A 68 " --> pdb=" O GLY A 64 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 69' Processing helix chain 'A' and resid 77 through 93 Processing helix chain 'A' and resid 104 through 119 removed outlier: 3.748A pdb=" N PHE A 108 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.767A pdb=" N LEU A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 163 Processing helix chain 'A' and resid 175 through 179 Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 296 through 307 Processing helix chain 'A' and resid 322 through 327 Processing helix chain 'A' and resid 348 through 363 removed outlier: 3.579A pdb=" N ALA A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 384 Processing helix chain 'A' and resid 384 through 401 removed outlier: 3.858A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 Processing helix chain 'A' and resid 415 through 433 removed outlier: 3.572A pdb=" N GLY A 425 " --> pdb=" O ASN A 421 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER A 433 " --> pdb=" O ILE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 481 removed outlier: 3.606A pdb=" N ALA A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 513 Processing helix chain 'A' and resid 527 through 534 removed outlier: 3.689A pdb=" N LEU A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 557 Processing helix chain 'A' and resid 579 through 592 removed outlier: 3.526A pdb=" N ALA A 583 " --> pdb=" O ASP A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 613 removed outlier: 3.515A pdb=" N SER A 612 " --> pdb=" O ASP A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 627 removed outlier: 3.554A pdb=" N ASP A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 638 Processing helix chain 'A' and resid 666 through 678 Processing helix chain 'A' and resid 689 through 700 Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 757 through 761 Processing helix chain 'B' and resid 51 through 56 removed outlier: 4.140A pdb=" N LYS B 54 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR B 55 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 69 removed outlier: 3.698A pdb=" N ILE B 68 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 64 through 69' Processing helix chain 'B' and resid 77 through 93 Processing helix chain 'B' and resid 104 through 119 removed outlier: 3.748A pdb=" N PHE B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 127 removed outlier: 3.767A pdb=" N LEU B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 163 Processing helix chain 'B' and resid 175 through 179 Processing helix chain 'B' and resid 180 through 196 Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 296 through 307 Processing helix chain 'B' and resid 322 through 327 Processing helix chain 'B' and resid 348 through 363 removed outlier: 3.579A pdb=" N ALA B 352 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 384 Processing helix chain 'B' and resid 384 through 401 removed outlier: 3.858A pdb=" N LYS B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 Processing helix chain 'B' and resid 415 through 433 removed outlier: 3.572A pdb=" N GLY B 425 " --> pdb=" O ASN B 421 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU B 431 " --> pdb=" O LYS B 427 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER B 433 " --> pdb=" O ILE B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 481 removed outlier: 3.606A pdb=" N ALA B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B 479 " --> pdb=" O GLN B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 513 Processing helix chain 'B' and resid 527 through 534 removed outlier: 3.689A pdb=" N LEU B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 557 Processing helix chain 'B' and resid 579 through 592 removed outlier: 3.526A pdb=" N ALA B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 613 removed outlier: 3.515A pdb=" N SER B 612 " --> pdb=" O ASP B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 627 removed outlier: 3.554A pdb=" N ASP B 618 " --> pdb=" O ALA B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 638 Processing helix chain 'B' and resid 666 through 678 Processing helix chain 'B' and resid 689 through 700 Processing helix chain 'B' and resid 740 through 742 No H-bonds generated for 'chain 'B' and resid 740 through 742' Processing helix chain 'B' and resid 757 through 761 Processing helix chain 'C' and resid 51 through 56 removed outlier: 4.140A pdb=" N LYS C 54 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR C 55 " --> pdb=" O GLN C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 69 removed outlier: 3.698A pdb=" N ILE C 68 " --> pdb=" O GLY C 64 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR C 69 " --> pdb=" O SER C 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 64 through 69' Processing helix chain 'C' and resid 77 through 93 Processing helix chain 'C' and resid 104 through 119 removed outlier: 3.748A pdb=" N PHE C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 removed outlier: 3.767A pdb=" N LEU C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 163 Processing helix chain 'C' and resid 175 through 179 Processing helix chain 'C' and resid 180 through 196 Processing helix chain 'C' and resid 234 through 244 Processing helix chain 'C' and resid 296 through 307 Processing helix chain 'C' and resid 322 through 327 Processing helix chain 'C' and resid 348 through 363 removed outlier: 3.579A pdb=" N ALA C 352 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 384 Processing helix chain 'C' and resid 384 through 401 removed outlier: 3.858A pdb=" N LYS C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 Processing helix chain 'C' and resid 415 through 433 removed outlier: 3.572A pdb=" N GLY C 425 " --> pdb=" O ASN C 421 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU C 431 " --> pdb=" O LYS C 427 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER C 433 " --> pdb=" O ILE C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 481 removed outlier: 3.606A pdb=" N ALA C 478 " --> pdb=" O PRO C 474 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 479 " --> pdb=" O GLN C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 513 Processing helix chain 'C' and resid 527 through 534 removed outlier: 3.689A pdb=" N LEU C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 557 Processing helix chain 'C' and resid 579 through 592 removed outlier: 3.526A pdb=" N ALA C 583 " --> pdb=" O ASP C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 613 removed outlier: 3.515A pdb=" N SER C 612 " --> pdb=" O ASP C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 627 removed outlier: 3.554A pdb=" N ASP C 618 " --> pdb=" O ALA C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 638 Processing helix chain 'C' and resid 666 through 678 Processing helix chain 'C' and resid 689 through 700 Processing helix chain 'C' and resid 740 through 742 No H-bonds generated for 'chain 'C' and resid 740 through 742' Processing helix chain 'C' and resid 757 through 761 Processing helix chain 'D' and resid 51 through 56 removed outlier: 4.140A pdb=" N LYS D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR D 55 " --> pdb=" O GLN D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 69 removed outlier: 3.698A pdb=" N ILE D 68 " --> pdb=" O GLY D 64 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 64 through 69' Processing helix chain 'D' and resid 77 through 93 Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.748A pdb=" N PHE D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.767A pdb=" N LEU D 127 " --> pdb=" O MET D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 163 Processing helix chain 'D' and resid 175 through 179 Processing helix chain 'D' and resid 180 through 196 Processing helix chain 'D' and resid 234 through 244 Processing helix chain 'D' and resid 296 through 307 Processing helix chain 'D' and resid 322 through 327 Processing helix chain 'D' and resid 348 through 363 removed outlier: 3.579A pdb=" N ALA D 352 " --> pdb=" O VAL D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 384 Processing helix chain 'D' and resid 384 through 401 removed outlier: 3.858A pdb=" N LYS D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 411 