Starting phenix.real_space_refine on Sat Aug 23 16:36:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8afh_15398/08_2025/8afh_15398.cif Found real_map, /net/cci-nas-00/data/ceres_data/8afh_15398/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8afh_15398/08_2025/8afh_15398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8afh_15398/08_2025/8afh_15398.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8afh_15398/08_2025/8afh_15398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8afh_15398/08_2025/8afh_15398.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.97, per 1000 atoms: 0.22 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: 0.77 Conformation dependent library (CDL) restraints added in 511.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.34 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: 2.00 Time building geometry restraints manager: 1.03 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: 0.01 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: 3.270 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: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 11.160 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.020 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.013 0.001 ARG B 404 TYR 0.018 0.002 TYR T 13 PHE 0.006 0.001 PHE I 840 TRP 0.023 0.003 TRP C 827 HIS 0.005 0.002 HIS K 350 Details of bonding type rmsd covalent geometry : bond 0.00581 (13682) covalent geometry : angle 0.69947 (18418) SS BOND : bond 0.00239 ( 8) SS BOND : angle 1.60641 ( 16) hydrogen bonds : bond 0.21907 ( 918) hydrogen bonds : angle 9.24467 ( 2586) *********************** 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 : 0.316 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: 0.1402 time to fit residues: 61.1183 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 : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.0020 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.4188 ------------------------------------------------------------------------------- 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 E 93 ASN J 805 ASN N 856 ASN N 869 ASN M 854 GLN P 98 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.179390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.166443 restraints weight = 19347.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.169792 restraints weight = 10693.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.172009 restraints weight = 6692.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.173479 restraints weight = 4551.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.174505 restraints weight = 3289.353| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13690 Z= 0.153 Angle : 0.579 7.329 18434 Z= 0.321 Chirality : 0.040 0.180 2082 Planarity : 0.005 0.097 2438 Dihedral : 4.723 22.008 1962 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.22 % Allowed : 11.53 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.21), residues: 1704 helix: 1.53 (0.18), residues: 754 sheet: -1.69 (0.22), residues: 476 loop : 0.41 (0.32), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 844 TYR 0.021 0.002 TYR T 810 PHE 0.005 0.001 PHE N 840 TRP 0.012 0.002 TRP I 827 HIS 0.003 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00321 (13682) covalent geometry : angle 0.57939 (18418) SS BOND : bond 0.00163 ( 8) SS BOND : angle 0.57910 ( 16) hydrogen bonds : bond 0.04814 ( 918) hydrogen bonds : angle 5.41223 ( 2586) *********************** 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 339 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 308 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 379 LYS cc_start: 0.8427 (tmtt) cc_final: 0.8077 (tmmt) REVERT: D 792 ARG cc_start: 0.7398 (ttt180) cc_final: 0.7164 (ttt-90) REVERT: C 844 ARG cc_start: 0.6659 (mtp85) cc_final: 0.6268 (mmm-85) REVERT: F 115 LEU cc_start: 0.7267 (tp) cc_final: 0.7064 (tp) REVERT: G 419 THR cc_start: 0.7725 (t) cc_final: 0.7435 (p) REVERT: I 817 GLN cc_start: 0.5905 (mp10) cc_final: 0.5613 (mp10) REVERT: I 872 TYR cc_start: 0.7871 (t80) cc_final: 0.7407 (t80) REVERT: J 858 LEU cc_start: 0.6335 (mt) cc_final: 0.5589 (tt) REVERT: L 384 ARG cc_start: 0.6670 (mtm180) cc_final: 0.6459 (mtp180) REVERT: L 395 MET cc_start: 0.5473 (ttm) cc_final: 0.5101 (mmm) REVERT: L 416 LEU cc_start: 0.8095 (tp) cc_final: 0.7767 (mp) REVERT: M 13 TYR cc_start: 0.5410 (m-80) cc_final: 0.4985 (m-80) REVERT: M 820 MET cc_start: 0.8126 (ttp) cc_final: 0.7539 (ttp) REVERT: M 839 ARG cc_start: 0.5831 (mtm-85) cc_final: 0.5535 (ttp-110) REVERT: O 107 GLU cc_start: 0.7022 (tm-30) cc_final: 0.6629 (tm-30) REVERT: P 107 GLU cc_start: 0.7568 (tt0) cc_final: 0.7108 (tt0) REVERT: Q 416 LEU cc_start: 0.7624 (mt) cc_final: 0.7362 (mt) REVERT: R 413 ILE cc_start: 0.7617 (mm) cc_final: 0.7269 (mm) REVERT: R 426 GLU cc_start: 0.6777 (mt-10) cc_final: 0.6442 (mt-10) REVERT: S 855 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6551 (mtm) REVERT: T 7 SER cc_start: 0.6952 (m) cc_final: 0.6451 (t) REVERT: T 807 MET cc_start: 0.7546 (mmm) cc_final: 0.7257 (mtt) REVERT: T 809 TRP cc_start: 0.7424 (m100) cc_final: 0.7030 (m100) REVERT: T 820 MET cc_start: 0.7415 (mmm) cc_final: 0.7073 (mmm) REVERT: T 875 SER cc_start: 0.7227 (p) cc_final: 0.6963 (p) REVERT: T 877 TYR cc_start: 0.7349 (m-80) cc_final: 0.6838 (m-80) outliers start: 31 outliers final: 16 residues processed: 323 average time/residue: 0.1215 time to fit residues: 53.3188 Evaluate side-chains 309 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 292 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 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 L residue 355 THR Chi-restraints excluded: chain N residue 2 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 157 optimal weight: 0.5980 chunk 131 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** C 831 ASN ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 856 ASN L 374 GLN N 805 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.168814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.157637 restraints weight = 19046.