Starting phenix.real_space_refine on Thu Jul 31 09:54:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8afh_15398/07_2025/8afh_15398.cif Found real_map, /net/cci-nas-00/data/ceres_data/8afh_15398/07_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_15398/07_2025/8afh_15398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8afh_15398/07_2025/8afh_15398.map" model { file = "/net/cci-nas-00/data/ceres_data/8afh_15398/07_2025/8afh_15398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8afh_15398/07_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-5711/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: 8.49, per 1000 atoms: 0.63 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: 3.33 Conformation dependent library (CDL) restraints added in 1.6 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: 1.41 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: 3.99 Time building geometry restraints manager: 3.97 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.070 Find NCS groups from input model: 0.610 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.450 ------------------------------------------------------------------------------- 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 : 1.318 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: 0.3438 time to fit residues: 149.0456 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 : 1.406 ------------------------------------------------------------------------------- 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 = 0.177378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.164887 restraints weight = 19343.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.167978 restraints weight = 11058.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.170092 restraints weight = 7118.462| |-----------------------------------------------------------------------------| r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 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 : 1.453 Fit side-chains revert: symmetry clash REVERT: B 379 LYS cc_start: 0.8423 (tmtt) cc_final: 0.7902 (tmmt) REVERT: B 384 ARG cc_start: 0.7035 (mtp180) cc_final: 0.6734 (mtp-110) REVERT: D 792 ARG cc_start: 0.7464 (ttt180) cc_final: 0.7231 (ttt-90) REVERT: G 419 THR cc_start: 0.7786 (t) cc_final: 0.7467 (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: 0.8077 (p) REVERT: I 872 TYR cc_start: 0.7923 (t80) cc_final: 0.7425 (t80) REVERT: J 858 LEU cc_start: 0.6443 (mt) cc_final: 0.5610 (tt) REVERT: L 395 MET cc_start: 0.5533 (ttm) cc_final: 0.5175 (mmm) REVERT: N 810 TYR cc_start: 0.7951 (m-80) cc_final: 0.7682 (m-10) REVERT: N 812 GLN cc_start: 0.6618 (tt0) cc_final: 0.6363 (tt0) REVERT: M 13 TYR cc_start: 0.5310 (m-80) cc_final: 0.4947 (m-80) REVERT: M 820 MET cc_start: 0.8106 (ttp) cc_final: 0.7773 (ttp) REVERT: M 866 TYR cc_start: 0.8030 (m-80) cc_final: 0.7823 (m-10) REVERT: O 107 GLU cc_start: 0.7065 (tm-30) cc_final: 0.6707 (tm-30) REVERT: P 107 GLU cc_start: 0.7602 (tt0) cc_final: 0.6782 (tt0) REVERT: Q 416 LEU cc_start: 0.7627 (mt) cc_final: 0.7364 (mt) REVERT: R 413 ILE cc_start: 0.7597 (mm) cc_final: 0.7242 (mm) REVERT: R 426 GLU cc_start: 0.6738 (mt-10) cc_final: 0.6408 (mt-10) REVERT: S 855 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6543 (mtm) REVERT: S 872 TYR cc_start: 0.7556 (t80) cc_final: 0.7354 (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: 0.7443 (m100) cc_final: 0.7113 (m100) REVERT: T 820 MET cc_start: 0.7573 (mmm) cc_final: 0.7204 (mmm) outliers start: 33 outliers final: 19 residues processed: 327 average time/residue: 0.3032 time to fit residues: 136.5748 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 : 1.479 ------------------------------------------------------------------------------- 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 = 0.170676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.159566 restraints weight = 18844.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.162232 restraints weight = 11383.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.164041 restraints weight = 7527.568| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 0.3912 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 6.281 18434 Z= 0.305 Chirality : 0.040 0.152 2082 Planarity : 0.004 0.060 2438 Dihedral : 4.521 19.123 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 : 14.76 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (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 0.015 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 0.04506 ( 918) hydrogen bonds : angle 5.05492 ( 2586) SS BOND : bond 0.00387 ( 8) SS BOND : angle 0.84574 ( 16) covalent geometry : bond 0.00362 (13682) covalent geometry : angle 0.55101 (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 : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 LEU cc_start: 