Starting phenix.real_space_refine on Thu May 15 16:22:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8afh_15398/05_2025/8afh_15398.cif Found real_map, /net/cci-nas-00/data/ceres_data/8afh_15398/05_2025/8afh_15398.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8afh_15398/05_2025/8afh_15398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8afh_15398/05_2025/8afh_15398.map" model { file = "/net/cci-nas-00/data/ceres_data/8afh_15398/05_2025/8afh_15398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8afh_15398/05_2025/8afh_15398.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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 46 5.16 5 C 8248 2.51 5 N 2564 2.21 5 O 2712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13570 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 739 Classifications: {'peptide': 96} Link IDs: {'TRANS': 95} Chain: "B" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 747 Classifications: {'peptide': 97} Link IDs: {'TRANS': 96} Chain: "D" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "C" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 600 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Chain: "F" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 600 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Chain: "G" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 333 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "H" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 299 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "I" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 860 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain breaks: 1 Chain: "J" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "K" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 739 Classifications: {'peptide': 96} Link IDs: {'TRANS': 95} Chain: "L" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 747 Classifications: {'peptide': 97} Link IDs: {'TRANS': 96} Chain: "N" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "M" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "O" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 600 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Chain: "P" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 600 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Chain: "Q" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 333 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "R" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 299 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "S" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 860 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain breaks: 1 Chain: "T" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Time building chain proxies: 9.13, per 1000 atoms: 0.67 Number of scatterers: 13570 At special positions: 0 Unit cell: (99.375, 271.625, 88.775, 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 46 16.00 O 2712 8.00 N 2564 7.00 C 8248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS D 795 " - pdb=" SG CYS D 868 " distance=2.03 Simple disulfide: pdb=" SG CYS C 795 " - pdb=" SG CYS C 868 " distance=2.03 Simple disulfide: pdb=" SG CYS I 795 " - pdb=" SG CYS I 868 " distance=2.03 Simple disulfide: pdb=" SG CYS J 795 " - pdb=" SG CYS J 868 " distance=2.03 Simple disulfide: pdb=" SG CYS N 795 " - pdb=" SG CYS N 868 " distance=2.03 Simple disulfide: pdb=" SG CYS M 795 " - pdb=" SG CYS M 868 " distance=2.03 Simple disulfide: pdb=" SG CYS S 795 " - pdb=" SG CYS S 868 " distance=2.03 Simple disulfide: pdb=" SG CYS T 795 " - pdb=" SG CYS T 868 " distance=2.03 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: 3.41 Conformation dependent library (CDL) restraints added in 1.8 seconds 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3296 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 26 sheets defined 50.3% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 350 through 357 removed outlier: 3.961A pdb=" N ASP A 354 " --> pdb=" O HIS A 350 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 357 " --> pdb=" O VAL A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 441 removed outlier: 3.646A pdb=" N GLU A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 432 removed outlier: 3.876A pdb=" N ALA B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL B 372 " --> pdb=" O ALA B 368 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU B 383 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG B 404 " --> pdb=" O ASP B 400 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 429 " --> pdb=" O SER B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 442 Processing helix chain 'B' and resid 443 through 446 Processing helix chain 'D' and resid 859 through 863 removed outlier: 3.554A pdb=" N THR D 863 " --> pdb=" O PRO D 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 863 removed outlier: 3.891A pdb=" N THR C 863 " --> pdb=" O PRO C 860 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 163 removed outlier: 3.828A pdb=" N LEU E 115 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 163 removed outlier: 3.592A pdb=" N ALA F 92 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 439 removed outlier: 3.796A pdb=" N ALA G 411 " --> pdb=" O ALA G 407 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS G 412 " --> pdb=" O THR G 408 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA G 418 " --> pdb=" O ALA G 414 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU G 426 " --> pdb=" O ARG G 422 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA G 427 " --> pdb=" O LEU G 423 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU G 429 " --> pdb=" O SER G 425 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA G 433 " --> pdb=" O LEU G 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 444 Processing helix chain 'H' and resid 405 through 431 removed outlier: 3.649A pdb=" N HIS H 409 " --> pdb=" O ASP H 405 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU H 410 " --> pdb=" O SER H 406 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE H 420 " --> pdb=" O LEU H 416 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU H 421 " --> pdb=" O GLN H 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 432 through 441 removed outlier: 3.588A pdb=" N ASP H 440 " --> pdb=" O ALA H 436 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG H 441 " --> pdb=" O ALA H 437 " (cutoff:3.500A) Processing helix chain 'I' and resid 859 through 863 removed outlier: 3.603A pdb=" N THR I 863 " --> pdb=" O PRO I 860 " (cutoff:3.500A) Processing helix chain 'J' and resid 859 through 863 removed outlier: 3.819A pdb=" N THR J 863 " --> pdb=" O PRO J 860 " (cutoff:3.500A) Processing helix chain 'K' and resid 351 through 357 removed outlier: 3.571A pdb=" N THR K 355 " --> pdb=" O ALA K 351 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG K 357 " --> pdb=" O VAL K 353 " (cutoff:3.500A) Processing helix chain 'K' and resid 357 through 441 removed outlier: 3.647A pdb=" N GLU K 362 " --> pdb=" O ALA K 358 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG K 363 " --> pdb=" O THR K 359 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA K 364 " --> pdb=" O ALA K 360 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA K 368 " --> pdb=" O ALA K 364 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS K 369 " --> pdb=" O ASP K 365 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL K 372 " --> pdb=" O ALA K 368 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER K 425 " --> pdb=" O GLU K 421 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU K 426 " --> pdb=" O ARG K 422 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG K 441 " --> pdb=" O ALA K 437 " (cutoff:3.500A) Processing helix chain 'L' and resid 352 through 432 removed outlier: 3.876A pdb=" N ALA L 356 " --> pdb=" O GLY L 352 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU L 362 " --> pdb=" O ALA L 358 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU L 367 " --> pdb=" O ARG L 363 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA L 371 " --> pdb=" O LEU L 367 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL L 372 " --> pdb=" O ALA L 368 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU L 383 " --> pdb=" O LYS L 379 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG L 404 " --> pdb=" O ASP L 400 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE L 420 " --> pdb=" O LEU L 416 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU L 429 " --> pdb=" O SER L 425 " (cutoff:3.500A) Processing helix chain 'L' and resid 432 through 442 Processing helix chain 'L' and resid 443 through 446 Processing helix