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.160233 restraints weight = 11522.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.162016 restraints weight = 7700.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.163231 restraints weight = 5515.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.164130 restraints weight = 4178.283| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13690 Z= 0.202 Angle : 0.597 8.649 18434 Z= 0.327 Chirality : 0.042 0.164 2082 Planarity : 0.005 0.062 2438 Dihedral : 4.701 22.809 1962 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.87 % Allowed : 14.61 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.21), residues: 1704 helix: 1.69 (0.17), residues: 766 sheet: -1.47 (0.22), residues: 470 loop : 0.41 (0.32), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 404 TYR 0.018 0.002 TYR D 832 PHE 0.010 0.002 PHE N 840 TRP 0.021 0.002 TRP C 827 HIS 0.004 0.001 HIS K 350 Details of bonding type rmsd covalent geometry : bond 0.00433 (13682) covalent geometry : angle 0.59697 (18418) SS BOND : bond 0.00501 ( 8) SS BOND : angle 0.94797 ( 16) hydrogen bonds : bond 0.04697 ( 918) hydrogen bonds : angle 5.20469 ( 2586) *********************** 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 368 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 314 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 384 ARG cc_start: 0.7144 (mtp180) cc_final: 0.6913 (mtp-110) REVERT: B 416 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8396 (mp) REVERT: B 439 ARG cc_start: 0.7111 (mtt180) cc_final: 0.6868 (mtt90) REVERT: C 825 THR cc_start: 0.7403 (OUTLIER) cc_final: 0.7016 (p) REVERT: C 833 VAL cc_start: 0.7573 (OUTLIER) cc_final: 0.7334 (m) REVERT: C 855 MET cc_start: 0.7470 (mtm) cc_final: 0.7014 (mtp) REVERT: G 419 THR cc_start: 0.7955 (t) cc_final: 0.7740 (p) REVERT: H 426 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6992 (mp0) REVERT: I 2 VAL cc_start: 0.7142 (m) cc_final: 0.6929 (p) REVERT: I 817 GLN cc_start: 0.6303 (mp10) cc_final: 0.5904 (mp10) REVERT: I 829 SER cc_start: 0.8524 (t) cc_final: 0.8127 (p) REVERT: J 858 LEU cc_start: 0.6963 (mt) cc_final: 0.5918 (tt) REVERT: K 350 HIS cc_start: 0.3474 (OUTLIER) cc_final: 0.3109 (m90) REVERT: K 422 ARG cc_start: 0.7690 (ttm-80) cc_final: 0.7335 (tpp-160) REVERT: L 363 ARG cc_start: 0.7588 (mmm-85) cc_final: 0.7189 (mmm-85) REVERT: L 395 MET cc_start: 0.5546 (ttm) cc_final: 0.5233 (mmm) REVERT: L 416 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7973 (mp) REVERT: N 792 ARG cc_start: 0.7798 (ttt180) cc_final: 0.7564 (ttt-90) REVERT: N 805 ASN cc_start: 0.5467 (OUTLIER) cc_final: 0.4853 (m110) REVERT: N 810 TYR cc_start: 0.7934 (m-80) cc_final: 0.7607 (m-80) REVERT: N 855 MET cc_start: 0.7775 (mmm) cc_final: 0.7470 (mmm) REVERT: N 877 TYR cc_start: 0.8026 (m-10) cc_final: 0.7777 (m-80) REVERT: M 820 MET cc_start: 0.7989 (ttp) cc_final: 0.7526 (ttp) REVERT: M 825 THR cc_start: 0.7284 (OUTLIER) cc_final: 0.6947 (p) REVERT: M 866 TYR cc_start: 0.8290 (m-80) cc_final: 0.7918 (m-10) REVERT: O 107 GLU cc_start: 0.6852 (tm-30) cc_final: 0.6484 (tm-30) REVERT: P 107 GLU cc_start: 0.7634 (tt0) cc_final: 0.6582 (tt0) REVERT: R 413 ILE cc_start: 0.7706 (mm) cc_final: 0.7322 (mm) REVERT: R 426 GLU cc_start: 0.6817 (mt-10) cc_final: 0.6313 (mt-10) REVERT: S 841 ILE cc_start: 0.6960 (mt) cc_final: 0.6750 (mm) REVERT: T 7 SER cc_start: 0.7263 (m) cc_final: 0.6849 (t) REVERT: T 809 TRP cc_start: 0.7521 (m100) cc_final: 0.6925 (m100) REVERT: T 820 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.7152 (ttm) REVERT: T 886 VAL cc_start: 0.7702 (m) cc_final: 0.7334 (p) outliers start: 54 outliers final: 31 residues processed: 337 average time/residue: 0.1090 time to fit residues: 50.9155 Evaluate side-chains 350 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 310 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 821 VAL Chi-restraints excluded: chain C residue 825 THR Chi-restraints excluded: chain C residue 833 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 429 LEU 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 831 ASN Chi-restraints excluded: chain J residue 833 VAL 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 805 ASN Chi-restraints excluded: chain N residue 865 VAL 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 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 140 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 142 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 101 optimal weight: 0.0970 chunk 83 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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** B 374 GLN D 3 GLN C 5 GLN ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN E 139 ASN L 350 HIS L 374 GLN P 98 GLN R 417 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.172437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.159037 restraints weight = 19692.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.162357 restraints weight = 11180.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.164554 restraints weight = 7196.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.166062 restraints weight = 5024.