0.8034 (tp) cc_final: 0.7792 (tp) REVERT: B 384 ARG cc_start: 0.7153 (mtp180) cc_final: 0.6862 (mtp-110) REVERT: B 416 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8438 (mp) REVERT: G 423 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6990 (mt) REVERT: H 426 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.7041 (mp0) REVERT: I 817 GLN cc_start: 0.6258 (mp10) cc_final: 0.5855 (mp10) REVERT: I 829 SER cc_start: 0.8526 (t) cc_final: 0.8109 (p) REVERT: J 858 LEU cc_start: 0.6935 (mt) cc_final: 0.5927 (tt) REVERT: K 350 HIS cc_start: 0.3457 (OUTLIER) cc_final: 0.3132 (m90) REVERT: K 422 ARG cc_start: 0.7528 (ttm-80) cc_final: 0.7253 (tpp-160) REVERT: L 363 ARG cc_start: 0.7526 (mmm-85) cc_final: 0.7168 (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: 0.8156 (m-10) cc_final: 0.7858 (m-80) REVERT: M 820 MET cc_start: 0.8080 (ttp) cc_final: 0.7576 (ttp) REVERT: M 825 THR cc_start: 0.7229 (OUTLIER) cc_final: 0.6880 (p) REVERT: M 866 TYR cc_start: 0.8151 (m-80) cc_final: 0.7857 (m-10) REVERT: O 107 GLU cc_start: 0.7028 (tm-30) cc_final: 0.6562 (tm-30) REVERT: O 156 LYS cc_start: 0.7459 (mttt) cc_final: 0.7074 (mttt) REVERT: P 107 GLU cc_start: 0.7914 (tt0) cc_final: 0.6785 (tt0) REVERT: Q 422 ARG cc_start: 0.6471 (tpt90) cc_final: 0.6263 (tpt170) REVERT: R 413 ILE cc_start: 0.7686 (mm) cc_final: 0.7304 (mm) REVERT: R 426 GLU cc_start: 0.6771 (mt-10) cc_final: 0.6364 (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: 0.7487 (OUTLIER) cc_final: 0.6992 (ttm) REVERT: T 886 VAL cc_start: 0.7682 (m) cc_final: 0.7293 (p) outliers start: 55 outliers final: 37 residues processed: 339 average time/residue: 0.3207 time to fit residues: 151.5383 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 : 1.555 ------------------------------------------------------------------------------- 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: 1.9990 chunk 161 optimal weight: 0.3980 chunk 87 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 66 optimal weight: 0.0770 chunk 119 optimal weight: 0.9990 chunk 147 optimal weight: 0.1980 overall best weight: 0.3938 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.170964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.159075 restraints weight = 18807.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.161955 restraints weight = 10920.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.163885 restraints weight = 7112.737| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13690 Z= 0.128 Angle : 0.487 5.891 18434 Z= 0.270 Chirality : 0.038 0.142 2082 Planarity : 0.003 0.053 2438 Dihedral : 4.194 17.945 1962 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.30 % Allowed : 17.26 % 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: 1.21 (0.21), residues: 1704 helix: 2.47 (0.17), residues: 766 sheet: -1.37 (0.23), residues: 486 loop : 0.70 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 827 HIS 0.002 0.001 HIS K 350 PHE 0.005 0.001 PHE S 840 TYR 0.011 0.001 TYR C 810 ARG 0.005 0.000 ARG F 145 Details of bonding type rmsd hydrogen bonds : bond 0.03999 ( 918) hydrogen bonds : angle 4.59522 ( 2586) SS BOND : bond 0.00481 ( 8) SS BOND : angle 0.69533 ( 16) covalent geometry : bond 0.00267 (13682) covalent geometry : angle 0.48712 (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 370 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 310 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 MET cc_start: 0.5731 (ttm) cc_final: 0.5324 (ttt) REVERT: A 422 ARG cc_start: 0.7312 (tpt90) cc_final: 0.6939 (tpp-160) REVERT: B 441 ARG cc_start: 0.6166 (mtt180) cc_final: 0.5954 (mtt180) REVERT: C 6 GLU cc_start: 0.6844 (mm-30) cc_final: 0.6310 (mm-30) REVERT: C 855 MET cc_start: 0.7574 (mtm) cc_final: 0.7122 (mtp) REVERT: H 426 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: H 435 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7752 (mt-10) REVERT: I 817 GLN cc_start: 0.6296 (mp10) cc_final: 0.5858 (mp10) REVERT: I 829 SER cc_start: 0.8416 (t) cc_final: 0.7970 (p) REVERT: J 858 LEU cc_start: 0.6891 (mt) cc_final: 0.5877 (tt) REVERT: J 869 ASN cc_start: 0.6885 (t0) cc_final: 0.6651 (m-40) REVERT: K 412 LYS cc_start: 0.7673 (ttmm) cc_final: 0.7391 (ttmm) REVERT: L 363 ARG cc_start: 0.7380 (mmm-85) cc_final: 0.7010 (mmm-85) REVERT: L 374 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.7025 (tp40) REVERT: L 416 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7836 (mp) REVERT: N 810 TYR cc_start: 0.7938 (m-80) cc_final: 0.7581 (m-80) REVERT: M 820 MET cc_start: 0.7921 (ttp) cc_final: 0.7484 (ttp) REVERT: M 825 THR cc_start: 0.7168 (OUTLIER) cc_final: 0.6768 (p) REVERT: M 866 TYR cc_start: 0.8235 (m-80) cc_final: 0.7917 (m-10) REVERT: O 107 GLU cc_start: 0.6901 (tm-30) cc_final: 0.6563 (tm-30) REVERT: O 156 LYS cc_start: 0.7353 (mttt) cc_final: 0.7033 (mttt) REVERT: P 107 GLU cc_start: 