chain 'N' and resid 859 through 863 removed outlier: 3.554A pdb=" N THR N 863 " --> pdb=" O PRO N 860 " (cutoff:3.500A) Processing helix chain 'M' and resid 859 through 863 removed outlier: 3.892A pdb=" N THR M 863 " --> pdb=" O PRO M 860 " (cutoff:3.500A) Processing helix chain 'O' and resid 86 through 163 removed outlier: 3.828A pdb=" N LEU O 115 " --> pdb=" O VAL O 111 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA O 116 " --> pdb=" O SER O 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 163 removed outlier: 3.592A pdb=" N ALA P 92 " --> pdb=" O ILE P 88 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN P 93 " --> pdb=" O ALA P 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 404 through 439 removed outlier: 3.796A pdb=" N ALA Q 411 " --> pdb=" O ALA Q 407 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS Q 412 " --> pdb=" O THR Q 408 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA Q 418 " --> pdb=" O ALA Q 414 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU Q 426 " --> pdb=" O ARG Q 422 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA Q 427 " --> pdb=" O LEU Q 423 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA Q 433 " --> pdb=" O LEU Q 429 " (cutoff:3.500A) Processing helix chain 'Q' and resid 440 through 444 Processing helix chain 'R' and resid 405 through 431 removed outlier: 3.648A pdb=" N HIS R 409 " --> pdb=" O ASP R 405 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU R 410 " --> pdb=" O SER R 406 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE R 420 " --> pdb=" O LEU R 416 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU R 421 " --> pdb=" O GLN R 417 " (cutoff:3.500A) Processing helix chain 'R' and resid 432 through 441 removed outlier: 3.588A pdb=" N ASP R 440 " --> pdb=" O ALA R 436 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG R 441 " --> pdb=" O ALA R 437 " (cutoff:3.500A) Processing helix chain 'S' and resid 859 through 863 removed outlier: 3.602A pdb=" N THR S 863 " --> pdb=" O PRO S 860 " (cutoff:3.500A) Processing helix chain 'T' and resid 859 through 863 removed outlier: 3.819A pdb=" N THR T 863 " --> pdb=" O PRO T 860 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 6 through 7 removed outlier: 3.710A pdb=" N VAL D 851 " --> pdb=" O CYS D 795 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 850 " --> pdb=" O ASP D 845 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.212A pdb=" N GLY D 10 " --> pdb=" O THR D 885 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N MET D 807 " --> pdb=" O VAL D 823 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL D 823 " --> pdb=" O MET D 807 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP D 809 " --> pdb=" O VAL D 821 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 870 through 872 Processing sheet with id=AA4, first strand: chain 'C' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.550A pdb=" N VAL C 12 " --> pdb=" O THR C 885 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 830 through 832 removed outlier: 7.030A pdb=" N TRP C 809 " --> pdb=" O VAL C 821 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VAL C 823 " --> pdb=" O MET C 807 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N MET C 807 " --> pdb=" O VAL C 823 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.613A pdb=" N VAL I 851 " --> pdb=" O CYS I 795 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.808A pdb=" N MET I 807 " --> pdb=" O VAL I 823 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL I 823 " --> pdb=" O MET I 807 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP I 809 " --> pdb=" O VAL I 821 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 870 through 872 removed outlier: 3.572A pdb=" N TYR I 872 " --> pdb=" O SER I 875 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AB2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.544A pdb=" N GLY J 10 " --> pdb=" O THR J 885 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.544A pdb=" N GLY J 10 " --> pdb=" O THR J 885 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 792 through 793 Processing sheet with id=AB5, first strand: chain 'N' and resid 6 through 7 removed outlier: 3.711A pdb=" N VAL N 851 " --> pdb=" O CYS N 795 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR N 850 " --> pdb=" O ASP N 845 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.212A pdb=" N GLY N 10 " --> pdb=" O THR N 885 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N MET N 807 " --> pdb=" O VAL N 823 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL N 823 " --> pdb=" O MET N 807 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP N 809 " --> pdb=" O VAL N 821 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 870 through 872 Processing sheet with id=AB8, first strand: chain 'M' and resid 5 through 7 Processing sheet with id=AB9, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.551A pdb=" N VAL M 12 " --> pdb=" O THR M 885 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 830 through 832 removed outlier: 7.030A pdb=" N TRP M 809 " --> pdb=" O VAL M 821 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VAL M 823 " --> pdb=" O MET M 807 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N MET M 807 " --> pdb=" O VAL M 823 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'S' and resid 5 through 6 removed outlier: 3.613A pdb=" N VAL S 851 " --> pdb=" O CYS S 795 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.810A pdb=" N MET S 807 " --> pdb=" O VAL S 823 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL S 823 " --> pdb=" O MET S 807 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP S 809 " --> pdb=" O VAL S 821 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'S' and resid 870 through 872 removed outlier: 3.571A pdb=" N TYR S 872 " --> pdb=" O SER S 875 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'T' and resid 4 through 6 Processing sheet with id=AC6, first strand: chain 'T' and resid 10 through 12 removed outlier: 6.545A pdb=" N GLY T 10 " --> pdb=" O THR T 885 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'T' and resid 10 through 12 removed outlier: 6.545A pdb=" N GLY T 10 " --> pdb=" O THR T 885 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'T' and resid 792 through 793 926 hydrogen bonds defined for protein. 2586 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.65 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4856 1.34 - 1.46: 2135 1.46 - 1.58: 6615 1.58 - 1.70: 0 1.70 - 1.81: 76 Bond restraints: 13682 Sorted by residual: bond pdb=" CB TRP M 827 " pdb=" CG TRP M 827 " ideal model delta sigma weight residual 1.498 1.446 0.052 3.10e-02 1.04e+03 2.81e+00 bond pdb=" CB TRP C 827 " pdb=" CG TRP C 827 " ideal model delta sigma weight residual 1.498 1.446 0.052 3.10e-02 1.04e+03 2.79e+00 bond pdb=" C TYR T 832 " pdb=" N VAL T 833 " ideal model delta sigma weight residual 1.334 1.317 0.017 1.29e-02 6.01e+03 1.74e+00 bond pdb=" CG1 ILE N 806 " pdb=" CD1 ILE N 806 " ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.69e+00 bond pdb=" CG1 ILE D 806 " pdb=" CD1 ILE D 806 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.67e+00 ... (remaining 13677 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 16816 1.17 - 2.35: 1354 2.35 - 3.52: 201 3.52 - 4.70: 33 4.70 - 5.87: 14 Bond angle restraints: 18418 Sorted by residual: angle pdb=" N ILE J 806 " pdb=" CA ILE J 806 " pdb=" C ILE J 806 " ideal model delta sigma weight residual 108.93 113.32 -4.39 1.35e+00 5.49e-01 1.06e+01 angle pdb=" N ILE T 806 " pdb=" CA ILE T 806 " pdb=" C ILE T 806 " ideal model delta sigma weight residual 108.93 113.32 -4.39 1.35e+00 5.49e-01 1.06e+01 angle pdb=" N ILE D 806 " pdb=" CA ILE D 806 " pdb=" C ILE D 806 " ideal model delta sigma weight residual 109.30 113.41 -4.11 1.31e+00 5.83e-01 9.83e+00 angle pdb=" N ILE N 806 " pdb=" CA ILE N 806 " pdb=" C ILE N 806 " ideal model delta sigma weight residual 109.30 113.37 -4.07 1.31e+00 5.83e-01 9.65e+00 angle pdb=" C ALA E 118 " pdb=" N GLU E 119 " pdb=" CA GLU E 119 " ideal model delta sigma weight residual 120.68 115.79 4.89 1.70e+00 3.46e-01 8.27e+00 ... (remaining 18413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 7573 17.25 - 34.51: 761 34.51 - 51.76: 92 51.76 - 69.02: 12 69.02 - 86.27: 28 Dihedral angle restraints: 8466 sinusoidal: 3382 harmonic: 5084 Sorted by residual: dihedral pdb=" CB CYS M 795 " pdb=" SG CYS M 795 " pdb=" SG CYS M 868 " pdb=" CB CYS M 868 " ideal model delta sinusoidal sigma weight residual 93.00 43.72 49.28 1 1.00e+01 1.00e-02 3.34e+01 dihedral pdb=" CB CYS C 795 " pdb=" SG CYS C 795 " pdb=" SG CYS C 868 " pdb=" CB CYS C 868 " ideal model delta sinusoidal sigma