Processing helix chain 'D' and resid 415 through 433 removed outlier: 3.572A pdb=" N GLY D 425 " --> pdb=" O ASN D 421 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU D 431 " --> pdb=" O LYS D 427 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER D 433 " --> pdb=" O ILE D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 481 removed outlier: 3.606A pdb=" N ALA D 478 " --> pdb=" O PRO D 474 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU D 479 " --> pdb=" O GLN D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 513 Processing helix chain 'D' and resid 527 through 534 removed outlier: 3.689A pdb=" N LEU D 531 " --> pdb=" O GLU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 557 Processing helix chain 'D' and resid 579 through 592 removed outlier: 3.526A pdb=" N ALA D 583 " --> pdb=" O ASP D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 613 removed outlier: 3.515A pdb=" N SER D 612 " --> pdb=" O ASP D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 627 removed outlier: 3.554A pdb=" N ASP D 618 " --> pdb=" O ALA D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 633 through 638 Processing helix chain 'D' and resid 666 through 678 Processing helix chain 'D' and resid 689 through 700 Processing helix chain 'D' and resid 740 through 742 No H-bonds generated for 'chain 'D' and resid 740 through 742' Processing helix chain 'D' and resid 757 through 761 Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 173 removed outlier: 6.926A pdb=" N MET A 100 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N THR A 205 " --> pdb=" O MET A 100 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N THR A 102 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL A 101 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL A 61 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL A 60 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N MET A 252 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS A 62 " --> pdb=" O MET A 252 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU A 249 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS A 315 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU A 251 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL A 312 " --> pdb=" O PHE A 336 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 744 through 749 removed outlier: 7.388A pdb=" N LEU A 450 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG A 445 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU A 452 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG A 443 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLN A 454 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 519 through 521 removed outlier: 6.867A pdb=" N LEU A 487 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 464 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU A 463 " --> pdb=" O ILE A 542 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 605 through 606 removed outlier: 3.574A pdb=" N ILE A 606 " --> pdb=" O GLU A 662 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 727 through 728 removed outlier: 3.633A pdb=" N GLY A 736 " --> pdb=" O SER A 728 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 168 through 173 removed outlier: 6.926A pdb=" N MET B 100 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N THR B 205 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N THR B 102 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL B 101 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 61 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL B 60 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N MET B 252 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS B 62 " --> pdb=" O MET B 252 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU B 249 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS B 315 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU B 251 " --> pdb=" O CYS B 315 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL B 312 " --> pdb=" O PHE B 336 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 744 through 749 removed outlier: 7.388A pdb=" N LEU B 450 " --> pdb=" O ARG B 445 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG B 445 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU B 452 " --> pdb=" O ARG B 443 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG B 443 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLN B 454 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 519 through 521 removed outlier: 6.867A pdb=" N LEU B 487 " --> pdb=" O SER B 520 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 464 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU B 463 " --> pdb=" O ILE B 542 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 605 through 606 removed outlier: 3.574A pdb=" N ILE B 606 " --> pdb=" O GLU B 662 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 727 through 728 removed outlier: 3.633A pdb=" N GLY B 736 " --> pdb=" O SER B 728 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 168 through 173 removed outlier: 6.926A pdb=" N MET C 100 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N THR C 205 " --> pdb=" O MET C 100 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N THR C 102 " --> pdb=" O THR C 205 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL C 101 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C 61 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL C 60 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N MET C 252 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS C 62 " --> pdb=" O MET C 252 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU C 249 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS C 315 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU C 251 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL C 312 " --> pdb=" O PHE C 336 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 744 through 749 removed outlier: 7.388A pdb=" N LEU C 450 " --> pdb=" O ARG C 445 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG C 445 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU C 452 " --> pdb=" O ARG C 443 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG C 443 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLN C 454 " --> pdb=" O LEU C 441 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 519 through 521 removed outlier: 6.867A pdb=" N LEU C 487 " --> pdb=" O SER C 520 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 464 " --> pdb=" O LEU C 488 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU C 463 " --> pdb=" O ILE C 542 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 605 through 606 removed outlier: 3.574A pdb=" N ILE C 606 " --> pdb=" O GLU C 662 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 727 through 728 removed outlier: 3.633A pdb=" N GLY C 736 " --> pdb=" O SER C 728 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 168 through 173 removed outlier: 6.926A pdb=" N MET D 100 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N THR D 205 " --> pdb=" O MET D 100 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N THR D 102 " --> pdb=" O THR D 205 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL D 101 " --> pdb=" O LEU D 59 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL D 61 " --> pdb=" O VAL D 101 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL D 60 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N MET D 252 " --> pdb=" O VAL D 60 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS D 62 " --> pdb=" O MET D 252 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU D 249 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS D 315 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU D 251 " --> pdb=" O CYS D 315 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL D 312 " --> pdb=" O PHE D 336 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 744 through 749 removed outlier: 7.388A pdb=" N LEU D 450 " --> pdb=" O ARG D 445 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG D 445 " --> pdb=" O LEU D 450 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU D 452 " --> pdb=" O ARG D 443 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG D 443 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLN D 454 " --> pdb=" O LEU D 441 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 519 through 521 removed outlier: 6.867A pdb=" N LEU D 487 " --> pdb=" O SER D 520 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL D 464 " --> pdb=" O LEU D 488 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU D 463 " --> pdb=" O ILE D 542 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 605 through 606 removed outlier: 3.574A pdb=" N ILE D 606 " --> pdb=" O GLU D 662 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 727 through 728 removed outlier: 3.633A pdb=" N GLY D 736 " --> pdb=" O SER D 728 " (cutoff:3.500A) 888 hydrogen bonds defined for protein. 