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.167095 restraints weight = 3740.857| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13690 Z= 0.165 Angle : 0.533 8.180 18434 Z= 0.293 Chirality : 0.040 0.150 2082 Planarity : 0.004 0.053 2438 Dihedral : 4.454 20.670 1962 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.58 % Allowed : 17.41 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.21), residues: 1704 helix: 2.11 (0.17), residues: 770 sheet: -1.42 (0.22), residues: 474 loop : 0.43 (0.32), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 145 TYR 0.014 0.001 TYR D 832 PHE 0.005 0.001 PHE N 840 TRP 0.011 0.001 TRP C 809 HIS 0.004 0.001 HIS K 350 Details of bonding type rmsd covalent geometry : bond 0.00350 (13682) covalent geometry : angle 0.53299 (18418) SS BOND : bond 0.00622 ( 8) SS BOND : angle 0.89169 ( 16) hydrogen bonds : bond 0.04181 ( 918) hydrogen bonds : angle 4.79641 ( 2586) *********************** 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: 64 poor density : 306 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 ARG cc_start: 0.7427 (tpt90) cc_final: 0.7024 (tpp-160) REVERT: A 423 LEU cc_start: 0.8133 (tp) cc_final: 0.7904 (mt) REVERT: D 820 MET cc_start: 0.7696 (tmm) cc_final: 0.7466 (tmm) REVERT: C 6 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6098 (mm-30) REVERT: C 855 MET cc_start: 0.7676 (mtm) cc_final: 0.7083 (mtp) REVERT: E 128 ARG cc_start: 0.6013 (tpt170) cc_final: 0.5702 (tpm170) REVERT: H 426 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: I 817 GLN cc_start: 0.6420 (mp10) cc_final: 0.5968 (mp10) REVERT: K 412 LYS cc_start: 0.7645 (ttmm) cc_final: 0.7374 (ttmm) REVERT: L 363 ARG cc_start: 0.7429 (mmm-85) cc_final: 0.7058 (mmm-85) REVERT: L 395 MET cc_start: 0.5523 (ttm) cc_final: 0.5286 (mmm) REVERT: L 416 LEU cc_start: 0.8153 (tp) cc_final: 0.7863 (mp) REVERT: L 431 GLU cc_start: 0.6800 (tp30) cc_final: 0.6446 (tp30) REVERT: L 438 ARG cc_start: 0.6702 (mtp180) cc_final: 0.6480 (mtp180) REVERT: N 810 TYR cc_start: 0.7870 (m-80) cc_final: 0.7546 (m-80) REVERT: M 13 TYR cc_start: 0.6010 (OUTLIER) cc_final: 0.4883 (t80) REVERT: M 820 MET cc_start: 0.8049 (ttp) cc_final: 0.7561 (ttp) REVERT: M 825 THR cc_start: 0.7234 (OUTLIER) cc_final: 0.6878 (p) REVERT: M 866 TYR cc_start: 0.8281 (m-80) cc_final: 0.7973 (m-80) REVERT: O 156 LYS cc_start: 0.7435 (mttt) cc_final: 0.7084 (mttt) REVERT: R 413 ILE cc_start: 0.7677 (mm) cc_final: 0.7284 (mm) REVERT: R 426 GLU cc_start: 0.6860 (mt-10) cc_final: 0.6261 (mt-10) REVERT: S 841 ILE cc_start: 0.6802 (mt) cc_final: 0.6594 (mm) REVERT: T 7 SER cc_start: 0.7775 (m) cc_final: 0.7236 (t) REVERT: T 809 TRP cc_start: 0.7547 (m100) cc_final: 0.6902 (m100) REVERT: T 886 VAL cc_start: 0.7697 (m) cc_final: 0.7234 (p) outliers start: 64 outliers final: 44 residues processed: 338 average time/residue: 0.1166 time to fit residues: 54.3483 Evaluate side-chains 346 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 299 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 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 886 VAL Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 429 LEU 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 831 ASN Chi-restraints excluded: chain J residue 833 VAL Chi-restraints excluded: chain K residue 425 SER Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 423 LEU Chi-restraints excluded: chain L residue 429 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 790 SER Chi-restraints excluded: chain N residue 835 SER Chi-restraints excluded: chain N residue 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 825 THR Chi-restraints excluded: chain O residue 163 SER Chi-restraints excluded: chain P residue 98 GLN Chi-restraints excluded: chain R residue 416 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 790 SER Chi-restraints excluded: chain S residue 820 MET Chi-restraints excluded: chain S residue 851 VAL 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 75 optimal weight: 0.0670 chunk 49 optimal weight: 2.9990 chunk 87 optimal weight: 0.4980 chunk 136 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 chunk 19 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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** B 374 GLN ** C 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 374 GLN L 409 HIS P 98 GLN ** R 417 GLN ** 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 = 0.4142 r_free = 0.4142 target = 0.172050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.158893 restraints weight = 19632.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.162072 restraints weight = 11259.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.164245 restraints weight = 7323.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.165736 restraints weight = 5129.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.166725 restraints weight = 3835.285| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13690 Z= 0.139 Angle : 0.508 8.889 18434 Z= 0.278 Chirality : 0.039 0.166 2082 Planarity : 0.004 0.050 2438 Dihedral : 4.271 19.023 1962 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.30 % Allowed : 18.98 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.21), residues: 1704 helix: 2.47 (0.17), residues: 766 sheet: -1.29 (0.23), residues: 474 loop : 0.49 (0.32), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 145 TYR 0.012 0.001 TYR T 810 PHE 0.005 0.001 PHE S 840 TRP 0.009 0.001 TRP C 809 HIS 0.003 0.001 HIS K 350 Details of bonding type rmsd covalent geometry : bond 0.00293 (13682) covalent geometry : angle 0.50796 (18418) SS BOND : bond 0.00311 ( 8) SS BOND : angle 0.75112 ( 16) hydrogen bonds : bond 0.03993 ( 918) hydrogen bonds : angle 4.59801 ( 2586) *********************** 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 363 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 303 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 ARG cc_start: 0.7416 (tpt90) cc_final: 0.7123 (tpp-160) REVERT: D 820 MET cc_start: 0.7757 (tmm) cc_final: 0.7410 (tmm) REVERT: C 6 GLU cc_start: 0.7038 (mm-30) cc_final: 0.5765 (mm-30) REVERT: C 855 MET cc_start: 0.7734 (mtm) cc_final: 0.6975 (mtp) REVERT: E 128 ARG cc_start: 0.6045 (tpt170) cc_final: 0.5742 (tpm170) REVERT: H 426 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: H 435 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7699 (mt-10) REVERT: I 817 GLN cc_start: 0.6429 (mp10) cc_final: 0.5995 (mp10) REVERT: I 829 SER cc_start: 0.8248 (t) cc_final: 0.7586 (p) REVERT: J 855 MET cc_start: 0.7595 (mmm) cc_final: 0.7382 (mmm) REVERT: K 412 LYS cc_start: 0.7607 (ttmm) cc_final: 0.7388 (ttmm) REVERT: L 416 LEU cc_start: 0.8231 (tp) cc_final: 0.7923 (mp) REVERT: L 431 GLU cc_start: 0.6904 (tp30) cc_final: 0.6560 (tp30) REVERT: L 439 ARG cc_start: 0.7795 (mtt180) cc_final: 0.7515 (mtt180) REVERT: N 810 TYR cc_start: 0.7885 (m-80) cc_final: 0.7637 (m-80) REVERT: N 818 ARG cc_start: 0.7875 (ptp-110) cc_final: 0.7632 (ptp-110) REVERT: M 13 TYR cc_start: 0.6086 (OUTLIER) cc_final: 0.5093 (t80) REVERT: M 825 THR cc_start: 0.7139 (OUTLIER) cc_final: 0.6792 (p) REVERT: M 866 TYR cc_start: 0.8274 (m-80) cc_final: 0.8038 (m-80) REVERT: O 156 LYS cc_start: 0.7401 (mttt) cc_final: 0.7046 (mttt) REVERT: P 146 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6804 (tp) REVERT: R 426 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6252 (mt-10) REVERT: S 841 ILE cc_start: 0.6813 (mt) cc_final: 0.6585 (mm) REVERT: T 7 SER cc_start: 0.7790 (m) cc_final: 0.7220 (t) REVERT: T 809 TRP cc_start: 0.7462 (m100) cc_final: 0.6876 (m100) REVERT: T 886 VAL cc_start: 0.7781 (OUTLIER) cc_final: 0.7249 (p) outliers start: 60 outliers final: 39 residues processed: 337 average time/residue: 0.1172 time to fit residues: 54.2396 Evaluate side-chains 342 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 298 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 LEU 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 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 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 429 LEU 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 833 VAL Chi-restraints excluded: chain L residue 355 THR 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 835 SER Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 13 TYR Chi-restraints excluded: chain M residue 794 SER Chi-restraints excluded: chain M residue 821 VAL Chi-restraints excluded: chain M residue 825 THR Chi-restraints excluded: chain O residue 163 SER 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 S residue 12 VAL Chi-restraints excluded: chain S residue 820 MET Chi-restraints excluded: chain S residue 835 SER Chi-restraints excluded: chain S residue 851 VAL 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 122 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 118 optimal weight: 0.0570 chunk 30 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 374 GLN ** R 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.180015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.166532 restraints weight = 19476.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.169956 restraints weight = 10966.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.172124 restraints weight = 6987.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.173608 restraints weight = 4884.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.174638 restraints weight = 3640.260| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13690 Z= 0.142 Angle : 0.514 8.799 18434 Z= 0.280 Chirality : 0.039 0.152 2082 Planarity : 0.003 0.047 2438 Dihedral : 4.235 18.069 1962 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.80 % Allowed : 19.05 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.21), residues: 1704 helix: 2.68 (0.17), residues: 764 sheet: -1.26 (0.24), residues: 408 loop : 0.23 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 404 TYR 0.014 0.001 TYR C 810 PHE 0.005 0.001 PHE S 840 TRP 0.024 0.001 TRP N 878 HIS 0.015 0.002 HIS L 409 Details of bonding type rmsd covalent geometry : bond 0.00301 (13682) covalent geometry : angle 0.51247 (18418) SS BOND : bond 0.00339 ( 8) SS BOND : angle 1.23629 ( 16) hydrogen bonds : bond 0.03957 ( 918) hydrogen bonds : angle 4.52035 ( 2586) *********************** 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 364 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 297 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 ARG cc_start: 0.7306 (tpt90) cc_final: 0.7010 (mmm160) REVERT: B 384 ARG cc_start: 0.7170 (mtp180) cc_final: 0.6644 (mtp-110) REVERT: B 416 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8372 (mp) REVERT: C 6 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6058 (mm-30) REVERT: C 809 TRP cc_start: 0.8355 (m100) cc_final: 0.7814 (m100) REVERT: C 855 MET cc_start: 0.7721 (mtm) cc_final: 0.7032 (mmm) REVERT: E 128 ARG cc_start: 0.6143 (tpt170) cc_final: 0.5807 (tpm170) REVERT: F 115 LEU cc_start: 0.6325 (tp) cc_final: 0.5805 (tp) REVERT: H 426 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: H 435 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7766 (mt-10) REVERT: I 817 GLN cc_start: 0.6428 (mp10) cc_final: 0.5952 (mp10) REVERT: J 855 MET cc_start: 0.7659 (mmm) cc_final: 0.6480 (mmm) REVERT: J 862 ASP cc_start: 0.7031 (m-30) cc_final: 0.6625 (m-30) REVERT: L 384 ARG cc_start: 0.6761 (mtp180) cc_final: 0.6543 (mtp180) REVERT: L 416 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7913 (mp) REVERT: L 431 GLU cc_start: 0.6938 (tp30) cc_final: 0.6520 (tp30) REVERT: L 439 ARG cc_start: 0.7834 (mtt180) cc_final: 0.7442 (mtt180) REVERT: N 810 TYR cc_start: 0.7874 (m-80) cc_final: 0.7628 (m-80) REVERT: N 818 ARG cc_start: 0.7884 (ptp-110) cc_final: 0.7585 (ptp-110) REVERT: N 839 ARG cc_start: 0.6409 (OUTLIER) cc_final: 0.6131 (ttp80) REVERT: M 13 TYR cc_start: 0.5792 (OUTLIER) cc_final: 0.4992 (t80) REVERT: M 825 THR cc_start: 0.7037 (OUTLIER) cc_final: 0.6727 (p) REVERT: M 866 TYR cc_start: 0.8311 (m-80) cc_final: 0.8021 (m-80) REVERT: O 156 LYS cc_start: 0.7428 (mttt) cc_final: 0.7041 (mttt) REVERT: R 426 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6171 (mt-10) REVERT: S 841 ILE cc_start: 0.6823 (mt) cc_final: 0.6599 (mm) REVERT: T 7 SER cc_start: 0.7802 (m) cc_final: 0.7245 (t) REVERT: T 809 TRP cc_start: 0.7471 (m100) cc_final: 0.7152 (m100) REVERT: T 886 VAL cc_start: 0.7567 (OUTLIER) cc_final: 0.7040 (p) outliers start: 67 outliers final: 47 residues processed: 333 average time/residue: 0.1255 time to fit residues: 57.0553 Evaluate side-chains 348 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 294 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 416 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain D residue 797 SER Chi-restraints excluded: chain D residue 824 VAL 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 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 H residue 429 LEU 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 833 VAL 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 416 LEU Chi-restraints excluded: chain L residue 423 LEU Chi-restraints excluded: chain L residue 429 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 790 SER Chi-restraints excluded: chain N residue 835 SER Chi-restraints excluded: chain N residue 839 ARG Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 13 TYR Chi-restraints excluded: chain M residue 794 SER Chi-restraints excluded: chain M residue 821 VAL Chi-restraints excluded: chain M residue 825 THR Chi-restraints excluded: chain M residue 851 VAL Chi-restraints excluded: chain P residue 124 GLU 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 820 MET 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 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 116 optimal weight: 0.9990 chunk 49 optimal weight: 0.0870 chunk 138 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 142 optimal weight: 0.5980 chunk 137 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 73 optimal weight: 0.1980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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** ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 374 GLN L 409 HIS M 854 GLN ** R 417 GLN ** 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 = 0.4270 r_free = 0.4270 target = 0.179389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.168010 restraints weight = 18480.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.170660 restraints weight = 10909.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.172470 restraints weight = 7199.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.173700 restraints weight = 5131.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.174496 restraints weight = 3859.585| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.5413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13690 Z= 0.149 Angle : 0.523 8.858 18434 Z= 0.282 Chirality : 0.039 0.142 2082 Planarity : 0.003 0.047 2438 Dihedral : 4.251 19.965 1962 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.58 % Allowed : 20.42 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.21), residues: 1704 helix: 2.77 (0.17), residues: 766 sheet: -1.25 (0.25), residues: 408 loop : 0.31 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 404 TYR 0.014 0.001 TYR C 810 PHE 0.005 0.001 PHE S 840 TRP 0.034 0.001 TRP N 878 HIS 0.004 0.001 HIS K 350 Details of bonding type rmsd covalent geometry : bond 0.00317 (13682) covalent geometry : angle 0.52133 (18418) SS BOND : bond 0.00171 ( 8) SS BOND : angle 1.48687 ( 16) hydrogen bonds : bond 0.03927 ( 918) hydrogen bonds : angle 4.50707 ( 2586) *********************** 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 367 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 303 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 ARG cc_start: 0.7451 (tpt90) cc_final: 0.7108 (tpp-160) REVERT: B 384 ARG cc_start: 0.7167 (mtp180) cc_final: 0.6632 (mtp-110) REVERT: B 416 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8418 (mp) REVERT: D 820 MET cc_start: 0.7801 (tmm) cc_final: 0.7447 (tmm) REVERT: C 6 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6154 (mm-30) REVERT: C 809 TRP cc_start: 0.8333 (m100) cc_final: 0.7813 (m100) REVERT: C 855 MET cc_start: 0.7698 (mtm) cc_final: 0.7050 (mmm) REVERT: E 128 ARG cc_start: 0.6035 (tpt170) cc_final: 0.5797 (tpm170) REVERT: G 426 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6646 (mt-10) REVERT: H 426 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: H 435 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7772 (mt-10) REVERT: I 817 GLN cc_start: 0.6516 (mp10) cc_final: 0.6049 (mp10) REVERT: J 855 MET cc_start: 0.7644 (mmm) cc_final: 0.7352 (mmm) REVERT: L 416 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7939 (mp) REVERT: L 431 GLU cc_start: 0.6865 (tp30) cc_final: 0.6438 (tp30) REVERT: L 435 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7390 (mm-30) REVERT: L 439 ARG cc_start: 0.7793 (mtt180) cc_final: 0.7430 (mtt180) REVERT: N 810 TYR cc_start: 0.7854 (m-80) cc_final: 0.7633 (m-80) REVERT: N 818 ARG cc_start: 0.7919 (ptp-110) cc_final: 0.7596 (ptp-110) REVERT: N 839 ARG cc_start: 0.6336 (OUTLIER) cc_final: 0.6061 (ttp80) REVERT: N 855 MET cc_start: 0.7495 (mmm) cc_final: 0.7148 (mtp) REVERT: M 13 TYR cc_start: 0.5845 (OUTLIER) cc_final: 0.5186 (t80) REVERT: M 825 THR cc_start: 0.6997 (OUTLIER) cc_final: 0.6651 (p) REVERT: M 831 ASN cc_start: 0.6845 (p0) cc_final: 0.6612 (p0) REVERT: M 832 TYR cc_start: 0.7739 (m-80) cc_final: 0.7126 (m-80) REVERT: O 156 LYS cc_start: 0.7381 (mttt) cc_final: 0.7073 (mttt) REVERT: R 426 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6454 (mt-10) REVERT: S 841 ILE cc_start: 0.6943 (mt) cc_final: 0.6708 (mm) REVERT: T 7 SER cc_start: 0.7860 (m) cc_final: 0.7294 (t) REVERT: T 809 TRP cc_start: 0.7463 (m100) cc_final: 0.7172 (m100) outliers start: 64 outliers final: 55 residues processed: 335 average time/residue: 0.1214 time to fit residues: 55.5875 Evaluate side-chains 358 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 297 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 797 SER Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain C residue 816 LYS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 825 THR Chi-restraints excluded: chain C residue 886 VAL 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 H residue 429 LEU 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 823 VAL Chi-restraints excluded: chain J residue 824 VAL Chi-restraints excluded: chain J residue 825 THR Chi-restraints excluded: chain J residue 833 VAL 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 416 LEU Chi-restraints excluded: chain L residue 423 LEU Chi-restraints excluded: chain L residue 429 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 790 SER Chi-restraints excluded: chain N residue 835 SER Chi-restraints excluded: chain N residue 839 ARG Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 13 TYR Chi-restraints excluded: chain M residue 794 SER Chi-restraints excluded: chain M residue 821 VAL Chi-restraints excluded: chain M residue 825 THR Chi-restraints excluded: chain M residue 851 VAL Chi-restraints excluded: chain P residue 124 GLU 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 420 ILE Chi-restraints excluded: chain R residue 422 ARG Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 820 MET Chi-restraints excluded: chain S residue 821 VAL Chi-restraints excluded: chain S residue 835 SER Chi-restraints excluded: chain S residue 851 VAL Chi-restraints excluded: chain S residue 886 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 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 124 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 77 optimal weight: 0.0020 chunk 129 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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** ** C 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 856 ASN L 374 GLN M 805 ASN M 854 GLN O 139 ASN ** R 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.177953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.166689 restraints weight = 18497.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.169362 restraints weight = 10946.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.171166 restraints weight = 7196.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.172375 restraints weight = 5091.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.173145 restraints weight = 3842.710| |-----------------------------------------------------------------------------| r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.5638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13690 Z= 0.164 Angle : 0.546 8.883 18434 Z= 0.295 Chirality : 0.040 0.153 2082 Planarity : 0.004 0.046 2438 Dihedral : 4.356 24.133 1962 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.23 % Allowed : 20.20 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.21), residues: 1704 helix: 2.67 (0.16), residues: 774 sheet: -1.31 (0.24), residues: 408 loop : 0.37 (0.30), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 404 TYR 0.021 0.002 TYR T 832 PHE 0.005 0.001 PHE S 840 TRP 0.031 0.001 TRP N 878 HIS 0.005 0.001 HIS K 350 Details of bonding type rmsd covalent geometry : bond 0.00352 (13682) covalent geometry : angle 0.54446 (18418) SS BOND : bond 0.00176 ( 8) SS BOND : angle 1.34786 ( 16) hydrogen bonds : bond 0.04014 ( 918) hydrogen bonds : angle 4.56713 ( 2586) *********************** 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 385 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 312 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 ARG cc_start: 0.7463 (tpt90) cc_final: 0.7168 (tpp-160) REVERT: B 384 ARG cc_start: 0.7168 (mtp180) cc_final: 0.6622 (mtp-110) REVERT: B 416 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8521 (mp) REVERT: D 820 MET cc_start: 0.7729 (tmm) cc_final: 0.7434 (tmm) REVERT: D 855 MET cc_start: 0.6474 (mtp) cc_final: 0.6157 (mtt) REVERT: C 6 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6376 (mm-30) REVERT: C 809 TRP cc_start: 0.8309 (m100) cc_final: 0.7604 (m100) REVERT: C 831 ASN cc_start: 0.7491 (m-40) cc_final: 0.7258 (m-40) REVERT: C 855 MET cc_start: 0.7546 (mtm) cc_final: 0.6973 (mmm) REVERT: G 416 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7952 (mp) REVERT: G 426 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6837 (mt-10) REVERT: G 429 LEU cc_start: 0.7947 (mp) cc_final: 0.7533 (tp) REVERT: H 426 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: H 435 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7728 (mt-10) REVERT: I 817 GLN cc_start: 0.6619 (mp10) cc_final: 0.6164 (mp10) REVERT: J 855 MET cc_start: 0.7707 (mmm) cc_final: 0.7372 (mmm) REVERT: L 416 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8024 (mp) REVERT: L 431 GLU cc_start: 0.6741 (tp30) cc_final: 0.6348 (tp30) REVERT: L 439 ARG cc_start: 0.7730 (mtt180) cc_final: 0.7299 (mtt180) REVERT: N 818 ARG cc_start: 0.7886 (ptp-110) cc_final: 0.7543 (ptp-110) REVERT: N 839 ARG cc_start: 0.6325 (OUTLIER) cc_final: 0.6011 (ttp80) REVERT: N 855 MET cc_start: 0.7584 (mmm) cc_final: 0.7180 (mtp) REVERT: M 13 TYR cc_start: 0.5838 (OUTLIER) cc_final: 0.5364 (t80) REVERT: M 825 THR cc_start: 0.6839 (OUTLIER) cc_final: 0.6554 (p) REVERT: O 156 LYS cc_start: 0.7279 (mttt) cc_final: 0.6950 (mttt) REVERT: R 426 GLU cc_start: 0.6622 (mt-10) cc_final: 0.6173 (mt-10) REVERT: S 841 ILE cc_start: 0.6997 (mt) cc_final: 0.6796 (mm) REVERT: T 7 SER cc_start: 0.7923 (m) cc_final: 0.7303 (t) REVERT: T 809 TRP cc_start: 0.7489 (m100) cc_final: 0.7096 (m100) REVERT: T 820 MET cc_start: 0.6862 (ttm) cc_final: 0.6392 (ttm) outliers start: 73 outliers final: 53 residues processed: 349 average time/residue: 0.1226 time to fit residues: 58.3505 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 : 0.464 ------------------------------------------------------------------------------- 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 443 ARG Chi-restraints excluded: chain D residue 797 