0.7600 (tt0) cc_final: 0.6568 (tt0) REVERT: Q 422 ARG cc_start: 0.6370 (tpt90) cc_final: 0.6122 (tpt170) REVERT: R 413 ILE cc_start: 0.7739 (mm) cc_final: 0.7343 (mm) REVERT: R 426 GLU cc_start: 0.6815 (mt-10) cc_final: 0.6132 (mt-10) REVERT: T 7 SER cc_start: 0.7531 (m) cc_final: 0.7004 (t) REVERT: T 809 TRP cc_start: 0.7531 (m100) cc_final: 0.6808 (m100) REVERT: T 886 VAL cc_start: 0.7732 (m) cc_final: 0.7263 (p) outliers start: 60 outliers final: 38 residues processed: 336 average time/residue: 0.3536 time to fit residues: 165.7616 Evaluate side-chains 343 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 301 time to evaluate : 1.595 ------------------------------------------------------------------------------- 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 7 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 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 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 374 GLN 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 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: 0.7980 chunk 144 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 136 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 59 optimal weight: 0.4980 chunk 108 optimal weight: 0.0570 chunk 88 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 62 optimal weight: 0.0670 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN C 5 GLN E 93 ASN E 139 ASN L 374 GLN R 417 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.170480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.158518 restraints weight = 18843.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.161391 restraints weight = 11038.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.163298 restraints weight = 7232.286| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13690 Z= 0.129 Angle : 0.493 9.042 18434 Z= 0.269 Chirality : 0.038 0.139 2082 Planarity : 0.003 0.050 2438 Dihedral : 4.094 16.970 1962 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.66 % Allowed : 18.27 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.21), residues: 1704 helix: 2.69 (0.17), residues: 768 sheet: -1.29 (0.22), residues: 486 loop : 0.78 (0.33), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 827 HIS 0.002 0.001 HIS K 350 PHE 0.005 0.001 PHE S 840 TYR 0.009 0.001 TYR N 832 ARG 0.006 0.000 ARG F 145 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 918) hydrogen bonds : angle 4.49257 ( 2586) SS BOND : bond 0.00191 ( 8) SS BOND : angle 0.84525 ( 16) covalent geometry : bond 0.00272 (13682) covalent geometry : angle 0.49262 (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 362 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 297 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 MET cc_start: 0.5897 (ttm) cc_final: 0.5473 (ttt) REVERT: A 422 ARG cc_start: 0.7316 (tpt90) cc_final: 0.7054 (tpp-160) REVERT: B 384 ARG cc_start: 0.7133 (mtp180) cc_final: 0.6597 (mtp-110) REVERT: B 441 ARG cc_start: 0.6222 (mtt180) cc_final: 0.5836 (mtt180) REVERT: C 6 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6111 (mm-30) REVERT: C 855 MET cc_start: 0.7525 (mtm) cc_final: 0.7063 (mtp) REVERT: G 423 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6970 (mt) REVERT: H 426 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: H 435 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7779 (mt-10) REVERT: I 817 GLN cc_start: 0.6351 (mp10) cc_final: 0.5916 (mp10) REVERT: I 829 SER cc_start: 0.8376 (t) cc_final: 0.7901 (p) REVERT: K 412 LYS cc_start: 0.7646 (ttmm) cc_final: 0.7396 (ttmm) REVERT: L 363 ARG cc_start: 0.7370 (mmm-85) cc_final: 0.6982 (mmm-85) REVERT: L 374 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6490 (mm110) REVERT: L 416 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7868 (mp) REVERT: L 439 ARG cc_start: 0.7743 (mtt180) cc_final: 0.7343 (mtt180) REVERT: N 810 TYR cc_start: 0.7910 (m-80) cc_final: 0.7659 (m-80) REVERT: M 13 TYR cc_start: 0.6042 (OUTLIER) cc_final: 0.4763 (t80) REVERT: M 825 THR cc_start: 0.7122 (OUTLIER) cc_final: 0.6749 (p) REVERT: M 866 TYR cc_start: 0.8346 (m-80) cc_final: 0.7967 (m-10) REVERT: O 156 LYS cc_start: 0.7358 (mttt) cc_final: 0.6994 (mttt) REVERT: P 107 GLU cc_start: 0.7657 (tt0) cc_final: 0.7215 (tt0) REVERT: P 146 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6855 (tp) REVERT: R 426 GLU cc_start: 0.6790 (mt-10) cc_final: 0.6151 (mt-10) REVERT: T 7 SER cc_start: 0.7567 (m) cc_final: 0.7148 (t) REVERT: T 886 VAL cc_start: 0.7517 (OUTLIER) cc_final: 0.7046 (p) outliers start: 65 outliers final: 42 residues processed: 330 average time/residue: 0.3517 time to fit residues: 159.5384 Evaluate side-chains 334 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 284 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 833 VAL 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 