2544 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.73 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7136 1.34 - 1.46: 3988 1.46 - 1.58: 9896 1.58 - 1.69: 0 1.69 - 1.81: 200 Bond restraints: 21220 Sorted by residual: bond pdb=" C GLY C 165 " pdb=" N VAL C 166 " ideal model delta sigma weight residual 1.335 1.314 0.021 1.41e-02 5.03e+03 2.20e+00 bond pdb=" C GLY A 165 " pdb=" N VAL A 166 " ideal model delta sigma weight residual 1.335 1.314 0.021 1.41e-02 5.03e+03 2.20e+00 bond pdb=" C GLY B 165 " pdb=" N VAL B 166 " ideal model delta sigma weight residual 1.335 1.314 0.021 1.41e-02 5.03e+03 2.20e+00 bond pdb=" C GLY D 165 " pdb=" N VAL D 166 " ideal model delta sigma weight residual 1.335 1.314 0.021 1.41e-02 5.03e+03 2.20e+00 bond pdb=" CG ARG C 544 " pdb=" CD ARG C 544 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.34e+00 ... (remaining 21215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 26864 1.29 - 2.58: 1600 2.58 - 3.87: 176 3.87 - 5.15: 60 5.15 - 6.44: 12 Bond angle restraints: 28712 Sorted by residual: angle pdb=" N VAL A 725 " pdb=" CA VAL A 725 " pdb=" C VAL A 725 " ideal model delta sigma weight residual 113.20 109.96 3.24 9.60e-01 1.09e+00 1.14e+01 angle pdb=" N VAL D 725 " pdb=" CA VAL D 725 " pdb=" C VAL D 725 " ideal model delta sigma weight residual 113.20 109.96 3.24 9.60e-01 1.09e+00 1.14e+01 angle pdb=" N VAL C 725 " pdb=" CA VAL C 725 " pdb=" C VAL C 725 " ideal model delta sigma weight residual 113.20 109.96 3.24 9.60e-01 1.09e+00 1.14e+01 angle pdb=" N VAL B 725 " pdb=" CA VAL B 725 " pdb=" C VAL B 725 " ideal model delta sigma weight residual 113.20 109.96 3.24 9.60e-01 1.09e+00 1.14e+01 angle pdb=" N ALA B 339 " pdb=" CA ALA B 339 " pdb=" C ALA B 339 " ideal model delta sigma weight residual 111.75 115.86 -4.11 1.28e+00 6.10e-01 1.03e+01 ... (remaining 28707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 11392 15.07 - 30.14: 1228 30.14 - 45.20: 296 45.20 - 60.27: 52 60.27 - 75.34: 32 Dihedral angle restraints: 13000 sinusoidal: 5068 harmonic: 7932 Sorted by residual: dihedral pdb=" CA VAL D 348 " pdb=" C VAL D 348 " pdb=" N GLU D 349 " pdb=" CA GLU D 349 " ideal model delta harmonic sigma weight residual -180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA VAL C 348 " pdb=" C VAL C 348 " pdb=" N GLU C 349 " pdb=" CA GLU C 349 " ideal model delta harmonic sigma weight residual 180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA VAL A 348 " pdb=" C VAL A 348 " pdb=" N GLU A 349 " pdb=" CA GLU A 349 " ideal model delta harmonic sigma weight residual 180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 12997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1960 0.031 - 0.062: 944 0.062 - 0.092: 280 0.092 - 0.123: 176 0.123 - 0.154: 28 Chirality restraints: 3388 Sorted by residual: chirality pdb=" CA PRO C 347 " pdb=" N PRO C 347 " pdb=" C PRO C 347 " pdb=" CB PRO C 347 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA PRO A 347 " pdb=" N PRO A 347 " pdb=" C PRO A 347 " pdb=" CB PRO A 347 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA PRO D 347 " pdb=" N PRO D 347 " pdb=" C PRO D 347 " pdb=" CB PRO D 347 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 3385 not shown) Planarity restraints: 3720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 643 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO A 644 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 644 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 644 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 643 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO B 644 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 644 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 644 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 643 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO C 644 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 644 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 644 " 0.028 5.00e-02 4.00e+02 ... (remaining 3717 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 408 2.64 - 3.21: 21410 3.21 - 3.77: 31480 3.77 - 4.34: 43910 4.34 - 4.90: 69802 Nonbonded interactions: 167010 Sorted by model distance: nonbonded pdb=" OG1 THR C 687 " pdb=" OD1 ASN C 689 " model vdw 2.076 3.040 nonbonded pdb=" OG1 THR B 687 " pdb=" OD1 ASN B 689 " model vdw 2.076 3.040 nonbonded pdb=" OG1 THR A 687 " pdb=" OD1 ASN A 689 " model vdw 2.076 3.040 nonbonded pdb=" OG1 THR D 687 " pdb=" OD1 ASN D 689 " model vdw 2.076 3.040 nonbonded pdb=" OG SER C 546 " pdb=" OD1 ASP C 548 " model vdw 2.150 3.040 ... (remaining 167005 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 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 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.370 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 0.035 21220 Z= 0.230 Angle : 0.687 6.442 28712 Z= 0.413 Chirality : 0.044 0.154 3388 Planarity : 0.005 0.052 3720 Dihedral : 13.935 75.336 7856 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.89 % Favored : 92.96 % Rotamer: Outliers : 0.18 % Allowed : 5.88 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.69 (0.13), residues: 2728 helix: -2.60 (0.12), residues: 1108 sheet: -3.38 (0.20), residues: 448 loop : -3.40 (0.16), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 370 TYR 0.009 0.001 TYR D 631 PHE 0.006 0.001 PHE D 108 TRP 0.006 0.001 TRP C 748 HIS 0.005 0.001 HIS A 707 Details of bonding type rmsd covalent geometry : bond 0.00486 (21220) covalent geometry : angle 0.68657 (28712) hydrogen bonds : bond 0.24942 ( 888) hydrogen bonds : angle 8.15143 ( 2544) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 292 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ASP cc_start: 0.8327 (t0) cc_final: 0.8091 (t0) REVERT: A 177 ASP cc_start: 0.7548 (m-30) cc_final: 0.7182 (m-30) REVERT: A 234 ASP cc_start: 0.8559 (t0) cc_final: 0.8335 (t0) REVERT: A 622 MET cc_start: 0.8941 (tpt) cc_final: 0.8585 (mmm) REVERT: B 158 ASP cc_start: 0.8326 (t0) cc_final: 0.8091 (t0) REVERT: B 177 ASP cc_start: 0.7549 (m-30) cc_final: 0.7183 (m-30) REVERT: B 234 ASP cc_start: 0.8560 (t0) cc_final: 0.8337 (t0) REVERT: B 622 MET cc_start: 0.8941 (tpt) cc_final: 0.8585 (mmm) REVERT: C 158 ASP cc_start: 0.8332 (t0) cc_final: 0.8092 (t0) REVERT: C 177 ASP cc_start: 0.7548 (m-30) cc_final: 0.7184 (m-30) REVERT: C 234 ASP cc_start: 0.8558 (t0) cc_final: 0.8335 (t0) REVERT: C 622 MET cc_start: 0.8940 (tpt) cc_final: 0.8586 (mmm) REVERT: D 158 ASP cc_start: 0.8330 (t0) cc_final: 0.8092 (t0) REVERT: D 177 ASP cc_start: 0.7550 (m-30) cc_final: 0.7184 (m-30) REVERT: D 234 ASP cc_start: 0.8558 (t0) cc_final: 0.8335 (t0) REVERT: D 622 MET cc_start: 0.8941 (tpt) cc_final: 0.8587 (mmm) outliers start: 4 outliers final: 0 residues processed: 296 average time/residue: 0.1530 time to fit residues: 69.7328 Evaluate side-chains 216 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN A 354 ASN A 369 GLN A 392 ASN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 HIS ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 HIS A 675 HIS B 344 ASN B 354 ASN B 369 GLN B 392 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 HIS B 675 HIS C 344 ASN C 354 ASN C 369 GLN C 392 ASN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 559 HIS ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 HIS C 675 HIS D 344 ASN D 354 ASN D 369 GLN D 392 ASN ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 559 HIS ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 HIS D 675 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.148603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.091958 restraints weight = 39541.