weight residual 93.00 43.76 49.24 1 1.00e+01 1.00e-02 3.33e+01 dihedral pdb=" CB CYS I 795 " pdb=" SG CYS I 795 " pdb=" SG CYS I 868 " pdb=" CB CYS I 868 " ideal model delta sinusoidal sigma weight residual 93.00 44.87 48.13 1 1.00e+01 1.00e-02 3.19e+01 ... (remaining 8463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1438 0.040 - 0.080: 476 0.080 - 0.120: 152 0.120 - 0.161: 7 0.161 - 0.201: 9 Chirality restraints: 2082 Sorted by residual: chirality pdb=" CB ILE J 842 " pdb=" CA ILE J 842 " pdb=" CG1 ILE J 842 " pdb=" CG2 ILE J 842 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE T 842 " pdb=" CA ILE T 842 " pdb=" CG1 ILE T 842 " pdb=" CG2 ILE T 842 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.45e-01 chirality pdb=" CB ILE S 842 " pdb=" CA ILE S 842 " pdb=" CG1 ILE S 842 " pdb=" CG2 ILE S 842 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.41e-01 ... (remaining 2079 not shown) Planarity restraints: 2438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS M 859 " 0.057 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO M 860 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO M 860 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO M 860 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 859 " 0.057 5.00e-02 4.00e+02 8.63e-02 1.19e+01 pdb=" N PRO C 860 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO C 860 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 860 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN L 417 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" CD GLN L 417 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLN L 417 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN L 417 " -0.013 2.00e-02 2.50e+03 ... (remaining 2435 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 549 2.71 - 3.26: 13767 3.26 - 3.80: 20842 3.80 - 4.35: 26626 4.35 - 4.90: 44512 Nonbonded interactions: 106296 Sorted by model distance: nonbonded pdb=" O THR L 424 " pdb=" ND2 ASN M 831 " model vdw 2.160 3.120 nonbonded pdb=" O THR B 424 " pdb=" ND2 ASN C 831 " model vdw 2.161 3.120 nonbonded pdb=" NH1 ARG D 799 " pdb=" OG SER D 800 " model vdw 2.201 3.120 nonbonded pdb=" NH1 ARG N 799 " pdb=" OG SER N 800 " model vdw 2.202 3.120 nonbonded pdb=" OD1 ASP I 802 " pdb=" NH2 ARG I 844 " model vdw 2.245 3.120 ... (remaining 106291 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 350 through 445) selection = chain 'K' selection = (chain 'L' and resid 350 through 445) } ncs_group { reference = (chain 'C' and resid 2 through 887) selection = (chain 'D' and resid 2 through 887) selection = chain 'I' selection = (chain 'J' and resid 2 through 887) selection = (chain 'M' and resid 2 through 887) selection = (chain 'N' and resid 2 through 887) selection = chain 'S' selection = (chain 'T' and resid 2 through 887) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'O' selection = chain 'P' } ncs_group { reference = (chain 'G' and resid 403 through 441) selection = chain 'H' selection = (chain 'Q' and resid 403 through 441) selection = chain 'R' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.240 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 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:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5983 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13690 Z= 0.273 Angle : 0.701 5.869 18434 Z= 0.431 Chirality : 0.044 0.201 2082 Planarity : 0.004 0.086 2438 Dihedral : 14.167 86.270 5146 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.20), residues: 1704 helix: -0.24 (0.18), residues: 758 sheet: -2.06 (0.22), residues: 478 loop : 0.03 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 827 HIS 0.005 0.002 HIS K 350 PHE 0.006 0.001 PHE I 840 TYR 0.018 0.002 TYR T 13 ARG 0.013 0.001 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.21907 ( 918) hydrogen bonds : angle 9.24467 ( 2586) SS BOND : bond 0.00239 ( 8) SS BOND : angle 1.60641 ( 16) covalent geometry : bond 0.00581 (13682) covalent geometry : angle 0.69947 (18418) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 369 LYS cc_start: 0.6832 (mtmm) cc_final: 0.6493 (mtmm) REVERT: B 376 LYS cc_start: 0.7593 (tppp) cc_final: 0.7317 (tppp) REVERT: D 792 ARG cc_start: 0.7445 (ttt180) cc_final: 0.7223 (ttm-80) REVERT: C 863 THR cc_start: 0.7906 (m) cc_final: 0.7567 (p) REVERT: G 415 GLU cc_start: 0.7209 (tp30) cc_final: 0.6804 (tp30) REVERT: G 419 THR cc_start: 0.7582 (t) cc_final: 0.7374 (p) REVERT: I 829 SER cc_start: 0.8178 (t) cc_final: 0.7899 (p) REVERT: I 854 GLN cc_start: 0.6504 (tp40) cc_final: 0.6114 (tp40) REVERT: J 855 MET cc_start: 0.7018 (mmm) cc_final: 0.6259 (mmm) REVERT: J 858 LEU cc_start: 0.6366 (mt) cc_final: 0.6031 (tt) REVERT: L 380 ARG cc_start: 0.7396 (ptp90) cc_final: 0.6907 (mtm110) REVERT: L 395 MET cc_start: 0.5951 (ttm) cc_final: 0.5577 (mmm) REVERT: L 416 LEU cc_start: 0.7606 (tp) cc_final: 0.7129 (mp) REVERT: N 860 PRO cc_start: 0.8040 (Cg_exo) cc_final: 0.7816 (Cg_endo) REVERT: M 820 MET cc_start: 0.7789 (ttp) cc_final: 0.7550 (ttp) REVERT: R 413 ILE cc_start: 0.7276 (mm) cc_final: 0.6827 (mm) REVERT: R 426 GLU cc_start: 0.6575 (mt-10) cc_final: 0.6323 (mt-10) REVERT: T 807 MET cc_start: 0.7422 (mmm) cc_final: 0.7205 (mtt) REVERT: T 871 ILE cc_start: 0.7862 (mp) cc_final: 0.7516 (mt) outliers start: 0 outliers final: 0 residues processed: 330 average time/residue: 0.3431 time to fit residues: 148.2744 Evaluate side-chains 305 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.4980 chunk 125 optimal weight: 0.6980 chunk 69 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 150 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN D 869 ASN C 831 ASN E 93 ASN J 805 ASN ** N 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 856 ASN N 869 ASN M 854 GLN P 98 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.177377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.164897 restraints weight = 19343.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.168052 restraints weight = 11051.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.170063 restraints weight = 7048.090| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6297 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13690 Z= 0.180 Angle : 0.603 7.527 18434 Z= 0.335 Chirality : 0.041 0.178 2082 Planarity : 0.006 0.103 2438 Dihedral : 4.811 21.591 1962 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.36 % Allowed : 11.46 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.21), residues: 1704 helix: 1.38 (0.18), residues: 762 sheet: -1.73 (0.22), residues: 476 loop : 0.31 (0.32), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 827 HIS 0.003 0.001 HIS A 350 PHE 0.006 0.002 PHE M 840 TYR 0.022 0.002 TYR T 810 ARG 0.009 0.001 ARG N 844 Details of bonding type rmsd hydrogen bonds : bond 0.04930 ( 918) hydrogen bonds : angle 5.49727 ( 2586) SS BOND : bond 0.00179 ( 8) SS BOND : angle 0.69408 ( 16) covalent geometry : bond 0.00376 (13682) covalent geometry : angle 0.60300 (18418) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 311 time to evaluate : 1.334 Fit side-chains revert: symmetry clash REVERT: B 379 LYS cc_start: 0.8419 (tmtt) cc_final: 0.7899 (tmmt) REVERT: B 384 ARG cc_start: 0.7035 (mtp180) cc_final: 0.6733 (mtp-110) REVERT: D 792 ARG cc_start: 0.7463 (ttt180) cc_final: 0.7230 (ttt-90) REVERT: G 419 THR cc_start: 0.7788 (t) cc_final: 0.7468 (p) REVERT: I 817 GLN cc_start: 0.6018 (mp10) cc_final: 0.5597 (mp10) REVERT: I 829 SER cc_start: 0.8545 (t) cc_final: 0.8075 (p) REVERT: I 872 TYR cc_start: 0.7925 (t80) cc_final: 0.7426 (t80) REVERT: J 858 LEU cc_start: 0.6446 (mt) cc_final: 0.5612 (tt) REVERT: L 395 MET cc_start: 0.5532 (ttm) cc_final: 0.5174 (mmm) REVERT: N 810 TYR cc_start: 0.7953 (m-80) cc_final: 0.7682 (m-10) REVERT: N 812 GLN cc_start: 0.6619 (tt0) cc_final: 0.6363 (tt0) REVERT: M 13 TYR cc_start: 0.5312 (m-80) cc_final: 0.4948 (m-80) REVERT: M 820 MET cc_start: 0.8107 (ttp) cc_final: 0.7773 (ttp) REVERT: M 866 TYR cc_start: 0.8029 (m-80) cc_final: 0.7821 (m-10) REVERT: O 107 GLU cc_start: 0.7063 (tm-30) cc_final: 0.6705 (tm-30) REVERT: P 107 GLU cc_start: 0.7602 (tt0) cc_final: 0.6780 (tt0) REVERT: Q 416 LEU cc_start: 0.7626 (mt) cc_final: 0.7363 (mt) REVERT: R 413 ILE cc_start: 0.7598 (mm) cc_final: 0.7244 (mm) REVERT: R 426 GLU cc_start: 0.6738 (mt-10) cc_final: 0.6409 (mt-10) REVERT: S 855 MET cc_start: 0.6934 (OUTLIER) cc_final: 0.6543 (mtm) REVERT: S 872 TYR cc_start: 0.7557 (t80) cc_final: 0.7355 (t80) REVERT: T 7 SER cc_start: 0.7034 (m) cc_final: 0.6561 (t) REVERT: T 807 MET cc_start: 0.7540 (mmm) cc_final: 0.7267 (mtt) REVERT: T 809 TRP cc_start: 0.7442 (m100) cc_final: 0.7111 (m100) REVERT: T 820 MET cc_start: 0.7573 (mmm) cc_final: 0.7205 (mmm) outliers start: 33 outliers final: 19 residues processed: 327 average time/residue: 0.2893 time to fit residues: 129.4964 Evaluate side-chains 317 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 297 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 835 SER Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain J residue 824 VAL Chi-restraints excluded: chain K residue 425 SER Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 824 VAL Chi-restraints excluded: chain N residue 835 SER Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain O residue 163 SER Chi-restraints excluded: chain P residue 98 GLN Chi-restraints excluded: chain S residue 855 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 24 optimal weight: 0.4980 chunk 138 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 55 optimal weight: 0.3980 chunk 50 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 162 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN E 93 ASN L 374 GLN ** N 805 ASN ** 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 = 0.4178 r_free = 0.4178 target = 0.170666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.159595 restraints weight = 18843.