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 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 L residue 355 THR Chi-restraints excluded: chain L residue 374 GLN 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 821 VAL Chi-restraints excluded: chain M residue 825 THR Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain R residue 416 LEU 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 869 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: 0.9980 chunk 75 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 125 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 146 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 62 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 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 ** H 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 374 GLN L 409 HIS M 854 GLN 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 = 0.4140 r_free = 0.4140 target = 0.167745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.155948 restraints weight = 19094.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.158802 restraints weight = 11171.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.160721 restraints weight = 7320.220| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.5107 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= 0.172 Angle : 0.539 8.399 18434 Z= 0.293 Chirality : 0.040 0.204 2082 Planarity : 0.004 0.049 2438 Dihedral : 4.269 18.141 1962 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.66 % Allowed : 19.41 % Favored : 75.93 % 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: 1.34 (0.21), residues: 1704 helix: 2.62 (0.17), residues: 764 sheet: -1.32 (0.22), residues: 474 loop : 0.61 (0.32), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP N 878 HIS 0.005 0.001 HIS K 350 PHE 0.005 0.001 PHE S 840 TYR 0.014 0.002 TYR N 832 ARG 0.007 0.001 ARG F 145 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 918) hydrogen bonds : angle 4.61995 ( 2586) SS BOND : bond 0.00247 ( 8) SS BOND : angle 1.20471 ( 16) covalent geometry : bond 0.00369 (13682) covalent geometry : angle 0.53783 (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 377 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 312 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 MET cc_start: 0.5837 (ttm) cc_final: 0.5631 (ttt) REVERT: A 422 ARG cc_start: 0.7314 (tpt90) cc_final: 0.7032 (mmm160) REVERT: B 384 ARG cc_start: 0.7159 (mtp180) cc_final: 0.6618 (mtp-110) REVERT: B 416 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8550 (mp) REVERT: B 441 ARG cc_start: 0.6254 (mtt180) cc_final: 0.5836 (mtt180) REVERT: C 6 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6554 (mm-30) REVERT: C 809 TRP cc_start: 0.8378 (m100) cc_final: 0.7622 (m100) REVERT: C 855 MET cc_start: 0.7437 (mtm) cc_final: 0.6932 (mtp) REVERT: G 423 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6973 (mt) REVERT: H 426 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: H 435 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7639 (mt-10) REVERT: I 817 GLN cc_start: 0.6407 (mp10) cc_final: 0.5982 (mp10) REVERT: K 350 HIS cc_start: 0.3549 (OUTLIER) cc_final: 0.3153 (m90) REVERT: L 363 ARG cc_start: 0.7437 (mmm-85) cc_final: 0.7049 (mmm-85) REVERT: L 374 GLN cc_start: 0.7091 (OUTLIER) cc_final: 0.6825 (tt0) REVERT: L 439 ARG cc_start: 0.7753 (mtt180) cc_final: 0.7460 (mtt180) REVERT: N 810 TYR cc_start: 0.7861 (m-80) cc_final: 0.7564 (m-80) REVERT: N 839 ARG cc_start: 0.6422 (OUTLIER) cc_final: 0.6138 (ttp80) REVERT: M 13 TYR cc_start: 0.5877 (OUTLIER) cc_final: 0.4979 (t80) REVERT: M 825 THR cc_start: 0.7036 (OUTLIER) cc_final: 0.6748 (p) REVERT: M 866 TYR cc_start: 0.8360 (m-80) cc_final: 0.8063 (m-80) REVERT: O 156 LYS cc_start: 0.7409 (mttt) cc_final: 0.7048 (mttt) REVERT: P 107 GLU cc_start: 0.7567 (tt0) cc_final: 0.7087 (tt0) REVERT: R 426 GLU cc_start: 0.6636 (mt-10) cc_final: 0.6018 (mt-10) REVERT: T 7 SER cc_start: 0.7640 (m) cc_final: 0.7199 (t) REVERT: T 809 TRP cc_start: 0.7378 (m100) cc_final: 0.7091 (m100) outliers start: 65 outliers final: 48 residues processed: 348 average time/residue: 0.3293 time to fit residues: 157.9094 Evaluate side-chains 361 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 305 time to evaluate : 1.440 ------------------------------------------------------------------------------- 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 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 816 LYS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 825 THR Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 103 LEU 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 350 HIS Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 374 GLN Chi-restraints excluded: chain L residue 409 HIS 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 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 P residue 143 ILE Chi-restraints excluded: chain R residue 416 LEU Chi-restraints excluded: chain R residue 420 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 96 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 57 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 M 854 GLN ** T 869 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 = 0.4271 r_free = 0.4271 target = 0.179695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.168277 restraints weight = 18537.