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.096193 restraints weight = 19487.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.098883 restraints weight = 12871.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.100657 restraints weight = 10097.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.101643 restraints weight = 8712.846| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 21220 Z= 0.345 Angle : 0.768 7.549 28712 Z= 0.400 Chirality : 0.048 0.171 3388 Planarity : 0.005 0.059 3720 Dihedral : 5.223 23.453 2932 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.24 % Favored : 90.62 % Rotamer: Outliers : 2.85 % Allowed : 16.93 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.50 (0.15), residues: 2728 helix: -1.21 (0.14), residues: 1164 sheet: -3.09 (0.22), residues: 444 loop : -3.13 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 635 TYR 0.012 0.002 TYR D 594 PHE 0.014 0.002 PHE D 335 TRP 0.004 0.001 TRP D 748 HIS 0.007 0.002 HIS C 559 Details of bonding type rmsd covalent geometry : bond 0.00792 (21220) covalent geometry : angle 0.76764 (28712) hydrogen bonds : bond 0.06849 ( 888) hydrogen bonds : angle 5.63653 ( 2544) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 220 time to evaluate : 0.829 Fit side-chains REVERT: A 119 MET cc_start: 0.8200 (tmm) cc_final: 0.7795 (tmm) REVERT: A 123 MET cc_start: 0.9184 (mmm) cc_final: 0.8966 (mmm) REVERT: A 177 ASP cc_start: 0.7887 (m-30) cc_final: 0.7597 (m-30) REVERT: A 234 ASP cc_start: 0.8724 (t0) cc_final: 0.8444 (t0) REVERT: A 503 MET cc_start: 0.6105 (tpp) cc_final: 0.5867 (tpp) REVERT: A 558 LEU cc_start: 0.8303 (pt) cc_final: 0.7719 (tp) REVERT: A 601 MET cc_start: 0.7436 (tmm) cc_final: 0.6978 (tmm) REVERT: A 622 MET cc_start: 0.8967 (tpt) cc_final: 0.8749 (mmt) REVERT: A 760 PHE cc_start: 0.7246 (m-80) cc_final: 0.6630 (m-80) REVERT: B 119 MET cc_start: 0.8197 (tmm) cc_final: 0.7792 (tmm) REVERT: B 123 MET cc_start: 0.9187 (mmm) cc_final: 0.8966 (mmm) REVERT: B 177 ASP cc_start: 0.7889 (m-30) cc_final: 0.7596 (m-30) REVERT: B 234 ASP cc_start: 0.8720 (t0) cc_final: 0.8439 (t0) REVERT: B 503 MET cc_start: 0.6110 (tpp) cc_final: 0.5870 (tpp) REVERT: B 558 LEU cc_start: 0.8297 (pt) cc_final: 0.7713 (tp) REVERT: B 601 MET cc_start: 0.7443 (tmm) cc_final: 0.6983 (tmm) REVERT: B 622 MET cc_start: 0.8967 (tpt) cc_final: 0.8748 (mmt) REVERT: B 760 PHE cc_start: 0.7248 (m-80) cc_final: 0.6631 (m-80) REVERT: C 119 MET cc_start: 0.8196 (tmm) cc_final: 0.7792 (tmm) REVERT: C 123 MET cc_start: 0.9189 (mmm) cc_final: 0.8966 (mmm) REVERT: C 177 ASP cc_start: 0.7883 (m-30) cc_final: 0.7590 (m-30) REVERT: C 234 ASP cc_start: 0.8727 (t0) cc_final: 0.8445 (t0) REVERT: C 503 MET cc_start: 0.6109 (tpp) cc_final: 0.5868 (tpp) REVERT: C 601 MET cc_start: 0.7440 (tmm) cc_final: 0.6981 (tmm) REVERT: C 622 MET cc_start: 0.8964 (tpt) cc_final: 0.8747 (mmt) REVERT: C 760 PHE cc_start: 0.7251 (m-80) cc_final: 0.6635 (m-80) REVERT: D 119 MET cc_start: 0.8197 (tmm) cc_final: 0.7795 (tmm) REVERT: D 123 MET cc_start: 0.9184 (mmm) cc_final: 0.8967 (mmm) REVERT: D 177 ASP cc_start: 0.7890 (m-30) cc_final: 0.7598 (m-30) REVERT: D 234 ASP cc_start: 0.8725 (t0) cc_final: 0.8444 (t0) REVERT: D 503 MET cc_start: 0.6104 (tpp) cc_final: 0.5868 (tpp) REVERT: D 601 MET cc_start: 0.7442 (tmm) cc_final: 0.6984 (tmm) REVERT: D 622 MET cc_start: 0.8967 (tpt) cc_final: 0.8748 (mmt) REVERT: D 760 PHE cc_start: 0.7253 (m-80) cc_final: 0.6633 (m-80) outliers start: 64 outliers final: 32 residues processed: 264 average time/residue: 0.1160 time to fit residues: 52.8910 Evaluate side-chains 224 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 749 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 232 optimal weight: 0.5980 chunk 271 optimal weight: 10.0000 chunk 270 optimal weight: 9.9990 chunk 202 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 112 optimal weight: 30.0000 chunk 77 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 162 optimal weight: 0.7980 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN A 361 GLN A 375 ASN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 ASN B 361 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 ASN C 361 GLN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 ASN D 361 GLN ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.152069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.095438 restraints weight = 38913.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.099908 restraints weight = 18933.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.102923 restraints weight = 12410.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.104686 restraints weight = 9616.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.105878 restraints weight = 8276.793| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 21220 Z= 0.210 Angle : 0.616 5.781 28712 Z= 0.323 Chirality : 0.045 0.159 3388 Planarity : 0.005 0.051 3720 Dihedral : 4.688 21.374 2932 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.30 % Favored : 93.55 % Rotamer: Outliers : 2.85 % Allowed : 19.16 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.16), residues: 2728 helix: -0.30 (0.15), residues: 1160 sheet: -2.66 (0.24), residues: 444 loop : -2.81 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 96 TYR 0.005 0.001 TYR A 164 PHE 0.010 0.001 PHE C 335 TRP 0.003 0.001 TRP D 748 HIS 0.004 0.001 HIS D 707 Details of bonding type rmsd covalent geometry : bond 0.00481 (21220) covalent geometry : angle 0.61596 (28712) hydrogen bonds : bond 0.05298 ( 888) hydrogen bonds : angle 4.92412 ( 2544) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 216 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8439 (tmm) cc_final: 0.7786 (tmm) REVERT: A 123 MET cc_start: 0.9157 (mmm) cc_final: 0.8927 (mmm) REVERT: A 158 ASP cc_start: 0.8371 (t0) cc_final: 0.8114 (t0) REVERT: A 177 ASP cc_start: 0.7797 (m-30) cc_final: 0.7504 (m-30) REVERT: A 361 GLN cc_start: 0.8994 (tt0) cc_final: 0.8766 (tt0) REVERT: A 622 MET cc_start: 0.8970 (tpt) cc_final: 0.8611 (mmm) REVERT: A 704 CYS cc_start: 0.8231 (p) cc_final: 0.7058 (p) REVERT: A 715 ASP cc_start: 0.6851 (t0) cc_final: 0.6139 (t0) REVERT: A 760 PHE cc_start: 0.7266 (m-80) cc_final: 0.6679 (m-80) REVERT: B 119 MET cc_start: 0.8443 (tmm) cc_final: 0.7787 (tmm) REVERT: B 123 MET cc_start: 0.9159 (mmm) cc_final: 0.8929 (mmm) REVERT: B 158 ASP cc_start: 0.8370 (t0) cc_final: 0.8118 (t0) REVERT: B 177 ASP cc_start: 0.7800 (m-30) cc_final: 0.7503 (m-30) REVERT: B 361 GLN cc_start: 0.8993 (tt0) cc_final: 0.8764 (tt0) REVERT: B 622 MET cc_start: 0.8978 (tpt) cc_final: 0.8615 (mmm) REVERT: B 704 CYS cc_start: 0.8237 (p) cc_final: 0.7064 (p) REVERT: B 715 ASP cc_start: 0.6852 (t0) cc_final: 0.6141 (t0) REVERT: B 760 PHE cc_start: 0.7273 (m-80) cc_final: 0.6685 (m-80) REVERT: C 119 MET cc_start: 0.8439 (tmm) cc_final: 0.7785 (tmm) REVERT: C 123 MET cc_start: 0.9157 (mmm) cc_final: 0.8927 (mmm) REVERT: C 158 ASP cc_start: 0.8376 (t0) cc_final: 0.8119 (t0) REVERT: C 177 ASP cc_start: 0.7797 (m-30) cc_final: 0.7501 (m-30) REVERT: C 361 GLN cc_start: 0.9001 (tt0) cc_final: 0.8772 (tt0) REVERT: C 622 MET cc_start: 0.8971 (tpt) cc_final: 0.8610 (mmm) REVERT: C 704 CYS cc_start: 0.8233 (p) cc_final: 0.7060 (p) REVERT: C 715 ASP cc_start: 0.6851 (t0) cc_final: 0.6143 (t0) REVERT: C 760 PHE cc_start: 0.7274 (m-80) cc_final: 0.6685 (m-80) REVERT: D 119 MET cc_start: 0.8441 (tmm) cc_final: 0.7784 (tmm) REVERT: D 123 MET cc_start: 0.9157 (mmm) cc_final: 0.8929 (mmm) REVERT: D 158 ASP cc_start: 0.8372 (t0) cc_final: 0.8118 (t0) REVERT: D 177 ASP cc_start: 0.7804 (m-30) cc_final: 0.7508 (m-30) REVERT: D 361 GLN cc_start: 0.8996 (tt0) cc_final: 0.8765 (tt0) REVERT: D 622 MET cc_start: 0.8974 (tpt) cc_final: 0.8612 (mmm) REVERT: D 704 CYS cc_start: 0.8234 (p) cc_final: 0.7060 (p) REVERT: D 715 ASP cc_start: 0.6847 (t0) cc_final: 0.6137 (t0) REVERT: D 760 PHE cc_start: 0.7267 (m-80) cc_final: 0.6682 (m-80) outliers start: 64 outliers final: 24 residues processed: 264 average time/residue: 0.1153 time to fit residues: 52.6495 Evaluate side-chains 236 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 212 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 749 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 191 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 200 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 217 optimal weight: 0.5980 chunk 272 optimal weight: 8.9990 chunk 142 optimal weight: 0.8980 chunk 240 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 263 optimal weight: 6.