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.162222 restraints weight = 11326.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.164003 restraints weight = 7537.189| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13690 Z= 0.171 Angle : 0.551 6.259 18434 Z= 0.305 Chirality : 0.040 0.152 2082 Planarity : 0.004 0.060 2438 Dihedral : 4.522 19.127 1962 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.94 % Allowed : 14.83 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.21), residues: 1704 helix: 1.91 (0.18), residues: 766 sheet: -1.47 (0.22), residues: 470 loop : 0.43 (0.32), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 809 HIS 0.003 0.001 HIS K 350 PHE 0.014 0.002 PHE N 840 TYR 0.015 0.002 TYR J 872 ARG 0.008 0.001 ARG Q 422 Details of bonding type rmsd hydrogen bonds : bond 0.04505 ( 918) hydrogen bonds : angle 5.05486 ( 2586) SS BOND : bond 0.00368 ( 8) SS BOND : angle 0.84501 ( 16) covalent geometry : bond 0.00363 (13682) covalent geometry : angle 0.55084 (18418) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 318 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 LEU cc_start: 0.8037 (tp) cc_final: 0.7794 (tp) REVERT: B 384 ARG cc_start: 0.7153 (mtp180) cc_final: 0.6860 (mtp-110) REVERT: B 416 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8437 (mp) REVERT: G 423 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6991 (mt) REVERT: H 426 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: I 817 GLN cc_start: 0.6257 (mp10) cc_final: 0.5856 (mp10) REVERT: I 829 SER cc_start: 0.8526 (t) cc_final: 0.8109 (p) REVERT: J 858 LEU cc_start: 0.6934 (mt) cc_final: 0.5926 (tt) REVERT: K 350 HIS cc_start: 0.3457 (OUTLIER) cc_final: 0.3134 (m90) REVERT: K 422 ARG cc_start: 0.7527 (ttm-80) cc_final: 0.7251 (tpp-160) REVERT: L 363 ARG cc_start: 0.7523 (mmm-85) cc_final: 0.7151 (mmm-85) REVERT: L 416 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7881 (mp) REVERT: N 810 TYR cc_start: 0.7956 (m-80) cc_final: 0.7628 (m-80) REVERT: N 877 TYR cc_start: 0.8160 (m-10) cc_final: 0.7862 (m-80) REVERT: M 820 MET cc_start: 0.8079 (ttp) cc_final: 0.7575 (ttp) REVERT: M 825 THR cc_start: 0.7232 (OUTLIER) cc_final: 0.6882 (p) REVERT: M 866 TYR cc_start: 0.8151 (m-80) cc_final: 0.7855 (m-10) REVERT: O 107 GLU cc_start: 0.7031 (tm-30) cc_final: 0.6565 (tm-30) REVERT: O 156 LYS cc_start: 0.7458 (mttt) cc_final: 0.7073 (mttt) REVERT: P 107 GLU cc_start: 0.7914 (tt0) cc_final: 0.6786 (tt0) REVERT: Q 422 ARG cc_start: 0.6470 (tpt90) cc_final: 0.6261 (tpt170) REVERT: R 413 ILE cc_start: 0.7685 (mm) cc_final: 0.7306 (mm) REVERT: R 426 GLU cc_start: 0.6770 (mt-10) cc_final: 0.6367 (mt-10) REVERT: T 7 SER cc_start: 0.7235 (m) cc_final: 0.6793 (t) REVERT: T 809 TRP cc_start: 0.7532 (m100) cc_final: 0.6921 (m100) REVERT: T 820 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.6993 (ttm) REVERT: T 886 VAL cc_start: 0.7683 (m) cc_final: 0.7295 (p) outliers start: 55 outliers final: 37 residues processed: 339 average time/residue: 0.2838 time to fit residues: 133.9560 Evaluate side-chains 352 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 308 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 797 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 825 THR Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 434 LEU Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain I residue 820 MET Chi-restraints excluded: chain I residue 869 ASN Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 824 VAL Chi-restraints excluded: chain J residue 825 THR Chi-restraints excluded: chain J residue 831 ASN Chi-restraints excluded: chain K residue 350 HIS Chi-restraints excluded: chain K residue 425 SER Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 416 LEU Chi-restraints excluded: chain L residue 429 LEU Chi-restraints excluded: chain N residue 790 SER Chi-restraints excluded: chain N residue 876 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 794 SER Chi-restraints excluded: chain M residue 825 THR Chi-restraints excluded: chain O residue 163 SER Chi-restraints excluded: chain P residue 98 GLN Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain R residue 416 LEU Chi-restraints excluded: chain S residue 790 SER Chi-restraints excluded: chain S residue 869 ASN Chi-restraints excluded: chain T residue 820 MET Chi-restraints excluded: chain T residue 823 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 71 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 56 optimal weight: 0.4980 chunk 66 optimal weight: 0.2980 chunk 119 optimal weight: 0.8980 chunk 147 optimal weight: 0.0040 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN B 409 HIS C 3 GLN C 5 GLN E 93 ASN L 350 HIS L 374 GLN ** N 805 ASN ** 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 = 0.4171 r_free = 0.4171 target = 0.170201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.158305 restraints weight = 18833.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.161182 restraints weight = 10951.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.163128 restraints weight = 7134.659| |-----------------------------------------------------------------------------| r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13690 Z= 0.139 Angle : 0.498 5.944 18434 Z= 0.276 Chirality : 0.039 0.143 2082 Planarity : 0.004 0.053 2438 Dihedral : 4.259 18.179 1962 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.37 % Allowed : 17.19 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.21), residues: 1704 helix: 2.40 (0.17), residues: 766 sheet: -1.41 (0.22), residues: 486 loop : 0.68 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 827 HIS 0.003 0.001 HIS K 350 PHE 0.005 0.001 PHE S 840 TYR 0.012 0.001 TYR C 810 ARG 0.005 0.000 ARG F 145 Details of bonding type rmsd hydrogen bonds : bond 0.04067 ( 918) hydrogen bonds : angle 4.65517 ( 2586) SS BOND : bond 0.00383 ( 8) SS BOND : angle 0.68163 ( 16) covalent geometry : bond 0.00293 (13682) covalent geometry : angle 0.49777 (18418) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 310 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 MET cc_start: 0.5722 (ttm) cc_final: 0.5307 (ttt) REVERT: A 422 ARG cc_start: 0.7333 (tpt90) cc_final: 0.6936 (tpp-160) REVERT: C 2 VAL cc_start: 0.7450 (OUTLIER) cc_final: 0.7134 (p) REVERT: C 6 GLU cc_start: 0.6873 (mm-30) cc_final: 0.6525 (mm-30) REVERT: C 855 MET cc_start: 0.7588 (mtm) cc_final: 0.7147 (mtp) REVERT: H 426 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.7002 (mp0) REVERT: I 817 GLN cc_start: 0.6332 (mp10) cc_final: 0.5919 (mp10) REVERT: I 829 SER cc_start: 0.8441 (t) cc_final: 0.8013 (p) REVERT: K 412 LYS cc_start: 0.7685 (ttmm) cc_final: 0.7414 (ttmm) REVERT: L 363 ARG cc_start: 0.7413 (mmm-85) cc_final: 0.7041 (mmm-85) REVERT: L 416 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7843 (mp) REVERT: N 810 TYR cc_start: 0.7932 (m-80) cc_final: 0.7619 (m-80) REVERT: M 820 MET cc_start: 0.7955 (ttp) cc_final: 0.7520 (ttp) REVERT: M 825 THR cc_start: 0.7212 (OUTLIER) cc_final: 0.6844 (p) REVERT: M 866 TYR cc_start: 0.8254 (m-80) cc_final: 0.7927 (m-10) REVERT: O 107 GLU cc_start: 0.6917 (tm-30) cc_final: 0.6469 (tm-30) REVERT: O 156 LYS cc_start: 0.7365 (mttt) cc_final: 0.7041 (mttt) REVERT: P 98 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7557 (mm110) REVERT: P 107 GLU cc_start: 0.7604 (tt0) cc_final: 0.6513 (tt0) REVERT: Q 422 ARG cc_start: 0.6379 (tpt90) cc_final: 0.6139 (tpt170) REVERT: R 413 ILE cc_start: 0.7742 (mm) cc_final: 0.7344 (mm) REVERT: R 426 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6143 (mt-10) REVERT: T 7 SER cc_start: 0.7572 (m) cc_final: 0.7041 (t) REVERT: T 809 TRP cc_start: 0.7539 (m100) cc_final: 0.6815 (m100) REVERT: T 886 VAL cc_start: 0.7732 (m) cc_final: 0.7263 (p) outliers start: 61 outliers final: 40 residues processed: 336 average time/residue: 0.3188 time to fit residues: 147.5869 Evaluate side-chains 348 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 303 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 867 SER Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 816 LYS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 825 THR Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 833 VAL Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain G residue 412 LYS Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain I residue 820 MET Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 824 VAL Chi-restraints excluded: chain J residue 831 ASN Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 416 LEU Chi-restraints excluded: chain L residue 423 LEU Chi-restraints excluded: chain L residue 429 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 790 SER Chi-restraints excluded: chain N residue 835 SER Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 13 TYR Chi-restraints excluded: chain M residue 794 SER Chi-restraints excluded: chain M residue 825 THR Chi-restraints excluded: chain O residue 103 LEU Chi-restraints excluded: chain O residue 163 SER Chi-restraints excluded: chain P residue 98 GLN Chi-restraints excluded: chain R residue 416 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 820 MET Chi-restraints excluded: chain S residue 851 VAL Chi-restraints excluded: chain S residue 869 ASN Chi-restraints excluded: chain T residue 855 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 51 optimal weight: 0.6980 chunk 144 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 108 optimal weight: 0.4980 chunk 88 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 62 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN E 93 ASN E 139 ASN L 374 GLN L 409 HIS ** N 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 417 GLN T 805 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.170691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.157864 restraints weight = 19444.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.161031 restraints weight = 11122.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.163046 restraints weight = 7156.287| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13690 Z= 0.174 Angle : 0.545 9.219 18434 Z= 0.296 Chirality : 0.040 0.146 2082 Planarity : 0.004 0.052 2438 Dihedral : 4.356 18.172 1962 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 5.59 % Allowed : 18.19 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.21), residues: 1704 helix: 2.46 (0.17), residues: 764 sheet: -1.39 (0.22), residues: 474 loop : 0.55 (0.32), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 827 HIS 0.004 0.001 HIS K 350 PHE 0.005 0.001 PHE S 840 TYR 0.015 0.002 TYR D 832 ARG 0.006 0.001 ARG F 145 Details of bonding type rmsd hydrogen bonds : bond 0.04184 ( 918) hydrogen bonds : angle 4.73268 ( 2586) SS BOND : bond 0.00487 ( 8) SS BOND : angle 1.02934 ( 16) covalent geometry : bond 0.00372 (13682) covalent geometry : angle 0.54428 (18418) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 307 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 MET cc_start: 0.5810 (ttm) cc_final: 0.5603 (ttt) REVERT: A 422 ARG cc_start: 0.7367 (tpt90) cc_final: 0.7115 (tpp-160) REVERT: B 416 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8479 (mp) REVERT: C 2 VAL cc_start: 0.7255 (OUTLIER) cc_final: 0.7043 (p) REVERT: C 6 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6285 (mm-30) REVERT: C 809 TRP cc_start: 0.8385 (m100) cc_final: 0.8070 (m100) REVERT: C 855 MET cc_start: 0.7406 (mtm) cc_final: 0.6828 (mtp) REVERT: G 423 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6926 (mt) REVERT: H 426 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6984 (mp0) REVERT: H 435 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7747 (mt-10) REVERT: I 817 GLN cc_start: 0.6488 (mp10) cc_final: 0.6029 (mp10) REVERT: K 412 LYS cc_start: 0.7667 (ttmm) cc_final: 0.7404 (ttmm) REVERT: L 363 ARG cc_start: 0.7450 (mmm-85) cc_final: 0.7050 (mmm-85) REVERT: L 416 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7912 (mp) REVERT: L 431 GLU cc_start: 0.6658 (tp30) cc_final: 0.6449 (tp30) REVERT: L 438 ARG cc_start: 0.6711 (mtp180) cc_final: 0.6507 (mtp180) REVERT: L 439 ARG cc_start: 0.7799 (mtt180) cc_final: 0.7505 (mtt180) REVERT: N 810 TYR cc_start: 0.7868 (m-80) cc_final: 0.7555 (m-80) REVERT: N 818 ARG cc_start: 0.7884 (ptp-110) cc_final: 0.7548 (ptp-110) REVERT: N 839 ARG cc_start: 0.6449 (OUTLIER) cc_final: 0.6147 (ttp80) REVERT: M 13 TYR cc_start: 0.6111 (OUTLIER) cc_final: 0.5049 (t80) REVERT: M 820 MET cc_start: 0.7999 (ttp) cc_final: 0.7532 (ttp) REVERT: M 825 THR cc_start: 0.7117 (OUTLIER) cc_final: 0.6766 (p) REVERT: M 866 TYR cc_start: 0.8359 (m-80) cc_final: 0.7926 (m-10) REVERT: O 107 GLU cc_start: 0.7036 (tm-30) cc_final: 0.6479 (tm-30) REVERT: O 156 LYS cc_start: 0.7459 (mttt) cc_final: 0.7100 (mttt) REVERT: P 107 GLU cc_start: 0.7676 (tt0) cc_final: 0.6428 (tt0) REVERT: R 417 GLN cc_start: 0.4976 (OUTLIER) cc_final: 0.2252 (tm130) REVERT: T 7 SER cc_start: 0.7678 (m) cc_final: 0.7240 (t) REVERT: T 809 TRP cc_start: 0.7368 (m100) cc_final: 0.6912 (m100) REVERT: T 886 VAL cc_start: 0.7537 (OUTLIER) cc_final: 0.7036 (p) outliers start: 78 outliers final: 51 residues processed: 349 average time/residue: 0.2903 time to fit residues: 138.1146 Evaluate side-chains 364 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 303 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 867 SER Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 816 LYS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 825 THR Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain I residue 820 MET Chi-restraints excluded: chain I residue 851 VAL Chi-restraints excluded: chain I residue 861 GLU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 824 VAL Chi-restraints excluded: chain J residue 825 THR Chi-restraints excluded: chain J residue 855 MET Chi-restraints excluded: chain K residue 425 SER Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 409 HIS Chi-restraints excluded: chain L residue 416 LEU Chi-restraints excluded: chain L residue 423 LEU Chi-restraints excluded: chain L residue 429 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 790 SER Chi-restraints excluded: chain N residue 835 SER Chi-restraints excluded: chain N residue 839 ARG Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 13 TYR Chi-restraints excluded: chain M residue 794 SER Chi-restraints excluded: chain M residue 821 VAL Chi-restraints excluded: chain M residue 825 THR Chi-restraints excluded: chain O residue 163 SER Chi-restraints excluded: chain P residue 98 GLN Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain R residue 416 LEU Chi-restraints excluded: chain R residue 417 GLN Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 820 MET Chi-restraints excluded: chain S residue 821 VAL Chi-restraints excluded: chain S residue 851 VAL Chi-restraints excluded: chain S residue 869 ASN Chi-restraints excluded: chain T residue 805 ASN Chi-restraints excluded: chain T residue 823 VAL Chi-restraints excluded: chain T residue 855 MET Chi-restraints excluded: chain T residue 886 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 159 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 125 optimal weight: 0.3980 chunk 105 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN C 854 GLN E 93 ASN L 374 GLN ** N 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 854 GLN P 98 GLN R 417 GLN T 805 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.179478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.168001 restraints weight = 18657.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.170731 restraints weight = 10936.