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.170989 restraints weight = 10868.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.172831 restraints weight = 7133.690| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13690 Z= 0.154 Angle : 0.529 8.820 18434 Z= 0.286 Chirality : 0.039 0.154 2082 Planarity : 0.003 0.047 2438 Dihedral : 4.274 22.447 1962 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.80 % Allowed : 21.13 % 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: 1.43 (0.21), residues: 1704 helix: 2.77 (0.17), residues: 764 sheet: -1.35 (0.24), residues: 408 loop : 0.28 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP N 878 HIS 0.007 0.001 HIS L 409 PHE 0.006 0.001 PHE S 840 TYR 0.014 0.001 TYR C 810 ARG 0.007 0.001 ARG L 438 Details of bonding type rmsd hydrogen bonds : bond 0.03983 ( 918) hydrogen bonds : angle 4.50747 ( 2586) SS BOND : bond 0.00219 ( 8) SS BOND : angle 1.13786 ( 16) covalent geometry : bond 0.00332 (13682) covalent geometry : angle 0.52814 (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 365 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 298 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 ARG cc_start: 0.7225 (tpt90) cc_final: 0.7020 (mmm160) REVERT: B 384 ARG cc_start: 0.7164 (mtp180) cc_final: 0.6622 (mtp-110) REVERT: B 416 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8570 (mp) REVERT: B 441 ARG cc_start: 0.6158 (mtt180) cc_final: 0.5735 (mtt180) REVERT: D 855 MET cc_start: 0.6410 (mtp) cc_final: 0.6112 (mtt) REVERT: C 6 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6223 (mm-30) REVERT: C 809 TRP cc_start: 0.8338 (m100) cc_final: 0.7824 (m100) REVERT: C 855 MET cc_start: 0.7238 (mtm) cc_final: 0.6734 (mtp) REVERT: G 423 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.7041 (mt) REVERT: H 426 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: H 435 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7595 (mt-10) REVERT: I 817 GLN cc_start: 0.6404 (mp10) cc_final: 0.6035 (mp10) REVERT: J 862 ASP cc_start: 0.6972 (m-30) cc_final: 0.6552 (m-30) REVERT: L 384 ARG cc_start: 0.6709 (mtp180) cc_final: 0.6485 (mpp-170) REVERT: L 416 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7945 (mp) REVERT: L 439 ARG cc_start: 0.7738 (mtt180) cc_final: 0.7511 (mtt180) REVERT: N 810 TYR cc_start: 0.7879 (m-80) cc_final: 0.7652 (m-80) REVERT: N 839 ARG cc_start: 0.6413 (OUTLIER) cc_final: 0.6135 (ttp80) REVERT: N 855 MET cc_start: 0.7597 (mmm) cc_final: 0.7171 (mtp) REVERT: M 13 TYR cc_start: 0.5949 (OUTLIER) cc_final: 0.5092 (t80) REVERT: M 825 THR cc_start: 0.6875 (OUTLIER) cc_final: 0.6642 (p) REVERT: M 866 TYR cc_start: 0.8302 (m-80) cc_final: 0.8087 (m-80) REVERT: O 156 LYS cc_start: 0.7352 (mttt) cc_final: 0.7019 (mttt) REVERT: P 107 GLU cc_start: 0.7532 (tt0) cc_final: 0.7313 (tt0) REVERT: P 146 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6871 (tp) REVERT: Q 429 LEU cc_start: 0.8188 (mt) cc_final: 0.7973 (tp) REVERT: R 426 GLU cc_start: 0.6600 (mt-10) cc_final: 0.6232 (mt-10) REVERT: T 7 SER cc_start: 0.7636 (m) cc_final: 0.7162 (t) REVERT: T 809 TRP cc_start: 0.7476 (m100) cc_final: 0.7120 (m100) outliers start: 67 outliers final: 45 residues processed: 334 average time/residue: 0.3364 time to fit residues: 154.2158 Evaluate side-chains 351 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 298 time to evaluate : 1.446 ------------------------------------------------------------------------------- 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 886 VAL Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 103 LEU 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 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 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 350 HIS 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 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 P residue 143 ILE Chi-restraints excluded: chain P residue 146 LEU 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 869 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: 0.9980 chunk 59 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 165 optimal weight: 0.2980 chunk 137 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 chunk 134 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN ** H 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 374 GLN M 854 GLN T 805 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.178578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.167216 restraints weight = 18720.