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN B 354 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 HIS ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 565 HIS ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN D 354 ASN ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 565 HIS ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.153712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.097010 restraints weight = 38265.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.101681 restraints weight = 18180.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.104779 restraints weight = 11738.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.106637 restraints weight = 9047.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.107714 restraints weight = 7740.957| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21220 Z= 0.148 Angle : 0.562 5.734 28712 Z= 0.295 Chirality : 0.043 0.153 3388 Planarity : 0.004 0.047 3720 Dihedral : 4.374 21.061 2932 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.87 % Favored : 93.99 % Rotamer: Outliers : 2.14 % Allowed : 20.05 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.16), residues: 2728 helix: 0.09 (0.16), residues: 1172 sheet: -2.39 (0.24), residues: 444 loop : -2.61 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 96 TYR 0.005 0.001 TYR B 164 PHE 0.010 0.001 PHE C 335 TRP 0.004 0.001 TRP C 748 HIS 0.005 0.001 HIS D 673 Details of bonding type rmsd covalent geometry : bond 0.00335 (21220) covalent geometry : angle 0.56197 (28712) hydrogen bonds : bond 0.04596 ( 888) hydrogen bonds : angle 4.62698 ( 2544) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 264 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7749 (tmm) REVERT: A 158 ASP cc_start: 0.8312 (t0) cc_final: 0.8076 (t0) REVERT: A 177 ASP cc_start: 0.7770 (m-30) cc_final: 0.7512 (m-30) REVERT: A 601 MET cc_start: 0.6968 (tmm) cc_final: 0.6253 (tmm) REVERT: A 622 MET cc_start: 0.8993 (tpt) cc_final: 0.8675 (mmm) REVERT: A 704 CYS cc_start: 0.8135 (p) cc_final: 0.6946 (p) REVERT: A 760 PHE cc_start: 0.7207 (m-80) cc_final: 0.6638 (m-80) REVERT: B 119 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7748 (tmm) REVERT: B 158 ASP cc_start: 0.8309 (t0) cc_final: 0.8077 (t0) REVERT: B 177 ASP cc_start: 0.7774 (m-30) cc_final: 0.7513 (m-30) REVERT: B 601 MET cc_start: 0.6978 (tmm) cc_final: 0.6262 (tmm) REVERT: B 622 MET cc_start: 0.8997 (tpt) cc_final: 0.8678 (mmm) REVERT: B 704 CYS cc_start: 0.8133 (p) cc_final: 0.6948 (p) REVERT: B 760 PHE cc_start: 0.7211 (m-80) cc_final: 0.6637 (m-80) REVERT: C 119 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7747 (tmm) REVERT: C 158 ASP cc_start: 0.8314 (t0) cc_final: 0.8080 (t0) REVERT: C 177 ASP cc_start: 0.7775 (m-30) cc_final: 0.7515 (m-30) REVERT: C 601 MET cc_start: 0.6969 (tmm) cc_final: 0.6252 (tmm) REVERT: C 622 MET cc_start: 0.8989 (tpt) cc_final: 0.8673 (mmm) REVERT: C 704 CYS cc_start: 0.8131 (p) cc_final: 0.6945 (p) REVERT: C 760 PHE cc_start: 0.7217 (m-80) cc_final: 0.6641 (m-80) REVERT: D 119 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7746 (tmm) REVERT: D 158 ASP cc_start: 0.8311 (t0) cc_final: 0.8075 (t0) REVERT: D 177 ASP cc_start: 0.7773 (m-30) cc_final: 0.7512 (m-30) REVERT: D 601 MET cc_start: 0.6964 (tmm) cc_final: 0.6247 (tmm) REVERT: D 622 MET cc_start: 0.8999 (tpt) cc_final: 0.8679 (mmm) REVERT: D 704 CYS cc_start: 0.8135 (p) cc_final: 0.6944 (p) REVERT: D 760 PHE cc_start: 0.7207 (m-80) cc_final: 0.6632 (m-80) outliers start: 48 outliers final: 28 residues processed: 296 average time/residue: 0.1204 time to fit residues: 59.9614 Evaluate side-chains 276 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 244 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 749 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 76 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 224 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 233 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 chunk 252 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 GLN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 GLN ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.153721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.096733 restraints weight = 37995.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.101380 restraints weight = 18133.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.104480 restraints weight = 11738.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.106329 restraints weight = 9054.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.107564 restraints weight = 7761.373| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 21220 Z= 0.158 Angle : 0.577 6.274 28712 Z= 0.303 Chirality : 0.044 0.154 3388 Planarity : 0.004 0.048 3720 Dihedral : 4.283 17.542 2932 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.01 % Favored : 93.84 % Rotamer: Outliers : 2.67 % Allowed : 20.59 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.16), residues: 2728 helix: 0.25 (0.16), residues: 1176 sheet: -2.49 (0.25), residues: 404 loop : -2.58 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 635 TYR 0.005 0.001 TYR D 55 PHE 0.009 0.001 PHE C 335 TRP 0.003 0.000 TRP D 748 HIS 0.008 0.001 HIS C 673 Details of bonding type rmsd covalent geometry : bond 0.00362 (21220) covalent geometry : angle 0.57728 (28712) hydrogen bonds : bond 0.04679 ( 888) hydrogen bonds : angle 4.45186 ( 2544) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 272 time to evaluate : 0.862 Fit side-chains REVERT: A 119 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7952 (tmm) REVERT: A 158 ASP cc_start: 0.8312 (t0) cc_final: 0.8068 (t0) REVERT: A 177 ASP cc_start: 0.7781 (m-30) cc_final: 0.7483 (m-30) REVERT: A 601 MET cc_start: 0.7037 (tmm) cc_final: 0.6386 (tmm) REVERT: A 622 MET cc_start: 0.8980 (tpt) cc_final: 0.8679 (mmm) REVERT: A 704 CYS cc_start: 0.8090 (p) cc_final: 0.6920 (p) REVERT: A 715 ASP cc_start: 0.6318 (t0) cc_final: 0.5397 (t0) REVERT: A 760 PHE cc_start: 0.7223 (m-80) cc_final: 0.6638 (m-80) REVERT: B 119 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7950 (tmm) REVERT: B 158 ASP cc_start: 0.8311 (t0) cc_final: 0.8068 (t0) REVERT: B 177 ASP cc_start: 0.7790 (m-30) cc_final: 0.7488 (m-30) REVERT: B 601 MET cc_start: 0.7037 (tmm) cc_final: 0.6384 (tmm) REVERT: B 622 MET cc_start: 0.8986 (tpt) cc_final: 0.8682 (mmm) REVERT: B 704 CYS cc_start: 0.8089 (p) cc_final: 0.6918 (p) REVERT: B 715 ASP cc_start: 0.6315 (t0) cc_final: 0.5399 (t0) REVERT: B 760 PHE cc_start: 0.7227 (m-80) cc_final: 0.6638 (m-80) REVERT: C 119 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7949 (tmm) REVERT: C 158 ASP cc_start: 0.8315 (t0) cc_final: 0.8072 (t0) REVERT: C 177 ASP cc_start: 0.7787 (m-30) cc_final: 0.7484 (m-30) REVERT: C 601 MET cc_start: 0.7034 (tmm) cc_final: 0.6383 (tmm) REVERT: C 622 MET cc_start: 0.8979 (tpt) cc_final: 0.8677 (mmm) REVERT: C 704 CYS cc_start: 0.8092 (p) cc_final: 0.6922 (p) REVERT: C 715 ASP cc_start: 0.6318 (t0) cc_final: 0.5400 (t0) REVERT: C 760 PHE cc_start: 0.7231 (m-80) cc_final: 0.6642 (m-80) REVERT: D 119 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.7948 (tmm) REVERT: D 158 ASP cc_start: 0.8312 (t0) cc_final: 0.8068 (t0) REVERT: D 177 ASP cc_start: 0.7788 (m-30) cc_final: 0.7488 (m-30) REVERT: D 601 MET cc_start: 0.7033 (tmm) cc_final: 0.6379 (tmm) REVERT: D 622 MET cc_start: 0.8983 (tpt) cc_final: 0.8681 (mmm) REVERT: D 704 CYS cc_start: 0.8086 (p) cc_final: 0.6916 (p) REVERT: D 715 ASP cc_start: 0.6316 (t0) cc_final: 0.5401 (t0) REVERT: D 760 PHE cc_start: 0.7216 (m-80) cc_final: 0.6629 (m-80) outliers start: 60 outliers final: 32 residues processed: 316 average time/residue: 0.1282 time to fit residues: 67.7778 Evaluate side-chains 288 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 252 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 385 GLU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 749 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 187 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 chunk 192 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 201 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 252 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.153794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.096106 restraints weight = 38147.