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.172552 restraints weight = 7163.531| |-----------------------------------------------------------------------------| r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13690 Z= 0.158 Angle : 0.527 8.718 18434 Z= 0.287 Chirality : 0.040 0.195 2082 Planarity : 0.003 0.048 2438 Dihedral : 4.282 18.238 1962 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.09 % Allowed : 19.77 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.21), residues: 1704 helix: 2.63 (0.17), residues: 764 sheet: -1.38 (0.24), residues: 408 loop : 0.20 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 827 HIS 0.004 0.001 HIS K 350 PHE 0.005 0.001 PHE S 840 TYR 0.014 0.001 TYR C 810 ARG 0.006 0.000 ARG L 438 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 918) hydrogen bonds : angle 4.59385 ( 2586) SS BOND : bond 0.00309 ( 8) SS BOND : angle 1.25203 ( 16) covalent geometry : bond 0.00337 (13682) covalent geometry : angle 0.52549 (18418) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 307 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 ARG cc_start: 0.7293 (tpt90) cc_final: 0.7012 (mmm160) REVERT: B 384 ARG cc_start: 0.7167 (mtp180) cc_final: 0.6622 (mtp-110) REVERT: C 6 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6127 (mm-30) REVERT: C 809 TRP cc_start: 0.8386 (m100) cc_final: 0.7840 (m100) REVERT: C 855 MET cc_start: 0.7502 (mtm) cc_final: 0.6979 (mtp) REVERT: G 416 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8072 (mp) REVERT: G 423 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.7044 (mt) REVERT: H 426 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7012 (mp0) REVERT: H 435 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7583 (mt-10) REVERT: I 817 GLN cc_start: 0.6397 (mp10) cc_final: 0.5998 (mp10) REVERT: L 416 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7922 (mp) REVERT: L 431 GLU cc_start: 0.6702 (tp30) cc_final: 0.6456 (tp30) REVERT: L 435 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7108 (mm-30) REVERT: N 810 TYR cc_start: 0.7887 (m-80) cc_final: 0.7630 (m-80) REVERT: N 818 ARG cc_start: 0.7853 (ptp-110) cc_final: 0.7563 (ptp-110) REVERT: N 839 ARG cc_start: 0.6440 (OUTLIER) cc_final: 0.6134 (ttp80) REVERT: M 13 TYR cc_start: 0.5845 (OUTLIER) cc_final: 0.4983 (t80) REVERT: M 825 THR cc_start: 0.6960 (OUTLIER) cc_final: 0.6728 (p) REVERT: M 866 TYR cc_start: 0.8335 (m-80) cc_final: 0.8091 (m-80) REVERT: O 156 LYS cc_start: 0.7372 (mttt) cc_final: 0.7022 (mttt) REVERT: P 107 GLU cc_start: 0.7742 (tt0) cc_final: 0.7379 (tt0) REVERT: R 417 GLN cc_start: 0.4246 (OUTLIER) cc_final: 0.1827 (tp-100) REVERT: R 421 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6392 (mp0) REVERT: R 426 GLU cc_start: 0.6657 (mt-10) cc_final: 0.6150 (mt-10) REVERT: T 7 SER cc_start: 0.7645 (m) cc_final: 0.7144 (t) REVERT: T 809 TRP cc_start: 0.7447 (m100) cc_final: 0.6947 (m100) outliers start: 71 outliers final: 49 residues processed: 346 average time/residue: 0.2919 time to fit residues: 137.9331 Evaluate side-chains 358 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 301 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain C residue 816 LYS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 825 THR Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain I residue 820 MET Chi-restraints excluded: chain I residue 851 VAL Chi-restraints excluded: chain I residue 861 GLU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 824 VAL Chi-restraints excluded: chain J residue 825 THR Chi-restraints excluded: chain J residue 855 MET Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain K residue 425 SER Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 416 LEU Chi-restraints excluded: chain L residue 423 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 790 SER Chi-restraints excluded: chain N residue 835 SER Chi-restraints excluded: chain N residue 839 ARG Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 13 TYR Chi-restraints excluded: chain M residue 794 SER Chi-restraints excluded: chain M residue 821 VAL Chi-restraints excluded: chain M residue 825 THR Chi-restraints excluded: chain M residue 851 VAL Chi-restraints excluded: chain P residue 98 GLN Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain R residue 416 LEU Chi-restraints excluded: chain R residue 417 GLN Chi-restraints excluded: chain R residue 422 ARG Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 820 MET Chi-restraints excluded: chain S residue 851 VAL Chi-restraints excluded: chain S residue 869 ASN Chi-restraints excluded: chain T residue 805 ASN Chi-restraints excluded: chain T residue 823 VAL Chi-restraints excluded: chain T residue 824 VAL Chi-restraints excluded: chain T residue 855 MET Chi-restraints excluded: chain T residue 886 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 96 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 148 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN C 831 ASN E 93 ASN ** H 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 374 GLN ** N 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 854 GLN P 98 GLN R 417 GLN T 805 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.177470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.166167 restraints weight = 18586.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.168862 restraints weight = 10962.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.170635 restraints weight = 7175.142| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13690 Z= 0.198 Angle : 0.570 8.676 18434 Z= 0.308 Chirality : 0.041 0.165 2082 Planarity : 0.004 0.062 2438 Dihedral : 4.440 19.099 1962 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.01 % Allowed : 20.92 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.20), residues: 1704 helix: 2.44 (0.17), residues: 766 sheet: -1.44 (0.24), residues: 408 loop : 0.25 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 809 HIS 0.005 0.001 HIS K 350 PHE 0.005 0.001 PHE S 840 TYR 0.018 0.002 TYR C 810 ARG 0.014 0.001 ARG L 438 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 918) hydrogen bonds : angle 4.70234 ( 2586) SS BOND : bond 0.00309 ( 8) SS BOND : angle 1.32056 ( 16) covalent geometry : bond 0.00429 (13682) covalent geometry : angle 0.56894 (18418) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 305 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 ARG cc_start: 0.7283 (tpt90) cc_final: 0.6910 (tpp-160) REVERT: B 416 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8603 (mp) REVERT: C 6 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6724 (mm-30) REVERT: C 809 TRP cc_start: 0.8351 (m100) cc_final: 0.7631 (m100) REVERT: C 855 MET cc_start: 0.7292 (mtm) cc_final: 0.6682 (mtp) REVERT: G 423 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7067 (mt) REVERT: H 426 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: H 435 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7680 (mt-10) REVERT: I 817 GLN cc_start: 0.6587 (mp10) cc_final: 0.6150 (mp10) REVERT: L 431 GLU cc_start: 0.6839 (tp30) cc_final: 0.6478 (tp30) REVERT: N 792 ARG cc_start: 0.7827 (ttt-90) cc_final: 0.7610 (ttt-90) REVERT: N 810 TYR cc_start: 0.7849 (m-80) cc_final: 0.7634 (m-80) REVERT: N 818 ARG cc_start: 0.7830 (ptp-110) cc_final: 0.7245 (ptp-110) REVERT: N 855 MET cc_start: 0.7650 (mmm) cc_final: 0.7148 (mtt) REVERT: M 13 TYR cc_start: 0.5869 (OUTLIER) cc_final: 0.5142 (t80) REVERT: M 866 TYR cc_start: 0.8316 (m-80) cc_final: 0.8081 (m-80) REVERT: O 156 LYS cc_start: 0.7382 (mttt) cc_final: 0.7047 (mttt) REVERT: R 417 GLN cc_start: 0.4639 (OUTLIER) cc_final: 0.2172 (tm130) REVERT: R 426 GLU cc_start: 0.6524 (mt-10) cc_final: 0.6013 (mt-10) REVERT: T 7 SER cc_start: 0.7856 (m) cc_final: 0.7337 (t) REVERT: T 809 TRP cc_start: 0.7477 (m100) cc_final: 0.6968 (m100) outliers start: 70 outliers final: 53 residues processed: 343 average time/residue: 0.2978 time to fit residues: 139.7849 Evaluate side-chains 359 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 301 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 816 LYS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 825 THR Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain I residue 820 MET Chi-restraints excluded: chain I residue 861 GLU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 824 VAL Chi-restraints excluded: chain J residue 825 THR Chi-restraints excluded: chain J residue 855 MET Chi-restraints excluded: chain K residue 425 SER Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 423 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 790 SER Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 13 TYR Chi-restraints excluded: chain M residue 794 SER Chi-restraints excluded: chain M residue 821 VAL Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain Q residue 405 ASP Chi-restraints excluded: chain R residue 416 LEU Chi-restraints excluded: chain R residue 417 GLN Chi-restraints excluded: chain R residue 422 ARG Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 820 MET Chi-restraints excluded: chain S residue 821 VAL Chi-restraints excluded: chain S residue 835 SER Chi-restraints excluded: chain S residue 851 VAL Chi-restraints excluded: chain S residue 868 CYS Chi-restraints excluded: chain S residue 869 ASN Chi-restraints excluded: chain T residue 805 ASN Chi-restraints excluded: chain T residue 823 VAL Chi-restraints excluded: chain T residue 824 VAL Chi-restraints excluded: chain T residue 855 MET Chi-restraints excluded: chain T residue 886 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 105 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 165 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 40 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN C 831 ASN L 374 GLN ** N 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 805 ASN M 854 GLN T 805 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.179092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.167812 restraints weight = 18651.