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.169907 restraints weight = 11018.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.171730 restraints weight = 7200.963| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.5551 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= 0.170 Angle : 0.553 8.638 18434 Z= 0.297 Chirality : 0.040 0.145 2082 Planarity : 0.003 0.046 2438 Dihedral : 4.383 26.324 1962 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.80 % Allowed : 21.99 % 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: 1.38 (0.20), residues: 1704 helix: 2.69 (0.17), residues: 764 sheet: -1.34 (0.24), residues: 408 loop : 0.29 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP N 878 HIS 0.005 0.001 HIS K 350 PHE 0.005 0.001 PHE S 840 TYR 0.024 0.002 TYR T 832 ARG 0.007 0.001 ARG L 391 Details of bonding type rmsd hydrogen bonds : bond 0.04059 ( 918) hydrogen bonds : angle 4.56039 ( 2586) SS BOND : bond 0.00413 ( 8) SS BOND : angle 1.50255 ( 16) covalent geometry : bond 0.00367 (13682) covalent geometry : angle 0.55109 (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 369 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 302 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 384 ARG cc_start: 0.7185 (mtp180) cc_final: 0.6638 (mtp-110) REVERT: B 416 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8562 (mp) REVERT: B 441 ARG cc_start: 0.6218 (mtt180) cc_final: 0.5766 (mtt180) REVERT: D 855 MET cc_start: 0.6450 (mtp) cc_final: 0.6137 (mtt) REVERT: C 6 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6146 (mm-30) REVERT: C 820 MET cc_start: 0.8370 (tmm) cc_final: 0.8126 (ttp) REVERT: C 827 TRP cc_start: 0.7470 (OUTLIER) cc_final: 0.6851 (m-10) REVERT: C 831 ASN cc_start: 0.7582 (m-40) cc_final: 0.7190 (m-40) REVERT: C 855 MET cc_start: 0.7196 (mtm) cc_final: 0.6711 (mtp) REVERT: G 423 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6982 (mt) REVERT: H 426 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: H 435 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7576 (mt-10) REVERT: I 817 GLN cc_start: 0.6611 (mp10) cc_final: 0.6147 (mp10) REVERT: L 374 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.7049 (tt0) REVERT: L 416 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7904 (mp) REVERT: L 438 ARG cc_start: 0.6530 (ttp-170) cc_final: 0.6278 (mtp180) REVERT: N 810 TYR cc_start: 0.7863 (m-80) cc_final: 0.7631 (m-80) REVERT: N 855 MET cc_start: 0.7581 (mmm) cc_final: 0.7228 (mtp) REVERT: M 13 TYR cc_start: 0.5845 (OUTLIER) cc_final: 0.5199 (t80) REVERT: M 825 THR cc_start: 0.6924 (OUTLIER) cc_final: 0.6662 (p) REVERT: M 832 TYR cc_start: 0.7693 (m-80) cc_final: 0.7204 (m-80) REVERT: O 156 LYS cc_start: 0.7403 (mttt) cc_final: 0.7046 (mttt) REVERT: P 107 GLU cc_start: 0.7485 (tt0) cc_final: 0.7249 (tt0) REVERT: Q 429 LEU cc_start: 0.8216 (mt) cc_final: 0.7978 (tp) REVERT: R 426 GLU cc_start: 0.6606 (mt-10) cc_final: 0.5984 (mt-10) REVERT: T 7 SER cc_start: 0.7731 (m) cc_final: 0.7234 (t) REVERT: T 809 TRP cc_start: 0.7480 (m100) cc_final: 0.7037 (m100) outliers start: 67 outliers final: 48 residues processed: 338 average time/residue: 0.3213 time to fit residues: 148.3180 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 : 1.480 ------------------------------------------------------------------------------- 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 103 LEU 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 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 350 HIS Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 374 GLN 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 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 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 420 ILE 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 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=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: 0.8980 chunk 162 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 160 optimal weight: 0.5980 chunk 138 optimal weight: 0.6980 chunk 148 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 817 GLN ** C 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN ** H 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 805 ASN M 854 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 = 0.4247 r_free = 0.4247 target = 0.177450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.166166 restraints weight = 18442.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.168842 restraints weight = 10969.