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.100709 restraints weight = 18294.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.103732 restraints weight = 11944.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.105574 restraints weight = 9300.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.106603 restraints weight = 8042.030| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 21220 Z= 0.182 Angle : 0.613 7.227 28712 Z= 0.318 Chirality : 0.045 0.156 3388 Planarity : 0.004 0.047 3720 Dihedral : 4.325 18.546 2932 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.16 % Favored : 93.70 % Rotamer: Outliers : 2.67 % Allowed : 22.33 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.16), residues: 2728 helix: 0.40 (0.16), residues: 1152 sheet: -2.16 (0.25), residues: 384 loop : -2.40 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 96 TYR 0.006 0.001 TYR D 164 PHE 0.010 0.001 PHE B 335 TRP 0.003 0.000 TRP D 264 HIS 0.008 0.001 HIS C 673 Details of bonding type rmsd covalent geometry : bond 0.00417 (21220) covalent geometry : angle 0.61343 (28712) hydrogen bonds : bond 0.04823 ( 888) hydrogen bonds : angle 4.48719 ( 2544) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 272 time to evaluate : 0.786 Fit side-chains REVERT: A 119 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.7980 (tmm) REVERT: A 158 ASP cc_start: 0.8306 (t0) cc_final: 0.8051 (t0) REVERT: A 177 ASP cc_start: 0.7789 (m-30) cc_final: 0.7488 (m-30) REVERT: A 601 MET cc_start: 0.7049 (tmm) cc_final: 0.6387 (tmm) REVERT: A 608 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7334 (mm-30) REVERT: A 622 MET cc_start: 0.8994 (tpt) cc_final: 0.8699 (mmm) REVERT: A 635 ARG cc_start: 0.6391 (ttm170) cc_final: 0.6102 (ttp-110) REVERT: A 704 CYS cc_start: 0.8092 (p) cc_final: 0.6931 (p) REVERT: A 715 ASP cc_start: 0.6325 (t0) cc_final: 0.5436 (t0) REVERT: A 760 PHE cc_start: 0.7234 (m-80) cc_final: 0.6687 (m-80) REVERT: B 119 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.7981 (tmm) REVERT: B 158 ASP cc_start: 0.8304 (t0) cc_final: 0.8049 (t0) REVERT: B 177 ASP cc_start: 0.7794 (m-30) cc_final: 0.7491 (m-30) REVERT: B 601 MET cc_start: 0.7053 (tmm) cc_final: 0.6388 (tmm) REVERT: B 608 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7335 (mm-30) REVERT: B 622 MET cc_start: 0.9001 (tpt) cc_final: 0.8703 (mmm) REVERT: B 635 ARG cc_start: 0.6395 (ttm170) cc_final: 0.6108 (ttp-110) REVERT: B 704 CYS cc_start: 0.8087 (p) cc_final: 0.6926 (p) REVERT: B 715 ASP cc_start: 0.6323 (t0) cc_final: 0.5435 (t0) REVERT: B 760 PHE cc_start: 0.7237 (m-80) cc_final: 0.6688 (m-80) REVERT: C 119 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.7978 (tmm) REVERT: C 158 ASP cc_start: 0.8313 (t0) cc_final: 0.8055 (t0) REVERT: C 177 ASP cc_start: 0.7795 (m-30) cc_final: 0.7494 (m-30) REVERT: C 601 MET cc_start: 0.7050 (tmm) cc_final: 0.6386 (tmm) REVERT: C 608 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7334 (mm-30) REVERT: C 622 MET cc_start: 0.8993 (tpt) cc_final: 0.8697 (mmm) REVERT: C 635 ARG cc_start: 0.6391 (ttm170) cc_final: 0.6100 (ttp-110) REVERT: C 704 CYS cc_start: 0.8089 (p) cc_final: 0.6928 (p) REVERT: C 715 ASP cc_start: 0.6325 (t0) cc_final: 0.5436 (t0) REVERT: C 760 PHE cc_start: 0.7238 (m-80) cc_final: 0.6689 (m-80) REVERT: D 119 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.7975 (tmm) REVERT: D 158 ASP cc_start: 0.8301 (t0) cc_final: 0.8048 (t0) REVERT: D 177 ASP cc_start: 0.7795 (m-30) cc_final: 0.7493 (m-30) REVERT: D 601 MET cc_start: 0.7048 (tmm) cc_final: 0.6384 (tmm) REVERT: D 608 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7335 (mm-30) REVERT: D 622 MET cc_start: 0.8998 (tpt) cc_final: 0.8701 (mmm) REVERT: D 635 ARG cc_start: 0.6390 (ttm170) cc_final: 0.6104 (ttp-110) REVERT: D 704 CYS cc_start: 0.8093 (p) cc_final: 0.6929 (p) REVERT: D 715 ASP cc_start: 0.6323 (t0) cc_final: 0.5434 (t0) REVERT: D 760 PHE cc_start: 0.7230 (m-80) cc_final: 0.6678 (m-80) outliers start: 60 outliers final: 32 residues processed: 316 average time/residue: 0.1263 time to fit residues: 67.0637 Evaluate side-chains 300 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 264 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 385 GLU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 749 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 184 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 63 optimal weight: 8.9990 chunk 126 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 216 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 ASN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 ASN ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.154196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.096705 restraints weight = 38458.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.101352 restraints weight = 18475.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.104335 restraints weight = 12052.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.106232 restraints weight = 9382.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.107298 restraints weight = 8080.342| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 21220 Z= 0.173 Angle : 0.621 12.094 28712 Z= 0.315 Chirality : 0.045 0.157 3388 Planarity : 0.004 0.048 3720 Dihedral : 4.271 19.033 2932 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.74 % Favored : 93.11 % Rotamer: Outliers : 2.67 % Allowed : 23.35 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.16), residues: 2728 helix: 0.36 (0.16), residues: 1152 sheet: -2.03 (0.25), residues: 384 loop : -2.30 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.005 0.001 TYR A 677 PHE 0.010 0.001 PHE B 335 TRP 0.002 0.000 TRP D 748 HIS 0.008 0.001 HIS A 673 Details of bonding type rmsd covalent geometry : bond 0.00397 (21220) covalent geometry : angle 0.62098 (28712) hydrogen bonds : bond 0.04667 ( 888) hydrogen bonds : angle 4.43676 ( 2544) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 276 time to evaluate : 0.800 Fit side-chains REVERT: A 119 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8068 (tmm) REVERT: A 158 ASP cc_start: 0.8284 (t0) cc_final: 0.8037 (t0) REVERT: A 177 ASP cc_start: 0.7797 (m-30) cc_final: 0.7484 (m-30) REVERT: A 601 MET cc_start: 0.7148 (tmm) cc_final: 0.6515 (tmm) REVERT: A 622 MET cc_start: 0.8982 (tpt) cc_final: 0.8653 (mmm) REVERT: A 704 CYS cc_start: 0.8087 (p) cc_final: 0.6990 (p) REVERT: A 715 ASP cc_start: 0.6296 (t0) cc_final: 0.5422 (t0) REVERT: A 760 PHE cc_start: 0.7248 (m-80) cc_final: 0.6731 (m-80) REVERT: B 119 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8062 (tmm) REVERT: B 158 ASP cc_start: 0.8275 (t0) cc_final: 0.8034 (t0) REVERT: B 177 ASP cc_start: 0.7798 (m-30) cc_final: 0.7484 (m-30) REVERT: B 601 MET cc_start: 0.7149 (tmm) cc_final: 0.6512 (tmm) REVERT: B 622 MET cc_start: 0.8987 (tpt) cc_final: 0.8657 (mmm) REVERT: B 704 CYS cc_start: 0.8083 (p) cc_final: 0.6986 (p) REVERT: B 715 ASP cc_start: 0.6292 (t0) cc_final: 0.5418 (t0) REVERT: B 760 PHE cc_start: 0.7244 (m-80) cc_final: 0.6727 (m-80) REVERT: C 119 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8061 (tmm) REVERT: C 158 ASP cc_start: 0.8285 (t0) cc_final: 0.8041 (t0) REVERT: C 177 ASP cc_start: 0.7800 (m-30) cc_final: 0.7483 (m-30) REVERT: C 601 MET cc_start: 0.7152 (tmm) cc_final: 0.6512 (tmm) REVERT: C 622 MET cc_start: 0.8981 (tpt) cc_final: 0.8654 (mmm) REVERT: C 704 CYS cc_start: 0.8086 (p) cc_final: 0.6989 (p) REVERT: C 715 ASP cc_start: 0.6301 (t0) cc_final: 0.5426 (t0) REVERT: C 760 PHE cc_start: 0.7246 (m-80) cc_final: 0.6730 (m-80) REVERT: D 119 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8059 (tmm) REVERT: D 158 ASP cc_start: 0.8279 (t0) cc_final: 