SER Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain C residue 816 LYS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 825 THR Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 429 LEU 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 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 L residue 355 THR Chi-restraints excluded: chain L residue 416 LEU Chi-restraints excluded: chain L residue 423 LEU Chi-restraints excluded: chain L residue 429 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 790 SER Chi-restraints excluded: chain N residue 835 SER Chi-restraints excluded: chain N residue 839 ARG Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 13 TYR Chi-restraints excluded: chain M residue 794 SER Chi-restraints excluded: chain M residue 821 VAL Chi-restraints excluded: chain M residue 825 THR Chi-restraints excluded: chain M residue 851 VAL Chi-restraints excluded: chain O residue 103 LEU Chi-restraints excluded: chain P residue 124 GLU 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 420 ILE Chi-restraints excluded: chain R residue 422 ARG Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 820 MET Chi-restraints excluded: chain S residue 821 VAL Chi-restraints excluded: chain S residue 835 SER Chi-restraints excluded: chain S residue 851 VAL Chi-restraints excluded: chain S residue 886 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 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 121 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 chunk 164 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 11 optimal weight: 0.0870 chunk 95 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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** C 831 ASN ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 374 GLN M 854 GLN ** R 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 831 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.178764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.167407 restraints weight = 18577.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.170005 restraints weight = 11021.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.171829 restraints weight = 7323.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.173067 restraints weight = 5238.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.173920 restraints weight = 3937.094| |-----------------------------------------------------------------------------| r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.5804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13690 Z= 0.150 Angle : 0.545 9.124 18434 Z= 0.293 Chirality : 0.040 0.199 2082 Planarity : 0.003 0.045 2438 Dihedral : 4.347 29.184 1962 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.58 % Allowed : 21.85 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.21), residues: 1704 helix: 2.82 (0.16), residues: 770 sheet: -1.20 (0.23), residues: 450 loop : 0.52 (0.32), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 404 TYR 0.016 0.001 TYR C 810 PHE 0.005 0.001 PHE S 840 TRP 0.030 0.001 TRP N 878 HIS 0.004 0.001 HIS K 350 Details of bonding type rmsd covalent geometry : bond 0.00323 (13682) covalent geometry : angle 0.54395 (18418) SS BOND : bond 0.00138 ( 8) SS BOND : angle 1.24539 ( 16) hydrogen bonds : bond 0.03928 ( 918) hydrogen bonds : angle 4.48370 ( 2586) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 308 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 ARG cc_start: 0.7454 (tpt90) cc_final: 0.7142 (tpp-160) REVERT: B 384 ARG cc_start: 0.7157 (mtp180) cc_final: 0.6595 (mtp-110) REVERT: B 416 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8525 (mp) REVERT: D 820 MET cc_start: 0.7737 (tmm) cc_final: 0.7416 (tmm) REVERT: D 855 MET cc_start: 0.6435 (mtp) cc_final: 0.6114 (mtt) REVERT: C 6 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6137 (mm-30) REVERT: C 855 MET cc_start: 0.7513 (mtm) cc_final: 0.7013 (mmm) REVERT: G 416 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7946 (mp) REVERT: G 426 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6841 (mt-10) REVERT: G 429 LEU cc_start: 0.7938 (mp) cc_final: 0.7542 (tp) REVERT: H 426 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7014 (mp0) REVERT: H 435 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7686 (mt-10) REVERT: I 817 GLN cc_start: 0.6611 (mp10) cc_final: 0.6176 (mp10) REVERT: J 862 ASP cc_start: 0.7162 (m-30) cc_final: 0.6480 (t0) REVERT: L 416 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8113 (mp) REVERT: L 431 GLU cc_start: 0.6755 (tp30) cc_final: 0.6380 (tp30) REVERT: L 439 ARG cc_start: 0.7724 (mtt180) cc_final: 0.7351 (mtt180) REVERT: N 818 ARG cc_start: 0.7925 (ptp-110) cc_final: 0.7620 (ptp-110) REVERT: N 839 ARG cc_start: 0.6366 (OUTLIER) cc_final: 0.6072 (ttp80) REVERT: N 855 MET cc_start: 0.7575 (mmm) cc_final: 0.7212 (mtp) REVERT: N 865 VAL cc_start: 0.8656 (OUTLIER) cc_final: 0.8416 (t) REVERT: N 880 GLN cc_start: 0.6657 (mt0) cc_final: 0.6325 (mt0) REVERT: M 13 TYR cc_start: 0.5923 (OUTLIER) cc_final: 0.5405 (t80) REVERT: M 825 THR cc_start: 0.6786 (OUTLIER) cc_final: 0.6532 (p) REVERT: M 832 TYR cc_start: 0.7672 (m-80) cc_final: 0.7181 (m-80) REVERT: O 156 LYS cc_start: 0.7263 (mttt) cc_final: 0.6983 (mttt) REVERT: R 413 ILE cc_start: 0.7690 (mm) cc_final: 0.7317 (mm) REVERT: R 426 GLU cc_start: 0.6608 (mt-10) cc_final: 0.6181 (mt-10) REVERT: S 841 ILE cc_start: 0.6979 (mt) cc_final: 0.6773 (mm) REVERT: T 7 SER cc_start: 0.7938 (m) cc_final: 0.7328 (t) REVERT: T 809 TRP cc_start: 0.7432 (m100) cc_final: 0.7136 (m100) outliers start: 64 outliers final: 53 residues processed: 338 average time/residue: 0.1393 time to fit residues: 63.9012 Evaluate side-chains 367 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 306 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 797 SER Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain C residue 816 LYS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 