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.170614 restraints weight = 7223.803| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.5710 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= 0.191 Angle : 0.580 8.623 18434 Z= 0.312 Chirality : 0.041 0.211 2082 Planarity : 0.004 0.046 2438 Dihedral : 4.520 28.970 1962 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.30 % Allowed : 22.35 % Favored : 73.35 % 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: 1.21 (0.20), residues: 1704 helix: 2.50 (0.16), residues: 770 sheet: -1.32 (0.23), residues: 450 loop : 0.34 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP N 878 HIS 0.006 0.001 HIS K 350 PHE 0.006 0.001 PHE S 840 TYR 0.027 0.002 TYR T 832 ARG 0.009 0.001 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.04164 ( 918) hydrogen bonds : angle 4.63450 ( 2586) SS BOND : bond 0.00185 ( 8) SS BOND : angle 1.40200 ( 16) covalent geometry : bond 0.00414 (13682) covalent geometry : angle 0.57882 (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 369 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 309 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 384 ARG cc_start: 0.7192 (mtp180) cc_final: 0.6655 (mtp-110) REVERT: B 416 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8604 (mp) REVERT: B 441 ARG cc_start: 0.6155 (mtt180) cc_final: 0.5707 (mtt180) REVERT: D 855 MET cc_start: 0.6476 (mtp) cc_final: 0.6177 (mtt) REVERT: C 6 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6601 (mp0) REVERT: C 831 ASN cc_start: 0.7681 (m-40) cc_final: 0.7403 (m-40) REVERT: C 855 MET cc_start: 0.7151 (mtm) cc_final: 0.6790 (mtp) REVERT: G 423 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.7043 (mt) REVERT: H 426 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6999 (mp0) REVERT: H 435 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7699 (mt-10) REVERT: I 817 GLN cc_start: 0.6692 (mp10) cc_final: 0.6281 (mp10) REVERT: L 416 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8019 (mp) REVERT: N 810 TYR cc_start: 0.7857 (m-80) cc_final: 0.7655 (m-80) REVERT: N 855 MET cc_start: 0.7696 (mmm) cc_final: 0.7207 (mtt) REVERT: N 877 TYR cc_start: 0.8034 (m-10) cc_final: 0.7786 (m-80) REVERT: N 880 GLN cc_start: 0.6570 (mt0) cc_final: 0.6230 (mt0) REVERT: M 13 TYR cc_start: 0.5773 (OUTLIER) cc_final: 0.5261 (t80) REVERT: M 832 TYR cc_start: 0.7749 (m-80) cc_final: 0.7196 (m-80) REVERT: O 156 LYS cc_start: 0.7333 (mttt) cc_final: 0.6977 (mttt) REVERT: P 107 GLU cc_start: 0.7594 (tt0) cc_final: 0.7339 (tt0) REVERT: Q 429 LEU cc_start: 0.8186 (mt) cc_final: 0.7974 (tp) REVERT: R 426 GLU cc_start: 0.6550 (mt-10) cc_final: 0.5917 (mt-10) REVERT: T 7 SER cc_start: 0.7906 (m) cc_final: 0.7387 (t) REVERT: T 809 TRP cc_start: 0.7481 (m100) cc_final: 0.7044 (m100) outliers start: 60 outliers final: 49 residues processed: 341 average time/residue: 0.3109 time to fit residues: 144.7589 Evaluate side-chains 363 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 309 time to evaluate : 1.571 ------------------------------------------------------------------------------- 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 799 ARG 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 886 VAL Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 103 LEU 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 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 350 HIS 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 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 805 ASN Chi-restraints excluded: chain M residue 821 VAL Chi-restraints excluded: chain M residue 855 MET Chi-restraints excluded: chain P residue 90 VAL 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 420 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 88 optimal weight: 1.9990 chunk 113 optimal weight: 0.0020 chunk 43 optimal weight: 0.5980 chunk 162 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 157 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 78 optimal weight: 0.0980 chunk 37 optimal weight: 3.9990 overall best weight: 0.3988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** M 854 GLN O 139 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.178532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.165949 restraints weight = 19328.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.168967 restraints weight = 11391.