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.170499 restraints weight = 10927.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.172209 restraints weight = 7149.004| |-----------------------------------------------------------------------------| r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.5564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13690 Z= 0.152 Angle : 0.535 8.834 18434 Z= 0.290 Chirality : 0.039 0.161 2082 Planarity : 0.003 0.046 2438 Dihedral : 4.390 23.598 1962 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.73 % Allowed : 21.49 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.20), residues: 1704 helix: 2.67 (0.17), residues: 766 sheet: -1.43 (0.24), residues: 408 loop : 0.34 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP S 827 HIS 0.005 0.001 HIS K 350 PHE 0.006 0.001 PHE S 840 TYR 0.016 0.001 TYR C 810 ARG 0.012 0.001 ARG L 438 Details of bonding type rmsd hydrogen bonds : bond 0.04027 ( 918) hydrogen bonds : angle 4.51051 ( 2586) SS BOND : bond 0.00222 ( 8) SS BOND : angle 1.34923 ( 16) covalent geometry : bond 0.00327 (13682) covalent geometry : angle 0.53407 (18418) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 299 time to evaluate : 1.339 Fit side-chains revert: symmetry clash REVERT: A 422 ARG cc_start: 0.7281 (tpt90) cc_final: 0.7034 (mmm160) REVERT: B 384 ARG cc_start: 0.7172 (mtp180) cc_final: 0.6608 (mtp-110) REVERT: B 416 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8567 (mp) REVERT: C 6 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6629 (mp0) REVERT: C 831 ASN cc_start: 0.7560 (OUTLIER) cc_final: 0.7329 (m-40) REVERT: C 855 MET cc_start: 0.7188 (mtm) cc_final: 0.6728 (mtp) REVERT: H 426 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: H 435 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7668 (mt-10) REVERT: I 817 GLN cc_start: 0.6631 (mp10) cc_final: 0.6211 (mp10) REVERT: L 391 ARG cc_start: 0.7139 (mtp-110) cc_final: 0.6902 (ttp80) REVERT: L 416 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8036 (mp) REVERT: L 431 GLU cc_start: 0.6722 (tp30) cc_final: 0.6355 (tp30) REVERT: N 792 ARG cc_start: 0.7794 (ttt-90) cc_final: 0.7580 (ttt-90) REVERT: N 810 TYR cc_start: 0.7883 (m-80) cc_final: 0.7679 (m-80) REVERT: N 855 MET cc_start: 0.7582 (mmm) cc_final: 0.7138 (mtp) REVERT: M 13 TYR cc_start: 0.5875 (OUTLIER) cc_final: 0.5241 (t80) REVERT: M 832 TYR cc_start: 0.7706 (m-80) cc_final: 0.7180 (m-80) REVERT: M 866 TYR cc_start: 0.8313 (m-80) cc_final: 0.8108 (m-80) REVERT: O 156 LYS cc_start: 0.7340 (mttt) cc_final: 0.7001 (mttt) REVERT: R 413 ILE cc_start: 0.7746 (mm) cc_final: 0.7420 (mm) REVERT: R 416 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7482 (mt) REVERT: R 421 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6481 (mp0) REVERT: R 426 GLU cc_start: 0.6709 (mt-10) cc_final: 0.6131 (mt-10) REVERT: T 7 SER cc_start: 0.7887 (m) cc_final: 0.7364 (t) REVERT: T 809 TRP cc_start: 0.7472 (m100) cc_final: 0.7159 (m100) REVERT: T 820 MET cc_start: 0.6832 (ttm) cc_final: 0.6606 (ttm) outliers start: 66 outliers final: 50 residues processed: 332 average time/residue: 0.3092 time to fit residues: 138.8712 Evaluate side-chains 352 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 296 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 816 LYS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 825 THR Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 831 ASN Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 147 ARG Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain I residue 820 MET Chi-restraints excluded: chain I residue 861 GLU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 824 VAL Chi-restraints excluded: chain J residue 825 THR Chi-restraints excluded: chain J residue 855 MET Chi-restraints excluded: chain K residue 425 SER Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 416 LEU Chi-restraints excluded: chain L residue 423 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 790 SER Chi-restraints excluded: chain N residue 835 SER Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 13 TYR Chi-restraints excluded: chain M residue 794 SER Chi-restraints excluded: chain M residue 821 VAL Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain Q residue 405 ASP Chi-restraints excluded: chain R residue 416 LEU Chi-restraints excluded: chain R residue 422 ARG Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 821 VAL Chi-restraints excluded: chain S residue 851 VAL Chi-restraints excluded: chain S residue 868 CYS Chi-restraints excluded: chain S residue 869 ASN Chi-restraints excluded: chain T residue 805 ASN Chi-restraints excluded: chain T residue 823 VAL Chi-restraints excluded: chain T residue 824 VAL Chi-restraints excluded: chain T residue 833 VAL Chi-restraints excluded: chain T residue 855 MET Chi-restraints excluded: chain T residue 886 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 160 optimal weight: 0.0970 chunk 138 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 3 GLN C 3 GLN C 831 ASN E 93 ASN L 374 GLN ** N 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 854 GLN O 139 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.178101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.166913 restraints weight = 18424.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.169565 restraints weight = 10903.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.171335 restraints weight = 7166.585| |-----------------------------------------------------------------------------| r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13690 Z= 0.169 Angle : 0.561 8.658 18434 Z= 0.302 Chirality : 0.041 0.204 2082 Planarity : 0.004 0.046 2438 Dihedral : 4.445 28.303 1962 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.58 % Allowed : 21.70 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.21), residues: 1704 helix: 2.67 (0.17), residues: 762 sheet: -1.38 (0.23), residues: 456 loop : 0.54 (0.31), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP S 827 HIS 0.004 0.001 HIS K 350 PHE 0.005 0.001 PHE S 840 TYR 0.020 0.002 TYR C 810 ARG 0.011 0.001 ARG L 438 Details of bonding type rmsd hydrogen bonds : bond 0.04081 ( 918) hydrogen bonds : angle 4.53277 ( 2586) SS BOND : bond 0.00215 ( 8) SS BOND : angle 1.35234 ( 16) covalent geometry : bond 0.00366 (13682) covalent geometry : angle 0.56002 (18418) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 308 time to evaluate : 1.483 Fit side-chains revert: symmetry clash REVERT: A 422 ARG cc_start: 0.7295 (tpt90) cc_final: 0.7052 (tpp-160) REVERT: B 384 ARG cc_start: 0.7178 (mtp180) cc_final: 0.6639 (mtp-110) REVERT: B 416 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8576 (mp) REVERT: C 6 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6048 (mm-30) REVERT: C 855 MET cc_start: 0.7166 (mtm) cc_final: 0.6689 (mtp) REVERT: H 426 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: H 435 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7584 (mt-10) REVERT: I 817 GLN cc_start: 0.6697 (mp10) cc_final: 0.6249 (mp10) REVERT: L 391 ARG cc_start: 0.7183 (mtp-110) cc_final: 0.6933 (ttp80) REVERT: L 416 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8006 (mp) REVERT: L 431 GLU cc_start: 0.6741 (tp30) cc_final: 0.6379 (tp30) REVERT: L 439 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7329 (mmt90) REVERT: N 792 ARG cc_start: 0.7797 (ttt-90) cc_final: 0.7589 (ttt-90) REVERT: N 810 TYR cc_start: 0.7869 (m-80) cc_final: 0.7655 (m-80) REVERT: N 855 MET cc_start: 0.7545 (mmm) cc_final: 0.7149 (mtp) REVERT: M 13 TYR cc_start: 0.5800 (OUTLIER) cc_final: 0.5254 (t80) REVERT: M 832 TYR cc_start: 0.7743 (m-80) cc_final: 0.7051 (m-80) REVERT: M 866 TYR cc_start: 0.8312 (m-80) cc_final: 0.8064 (m-80) REVERT: O 156 LYS cc_start: 0.7335 (mttt) cc_final: 0.6990 (mttt) REVERT: R 426 GLU cc_start: 0.6671 (mt-10) cc_final: 0.6097 (mt-10) REVERT: T 7 SER cc_start: 