0.8035 (t0) REVERT: D 177 ASP cc_start: 0.7801 (m-30) cc_final: 0.7486 (m-30) REVERT: D 601 MET cc_start: 0.7152 (tmm) cc_final: 0.6513 (tmm) REVERT: D 622 MET cc_start: 0.8979 (tpt) cc_final: 0.8652 (mmm) REVERT: D 704 CYS cc_start: 0.8083 (p) cc_final: 0.6983 (p) REVERT: D 715 ASP cc_start: 0.6305 (t0) cc_final: 0.5428 (t0) REVERT: D 760 PHE cc_start: 0.7240 (m-80) cc_final: 0.6720 (m-80) outliers start: 60 outliers final: 40 residues processed: 316 average time/residue: 0.1358 time to fit residues: 70.8688 Evaluate side-chains 304 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 260 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 749 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 245 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 234 optimal weight: 9.9990 chunk 226 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 222 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 119 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 191 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 ASN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 ASN ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 GLN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 ASN ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.152459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.094341 restraints weight = 37933.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.098500 restraints weight = 19363.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.101113 restraints weight = 13042.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.102826 restraints weight = 10394.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.103834 restraints weight = 9103.868| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 21220 Z= 0.238 Angle : 0.683 11.611 28712 Z= 0.348 Chirality : 0.046 0.148 3388 Planarity : 0.004 0.049 3720 Dihedral : 4.533 19.132 2932 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.18 % Favored : 92.67 % Rotamer: Outliers : 2.85 % Allowed : 24.29 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.16), residues: 2728 helix: 0.08 (0.16), residues: 1160 sheet: -2.01 (0.25), residues: 384 loop : -2.38 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.007 0.001 TYR C 677 PHE 0.011 0.002 PHE B 335 TRP 0.002 0.001 TRP C 768 HIS 0.008 0.001 HIS A 673 Details of bonding type rmsd covalent geometry : bond 0.00550 (21220) covalent geometry : angle 0.68251 (28712) hydrogen bonds : bond 0.05227 ( 888) hydrogen bonds : angle 4.59835 ( 2544) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 232 time to evaluate : 0.789 Fit side-chains REVERT: A 119 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8054 (tmm) REVERT: A 158 ASP cc_start: 0.8359 (t0) cc_final: 0.8113 (t0) REVERT: A 177 ASP cc_start: 0.7875 (m-30) cc_final: 0.7545 (m-30) REVERT: A 601 MET cc_start: 0.7200 (tmm) cc_final: 0.6556 (tmm) REVERT: A 622 MET cc_start: 0.8996 (tpt) cc_final: 0.8654 (mmm) REVERT: A 704 CYS cc_start: 0.8155 (OUTLIER) cc_final: 0.6965 (p) REVERT: A 715 ASP cc_start: 0.6350 (t0) cc_final: 0.5387 (t0) REVERT: A 760 PHE cc_start: 0.7302 (m-80) cc_final: 0.6783 (m-80) REVERT: B 119 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8050 (tmm) REVERT: B 158 ASP cc_start: 0.8356 (t0) cc_final: 0.8111 (t0) REVERT: B 177 ASP cc_start: 0.7876 (m-30) cc_final: 0.7546 (m-30) REVERT: B 601 MET cc_start: 0.7204 (tmm) cc_final: 0.6556 (tmm) REVERT: B 622 MET cc_start: 0.8999 (tpt) cc_final: 0.8656 (mmm) REVERT: B 704 CYS cc_start: 0.8150 (OUTLIER) cc_final: 0.6963 (p) REVERT: B 715 ASP cc_start: 0.6349 (t0) cc_final: 0.5384 (t0) REVERT: B 760 PHE cc_start: 0.7306 (m-80) cc_final: 0.6784 (m-80) REVERT: C 119 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8049 (tmm) REVERT: C 158 ASP cc_start: 0.8359 (t0) cc_final: 0.8110 (t0) REVERT: C 177 ASP cc_start: 0.7875 (m-30) cc_final: 0.7548 (m-30) REVERT: C 601 MET cc_start: 0.7197 (tmm) cc_final: 0.6551 (tmm) REVERT: C 622 MET cc_start: 0.8997 (tpt) cc_final: 0.8654 (mmm) REVERT: C 704 CYS cc_start: 0.8151 (OUTLIER) cc_final: 0.6960 (p) REVERT: C 715 ASP cc_start: 0.6354 (t0) cc_final: 0.5387 (t0) REVERT: C 760 PHE cc_start: 0.7307 (m-80) cc_final: 0.6785 (m-80) REVERT: D 119 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8045 (tmm) REVERT: D 158 ASP cc_start: 0.8357 (t0) cc_final: 0.8110 (t0) REVERT: D 177 ASP cc_start: 0.7877 (m-30) cc_final: 0.7548 (m-30) REVERT: D 601 MET cc_start: 0.7199 (tmm) cc_final: 0.6553 (tmm) REVERT: D 622 MET cc_start: 0.8990 (tpt) cc_final: 0.8651 (mmm) REVERT: D 704 CYS cc_start: 0.8152 (OUTLIER) cc_final: 0.6964 (p) REVERT: D 715 ASP cc_start: 0.6350 (t0) cc_final: 0.5385 (t0) REVERT: D 760 PHE cc_start: 0.7304 (m-80) cc_final: 0.6783 (m-80) outliers start: 64 outliers final: 44 residues processed: 276 average time/residue: 0.1285 time to fit residues: 59.0973 Evaluate side-chains 278 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 226 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 704 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 704 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 704 CYS Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 749 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 228 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 263 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 208 optimal weight: 0.8980 chunk 240 optimal weight: 9.9990 chunk 153 optimal weight: 3.9990 chunk 266 optimal weight: 6.9990 chunk 264 optimal weight: 2.9990 chunk 223 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 ASN C 375 ASN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.154609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.097528 restraints weight = 36905.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.101643 restraints weight = 18499.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.104458 restraints weight = 12302.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.106075 restraints weight = 9631.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.107142 restraints weight = 8369.321| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21220 Z= 0.146 Angle : 0.635 11.015 28712 Z= 0.322 Chirality : 0.044 0.142 3388 Planarity : 0.004 0.047 3720 Dihedral : 4.211 18.672 2932 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.24 % Favored : 94.61 % Rotamer: Outliers : 2.45 % Allowed : 25.58 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.16), residues: 2728 helix: 0.14 (0.15), residues: 1176 sheet: -1.89 (0.24), residues: 436 loop : -2.07 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 551 TYR 0.005 0.001 TYR D 164 PHE 0.009 0.001 PHE B 335 TRP 0.004 0.001 TRP D 748 HIS 0.009 0.001 HIS A 673 Details of bonding type rmsd covalent geometry : bond 0.00332 (21220) covalent geometry : angle 0.63464 (28712) hydrogen bonds : bond 0.04448 ( 888) hydrogen bonds : angle 4.48815 ( 2544) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 261 time to evaluate : 0.831 Fit side-chains REVERT: A 119 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8077 (tmm) REVERT: A 158 ASP cc_start: 0.8147 (t0) cc_final: 0.7916 (t0) REVERT: A 177 ASP cc_start: 0.7797 (m-30) cc_final: 0.7454 (m-30) REVERT: A 601 MET cc_start: 0.7074 (tmm) cc_final: 0.6474 (tmm) REVERT: A 622 MET cc_start: 0.8932 (tpt) cc_final: 0.8607 (mmm) REVERT: A 669 GLU cc_start: 0.7516 (pt0) cc_final: 0.7270 (tp30) REVERT: A 704 CYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7061 (p) REVERT: A 715 ASP cc_start: 0.6165 (t0) cc_final: 0.5379 (t0) REVERT: A 760 PHE cc_start: 0.7207 (m-80) cc_final: 0.6664 (m-80) REVERT: B 119 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8075 (tmm) REVERT: B 158 ASP cc_start: 0.8142 (t0) cc_final: 0.7915 (t0) REVERT: B 177 ASP cc_start: 0.7795 (m-30) cc_final: 0.7451 (m-30) REVERT: B 601 MET cc_start: 0.7068 (tmm) cc_final: 0.6467 (tmm) REVERT: B 622 MET cc_start: 0.8956 (tpt) cc_final: 0.8653 (mmm) REVERT: B 669 GLU cc_start: 0.7530 (pt0) cc_final: 0.7296 (tp30) REVERT: B 704 CYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7058 (p) REVERT: B 715 ASP cc_start: 0.6151 (t0) cc_final: 0.5370 (t0) REVERT: B 760 PHE cc_start: 0.7214 (m-80) cc_final: 0.6666 (m-80) REVERT: C 119 