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.170958 restraints weight = 7507.214| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.5829 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= 0.133 Angle : 0.541 8.981 18434 Z= 0.289 Chirality : 0.039 0.195 2082 Planarity : 0.003 0.044 2438 Dihedral : 4.307 30.373 1962 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % 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 : 0.06 % 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: 1.53 (0.21), residues: 1704 helix: 2.84 (0.17), residues: 766 sheet: -1.22 (0.23), residues: 450 loop : 0.44 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP N 878 HIS 0.004 0.001 HIS K 350 PHE 0.004 0.001 PHE I 840 TYR 0.023 0.001 TYR T 832 ARG 0.012 0.001 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 918) hydrogen bonds : angle 4.38972 ( 2586) SS BOND : bond 0.00142 ( 8) SS BOND : angle 1.24031 ( 16) covalent geometry : bond 0.00283 (13682) covalent geometry : angle 0.53980 (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 358 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 298 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 384 ARG cc_start: 0.7162 (mtp180) cc_final: 0.6632 (mtp-110) REVERT: B 416 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8532 (mp) REVERT: B 441 ARG cc_start: 0.6218 (mtt180) cc_final: 0.5755 (mtt180) REVERT: D 855 MET cc_start: 0.6419 (mtp) cc_final: 0.6115 (mtt) REVERT: C 6 GLU cc_start: 0.7039 (mm-30) cc_final: 0.6289 (mm-30) REVERT: C 809 TRP cc_start: 0.8269 (m100) cc_final: 0.7460 (m100) REVERT: C 827 TRP cc_start: 0.7396 (OUTLIER) cc_final: 0.7155 (m-10) REVERT: C 831 ASN cc_start: 0.7572 (m-40) cc_final: 0.7261 (m-40) REVERT: C 855 MET cc_start: 0.7126 (mtm) cc_final: 0.6522 (mtp) REVERT: F 151 LEU cc_start: 0.7195 (mt) cc_final: 0.6911 (mm) REVERT: H 426 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: H 435 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7714 (mt-10) REVERT: I 817 GLN cc_start: 0.6648 (mp10) cc_final: 0.6238 (mp10) REVERT: J 869 ASN cc_start: 0.7391 (t0) cc_final: 0.6882 (m110) REVERT: L 374 GLN cc_start: 0.7222 (tp40) cc_final: 0.6921 (tt0) REVERT: L 391 ARG cc_start: 0.7129 (mtp-110) cc_final: 0.6900 (ttp80) REVERT: L 416 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7991 (mp) REVERT: N 855 MET cc_start: 0.7567 (mmm) cc_final: 0.7232 (mtp) REVERT: N 877 TYR cc_start: 0.8030 (m-10) cc_final: 0.7821 (m-80) REVERT: N 880 GLN cc_start: 0.6707 (mt0) cc_final: 0.6345 (mt0) REVERT: M 13 TYR cc_start: 0.5773 (OUTLIER) cc_final: 0.5193 (t80) REVERT: M 832 TYR cc_start: 0.7682 (m-80) cc_final: 0.7221 (m-80) REVERT: O 156 LYS cc_start: 0.7296 (mttt) cc_final: 0.6943 (mttt) REVERT: P 107 GLU cc_start: 0.7483 (tt0) cc_final: 0.7241 (tt0) REVERT: R 426 GLU cc_start: 0.6699 (mt-10) cc_final: 0.6278 (mt-10) REVERT: T 7 SER cc_start: 0.7741 (m) cc_final: 0.7254 (t) REVERT: T 809 TRP cc_start: 0.7480 (m100) cc_final: 0.7004 (m100) REVERT: T 820 MET cc_start: 0.6813 (ttm) cc_final: 0.6573 (ttm) outliers start: 60 outliers final: 46 residues processed: 333 average time/residue: 0.3155 time to fit residues: 143.9476 Evaluate side-chains 345 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 294 time to evaluate : 1.534 ------------------------------------------------------------------------------- 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 B residue 446 MET Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 3 GLN 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 103 LEU 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 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 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 350 HIS 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 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 90 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 T residue 823 VAL Chi-restraints excluded: chain T residue 824 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 51 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 115 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN ** L 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 805 ASN M 854 GLN ** M 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.225645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.215000 restraints weight = 20222.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.216878 restraints weight = 12158.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.218371 restraints weight = 8130.201| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.5919 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= 0.177 Angle : 0.574 9.557 18434 Z= 0.309 Chirality : 0.041 0.191 2082 Planarity : 0.004 0.052 2438 Dihedral : 4.401 30.097 1962 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.94 % Allowed : 23.28 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.40 (0.21), residues: 1704 helix: 2.72 (0.17), residues: 768 sheet: -1.31 (0.23), residues: 450 loop : 0.42 (0.31), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP S 827 HIS 0.005 0.001 HIS K 350 PHE 0.006 0.001 PHE I 840 TYR 0.025 0.002 TYR T 832 ARG 0.010 0.001 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.04055 ( 918) hydrogen bonds : angle 4.49918 ( 2586) SS BOND : bond 0.00165 ( 8) SS BOND : angle 1.38569 ( 16) covalent geometry : bond 0.00383 (13682) covalent geometry : angle 0.57319 (18418) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4813.05 seconds wall clock time: 86 minutes 27.89 seconds (5187.89 seconds total)