0.7927 (m) cc_final: 0.7385 (t) REVERT: T 809 TRP cc_start: 0.7506 (m100) cc_final: 0.7135 (m100) REVERT: T 820 MET cc_start: 0.6914 (ttm) cc_final: 0.6693 (ttm) outliers start: 64 outliers final: 51 residues processed: 340 average time/residue: 0.3049 time to fit residues: 141.0855 Evaluate side-chains 360 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 304 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 816 LYS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 825 THR Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 147 ARG Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain I residue 820 MET Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 824 VAL Chi-restraints excluded: chain J residue 825 THR Chi-restraints excluded: chain J residue 855 MET Chi-restraints excluded: chain K residue 425 SER Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 416 LEU Chi-restraints excluded: chain L residue 423 LEU Chi-restraints excluded: chain L residue 439 ARG Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 790 SER Chi-restraints excluded: chain N residue 835 SER Chi-restraints excluded: chain N residue 845 ASP Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 13 TYR Chi-restraints excluded: chain M residue 794 SER Chi-restraints excluded: chain M residue 821 VAL Chi-restraints excluded: chain M residue 851 VAL Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain Q residue 405 ASP Chi-restraints excluded: chain R residue 416 LEU Chi-restraints excluded: chain R residue 422 ARG Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 821 VAL Chi-restraints excluded: chain S residue 851 VAL Chi-restraints excluded: chain S residue 868 CYS Chi-restraints excluded: chain S residue 869 ASN Chi-restraints excluded: chain T residue 823 VAL Chi-restraints excluded: chain T residue 824 VAL Chi-restraints excluded: chain T residue 833 VAL Chi-restraints excluded: chain T residue 855 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 88 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 43 optimal weight: 0.2980 chunk 162 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 78 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN E 93 ASN L 374 GLN ** N 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 854 GLN 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 = 0.178512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.167321 restraints weight = 18491.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.169945 restraints weight = 10894.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.171731 restraints weight = 7184.271| |-----------------------------------------------------------------------------| r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6412 moved from start: 0.5807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13690 Z= 0.160 Angle : 0.562 9.466 18434 Z= 0.301 Chirality : 0.040 0.171 2082 Planarity : 0.004 0.045 2438 Dihedral : 4.433 27.617 1962 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.30 % Allowed : 22.49 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.21), residues: 1704 helix: 2.70 (0.17), residues: 768 sheet: -1.38 (0.23), residues: 456 loop : 0.54 (0.32), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP N 878 HIS 0.005 0.001 HIS K 350 PHE 0.005 0.001 PHE S 840 TYR 0.021 0.001 TYR C 810 ARG 0.012 0.001 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 918) hydrogen bonds : angle 4.47919 ( 2586) SS BOND : bond 0.00140 ( 8) SS BOND : angle 1.27401 ( 16) covalent geometry : bond 0.00345 (13682) covalent geometry : angle 0.56075 (18418) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 303 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 ARG cc_start: 0.7260 (tpt90) cc_final: 0.7027 (tpp-160) REVERT: B 384 ARG cc_start: 0.7177 (mtp180) cc_final: 0.6635 (mtp-110) REVERT: B 416 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8531 (mp) REVERT: C 6 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6085 (mm-30) REVERT: C 855 MET cc_start: 0.7153 (mtm) cc_final: 0.6678 (mtp) REVERT: E 128 ARG cc_start: 0.6119 (tpm170) cc_final: 0.5474 (tpm170) REVERT: H 426 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: H 435 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7724 (mt-10) REVERT: I 817 GLN cc_start: 0.6660 (mp10) cc_final: 0.6248 (mp10) REVERT: L 391 ARG cc_start: 0.7169 (mtp-110) cc_final: 0.6952 (ttp80) REVERT: L 416 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8001 (mp) REVERT: L 431 GLU cc_start: 0.6730 (tp30) cc_final: 0.6346 (tp30) REVERT: N 792 ARG cc_start: 0.7800 (ttt-90) cc_final: 0.7588 (ttt-90) REVERT: N 810 TYR cc_start: 0.7873 (m-80) cc_final: 0.7625 (m-80) REVERT: N 855 MET cc_start: 0.7552 (mmm) cc_final: 0.7158 (mtp) REVERT: M 13 TYR cc_start: 0.5875 (OUTLIER) cc_final: 0.5291 (t80) REVERT: M 866 TYR cc_start: 0.8290 (m-80) cc_final: 0.8054 (m-80) REVERT: O 156 LYS cc_start: 0.7294 (mttt) cc_final: 0.6950 (mttt) REVERT: R 426 GLU cc_start: 0.6833 (mt-10) cc_final: 0.6193 (mt-10) REVERT: T 7 SER cc_start: 0.7954 (m) cc_final: 0.7390 (t) REVERT: T 809 TRP cc_start: 0.7503 (m100) cc_final: 0.7148 (m100) REVERT: T 820 MET cc_start: 0.6880 (ttm) cc_final: 0.6662 (ttm) outliers start: 60 outliers final: 53 residues processed: 334 average time/residue: 0.3078 time to fit residues: 139.3165 Evaluate side-chains 359 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 302 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 816 LYS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 825 THR Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 147 ARG Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain I residue 820 MET Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 824 VAL Chi-restraints excluded: chain J residue 825 THR Chi-restraints excluded: chain J residue 855 MET Chi-restraints excluded: chain K residue 425 SER Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 416 LEU Chi-restraints excluded: chain L residue 423 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 790 SER Chi-restraints excluded: chain N residue 835 SER Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 13 TYR Chi-restraints excluded: chain M residue 794 SER Chi-restraints excluded: chain M residue 821 VAL Chi-restraints excluded: chain M residue 851 VAL Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain Q residue 405 ASP Chi-restraints excluded: chain R residue 416 LEU Chi-restraints excluded: chain R residue 422 ARG Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 820 MET Chi-restraints excluded: chain S residue 821 VAL Chi-restraints excluded: chain S residue 851 VAL Chi-restraints excluded: chain S residue 868 CYS Chi-restraints excluded: chain S residue 869 ASN Chi-restraints excluded: chain T residue 805 ASN Chi-restraints excluded: chain T residue 823 VAL Chi-restraints excluded: chain T residue 824 VAL Chi-restraints excluded: chain T residue 833 VAL Chi-restraints excluded: chain T residue 855 MET Chi-restraints excluded: chain T residue 886 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 51 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 115 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN C 817 GLN E 93 ASN L 374 GLN L 409 HIS ** N 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 854 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.177617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.166427 restraints weight = 18596.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.169065 restraints weight = 10974.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.170839 restraints weight = 7246.904| |-----------------------------------------------------------------------------| r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.5904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13690 Z= 0.174 Angle : 0.580 10.029 18434 Z= 0.311 Chirality : 0.041 0.158 2082 Planarity : 0.004 0.046 2438 Dihedral : 4.465 29.346 1962 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.66 % Allowed : 22.13 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.21), residues: 1704 helix: 2.70 (0.17), residues: 762 sheet: -1.41 (0.23), residues: 456 loop : 0.56 (0.31), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP S 827 HIS 0.004 0.001 HIS K 350 PHE 0.005 0.001 PHE S 840 TYR 0.021 0.002 TYR C 810 ARG 0.010 0.001 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 918) hydrogen bonds : angle 4.53209 ( 2586) SS BOND : bond 0.00146 ( 8) SS BOND : angle 1.29246 ( 16) covalent geometry : bond 0.00376 (13682) covalent geometry : angle 0.57882 (18418) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4439.32 seconds wall clock time: 78 minutes 20.82 seconds (4700.82 seconds total)