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8073 (tmm) REVERT: C 158 ASP cc_start: 0.8154 (t0) cc_final: 0.7930 (t0) REVERT: C 177 ASP cc_start: 0.7796 (m-30) cc_final: 0.7452 (m-30) REVERT: C 601 MET cc_start: 0.7071 (tmm) cc_final: 0.6469 (tmm) REVERT: C 622 MET cc_start: 0.8930 (tpt) cc_final: 0.8606 (mmm) REVERT: C 669 GLU cc_start: 0.7526 (pt0) cc_final: 0.7297 (tp30) REVERT: C 704 CYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7060 (p) REVERT: C 715 ASP cc_start: 0.6166 (t0) cc_final: 0.5379 (t0) REVERT: C 760 PHE cc_start: 0.7203 (m-80) cc_final: 0.6658 (m-80) REVERT: D 119 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8071 (tmm) REVERT: D 158 ASP cc_start: 0.8150 (t0) cc_final: 0.7921 (t0) REVERT: D 177 ASP cc_start: 0.7796 (m-30) cc_final: 0.7454 (m-30) REVERT: D 601 MET cc_start: 0.7072 (tmm) cc_final: 0.6468 (tmm) REVERT: D 622 MET cc_start: 0.8929 (tpt) cc_final: 0.8604 (mmm) REVERT: D 669 GLU cc_start: 0.7533 (pt0) cc_final: 0.7300 (tp30) REVERT: D 704 CYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7058 (p) REVERT: D 715 ASP cc_start: 0.6162 (t0) cc_final: 0.5378 (t0) REVERT: D 760 PHE cc_start: 0.7210 (m-80) cc_final: 0.6661 (m-80) outliers start: 55 outliers final: 41 residues processed: 292 average time/residue: 0.1256 time to fit residues: 61.0422 Evaluate side-chains 305 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 256 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 704 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 704 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 704 CYS Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 749 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 165 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 138 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 199 optimal weight: 7.9990 chunk 166 optimal weight: 0.3980 chunk 93 optimal weight: 0.3980 chunk 222 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 212 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 HIS ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.154988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.096286 restraints weight = 37934.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.100660 restraints weight = 19222.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.103457 restraints weight = 12881.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.105192 restraints weight = 10154.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.106171 restraints weight = 8842.692| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 21220 Z= 0.156 Angle : 0.641 11.203 28712 Z= 0.324 Chirality : 0.044 0.140 3388 Planarity : 0.004 0.047 3720 Dihedral : 4.174 19.077 2932 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.68 % Favored : 94.24 % Rotamer: Outliers : 2.45 % Allowed : 25.49 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.16), residues: 2728 helix: 0.21 (0.16), residues: 1184 sheet: -1.82 (0.24), residues: 436 loop : -2.03 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 635 TYR 0.005 0.001 TYR B 157 PHE 0.009 0.001 PHE A 335 TRP 0.003 0.000 TRP D 748 HIS 0.025 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00357 (21220) covalent geometry : angle 0.64103 (28712) hydrogen bonds : bond 0.04491 ( 888) hydrogen bonds : angle 4.47308 ( 2544) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 262 time to evaluate : 0.840 Fit side-chains REVERT: A 119 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8089 (tmm) REVERT: A 158 ASP cc_start: 0.8163 (t0) cc_final: 0.7925 (t0) REVERT: A 177 ASP cc_start: 0.7806 (m-30) cc_final: 0.7487 (m-30) REVERT: A 601 MET cc_start: 0.7209 (tmm) cc_final: 0.6536 (tmm) REVERT: A 622 MET cc_start: 0.8980 (tpt) cc_final: 0.8682 (mmm) REVERT: A 669 GLU cc_start: 0.7425 (pt0) cc_final: 0.7139 (tp30) REVERT: A 704 CYS cc_start: 0.7880 (OUTLIER) cc_final: 0.6952 (p) REVERT: A 715 ASP cc_start: 0.6057 (t0) cc_final: 0.5303 (t0) REVERT: A 760 PHE cc_start: 0.7190 (m-80) cc_final: 0.6689 (m-80) REVERT: B 119 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8086 (tmm) REVERT: B 158 ASP cc_start: 0.8158 (t0) cc_final: 0.7919 (t0) REVERT: B 177 ASP cc_start: 0.7809 (m-30) cc_final: 0.7492 (m-30) REVERT: B 601 MET cc_start: 0.7209 (tmm) cc_final: 0.6534 (tmm) REVERT: B 622 MET cc_start: 0.8978 (tpt) cc_final: 0.8682 (mmm) REVERT: B 669 GLU cc_start: 0.7424 (pt0) cc_final: 0.7156 (tp30) REVERT: B 704 CYS cc_start: 0.7873 (OUTLIER) cc_final: 0.6946 (p) REVERT: B 715 ASP cc_start: 0.6048 (t0) cc_final: 0.5299 (t0) REVERT: B 760 PHE cc_start: 0.7197 (m-80) cc_final: 0.6694 (m-80) REVERT: C 119 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8087 (tmm) REVERT: C 158 ASP cc_start: 0.8167 (t0) cc_final: 0.7929 (t0) REVERT: C 177 ASP cc_start: 0.7805 (m-30) cc_final: 0.7484 (m-30) REVERT: C 601 MET cc_start: 0.7204 (tmm) cc_final: 0.6531 (tmm) REVERT: C 622 MET cc_start: 0.8978 (tpt) cc_final: 0.8682 (mmm) REVERT: C 669 GLU cc_start: 0.7422 (pt0) cc_final: 0.7154 (tp30) REVERT: C 704 CYS cc_start: 0.7881 (OUTLIER) cc_final: 0.6951 (p) REVERT: C 715 ASP cc_start: 0.6053 (t0) cc_final: 0.5304 (t0) REVERT: C 760 PHE cc_start: 0.7188 (m-80) cc_final: 0.6685 (m-80) REVERT: D 119 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8084 (tmm) REVERT: D 158 ASP cc_start: 0.8165 (t0) cc_final: 0.7927 (t0) REVERT: D 177 ASP cc_start: 0.7806 (m-30) cc_final: 0.7487 (m-30) REVERT: D 601 MET cc_start: 0.7209 (tmm) cc_final: 0.6532 (tmm) REVERT: D 622 MET cc_start: 0.8978 (tpt) cc_final: 0.8680 (mmm) REVERT: D 669 GLU cc_start: 0.7427 (pt0) cc_final: 0.7157 (tp30) REVERT: D 704 CYS cc_start: 0.7876 (OUTLIER) cc_final: 0.6947 (p) REVERT: D 715 ASP cc_start: 0.6059 (t0) cc_final: 0.5306 (t0) REVERT: D 760 PHE cc_start: 0.7202 (m-80) cc_final: 0.6699 (m-80) outliers start: 55 outliers final: 41 residues processed: 297 average time/residue: 0.1344 time to fit residues: 66.0939 Evaluate side-chains 297 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 248 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 704 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 704 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 704 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 704 CYS Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 749 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 146 optimal weight: 0.0270 chunk 78 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 201 optimal weight: 10.0000 chunk 185 optimal weight: 6.9990 chunk 261 optimal weight: 0.7980 chunk 103 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 223 optimal weight: 2.9990 chunk 191 optimal weight: 10.0000 overall best weight: 1.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 GLN C 354 ASN ** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 559 HIS ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.155466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.097385 restraints weight = 37612.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.101647 restraints weight = 18900.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.104586 restraints weight = 12587.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.106245 restraints weight = 9876.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.107397 restraints weight = 8545.493| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 21220 Z= 0.157 Angle : 0.654 10.305 28712 Z= 0.331 Chirality : 0.044 0.139 3388 Planarity : 0.004 0.047 3720 Dihedral : 4.122 17.772 2932 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.68 % Favored : 94.21 % Rotamer: Outliers : 2.54 % Allowed : 26.25 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.16), residues: 2728 helix: 0.28 (0.16), residues: 1180 sheet: -1.75 (0.24), residues: 436 loop : -1.96 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 551 TYR 0.006 0.001 TYR A 677 PHE 0.009 0.001 PHE B 335 TRP 0.003 0.000 TRP D 748 HIS 0.023 0.001 HIS D 559 Details of bonding type rmsd covalent geometry : bond 0.00359 (21220) covalent geometry : angle 0.65379 (28712) hydrogen bonds : bond 0.04479 ( 888) hydrogen bonds : angle 4.46815 ( 2544) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4292.36 seconds wall clock time: 74 minutes 47.57 seconds (4487.57 seconds total)