825 THR Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 147 ARG Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 143 ILE 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 H residue 429 LEU Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain I residue 820 MET Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 823 VAL 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 L residue 355 THR Chi-restraints excluded: chain L residue 416 LEU Chi-restraints excluded: chain L residue 423 LEU Chi-restraints excluded: chain L residue 429 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 790 SER Chi-restraints excluded: chain N residue 835 SER Chi-restraints excluded: chain N residue 839 ARG Chi-restraints excluded: chain N residue 845 ASP Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 13 TYR Chi-restraints excluded: chain M residue 794 SER Chi-restraints excluded: chain M residue 821 VAL Chi-restraints excluded: chain M residue 825 THR Chi-restraints excluded: chain M residue 851 VAL Chi-restraints excluded: chain O residue 103 LEU Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 124 GLU Chi-restraints excluded: chain Q residue 405 ASP Chi-restraints excluded: chain R residue 416 LEU Chi-restraints excluded: chain R residue 422 ARG Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 820 MET Chi-restraints excluded: chain S residue 821 VAL Chi-restraints excluded: chain S residue 835 SER Chi-restraints excluded: chain S residue 851 VAL Chi-restraints excluded: chain S residue 886 VAL Chi-restraints excluded: chain T residue 824 VAL Chi-restraints excluded: chain T residue 855 MET Chi-restraints excluded: chain T residue 875 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 101 optimal weight: 0.0870 chunk 107 optimal weight: 0.1980 chunk 102 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 162 optimal weight: 0.0970 chunk 158 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 350 HIS B 409 HIS ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 374 GLN M 854 GLN ** R 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 831 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.180714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.169482 restraints weight = 18361.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.172114 restraints weight = 10899.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.173911 restraints weight = 7204.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.175126 restraints weight = 5126.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.175972 restraints weight = 3839.820| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.5921 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= 0.122 Angle : 0.530 9.518 18434 Z= 0.283 Chirality : 0.039 0.193 2082 Planarity : 0.003 0.051 2438 Dihedral : 4.235 28.246 1962 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.37 % Allowed : 22.35 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.21), residues: 1704 helix: 3.02 (0.17), residues: 776 sheet: -1.12 (0.23), residues: 450 loop : 0.53 (0.32), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 404 TYR 0.015 0.001 TYR C 810 PHE 0.005 0.001 PHE S 840 TRP 0.026 0.001 TRP S 827 HIS 0.003 0.001 HIS K 350 Details of bonding type rmsd covalent geometry : bond 0.00255 (13682) covalent geometry : angle 0.52862 (18418) SS BOND : bond 0.00196 ( 8) SS BOND : angle 1.19368 ( 16) hydrogen bonds : bond 0.03773 ( 918) hydrogen bonds : angle 4.34684 ( 2586) ********************** 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 359 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 298 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 395 MET cc_start: 0.6112 (ppp) cc_final: 0.5900 (ppp) REVERT: A 422 ARG cc_start: 0.7418 (tpt90) cc_final: 0.7058 (tpp-160) REVERT: B 384 ARG cc_start: 0.7145 (mtp180) cc_final: 0.6571 (mtp-110) REVERT: D 820 MET cc_start: 0.7746 (tmm) cc_final: 0.7428 (tmm) REVERT: D 855 MET cc_start: 0.6376 (mtp) cc_final: 0.6087 (mtt) REVERT: C 6 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6189 (mm-30) REVERT: C 855 MET cc_start: 0.7484 (mtm) cc_final: 0.6951 (mmm) REVERT: F 151 LEU cc_start: 0.7118 (mt) cc_final: 0.6847 (mm) REVERT: G 416 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7954 (mp) REVERT: G 426 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6805 (mt-10) REVERT: G 429 LEU cc_start: 0.7935 (mp) cc_final: 0.7541 (tt) REVERT: H 426 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: H 435 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7696 (mt-10) REVERT: I 817 GLN cc_start: 0.6526 (mp10) cc_final: 0.6122 (mp10) REVERT: J 862 ASP cc_start: 0.7129 (m-30) cc_final: 0.6441 (t0) REVERT: K 412 LYS cc_start: 0.7724 (ttmm) cc_final: 0.7377 (ttmm) REVERT: L 416 LEU cc_start: 0.8324 (tp) cc_final: 0.8017 (mp) REVERT: L 431 GLU cc_start: 0.6712 (tp30) cc_final: 0.6301 (tp30) REVERT: N 818 ARG cc_start: 0.7888 (ptp-110) cc_final: 0.7575 (ptp-110) REVERT: N 839 ARG cc_start: 0.6381 (OUTLIER) cc_final: 0.6144 (ttp80) REVERT: N 855 MET cc_start: 0.7697 (mmm) cc_final: 0.7361 (mtp) REVERT: N 877 TYR cc_start: 0.8083 (m-10) cc_final: 0.7843 (m-80) REVERT: M 13 TYR cc_start: 0.5630 (OUTLIER) cc_final: 0.5204 (t80) REVERT: M 825 THR cc_start: 0.6680 (OUTLIER) cc_final: 0.6360 (p) REVERT: M 832 TYR cc_start: 0.7622 (m-80) cc_final: 0.7173 (m-80) REVERT: O 156 LYS cc_start: 0.7262 (mttt) cc_final: 0.6952 (mttt) REVERT: R 413 ILE cc_start: 0.7670 (mm) cc_final: 0.7288 (mm) REVERT: R 426 GLU cc_start: 0.6587 (mt-10) cc_final: 0.6178 (mt-10) REVERT: S 841 ILE cc_start: 0.6939 (mt) cc_final: 0.6732 (mm) REVERT: T 7 SER cc_start: 0.7897 (m) cc_final: 0.7303 (t) REVERT: T 809 TRP cc_start: 0.7427 (m100) cc_final: 0.7149 (m100) REVERT: T 820 MET cc_start: 0.6764 (ttm) cc_final: 0.6232 (ttm) outliers start: 61 outliers final: 50 residues processed: 328 average time/residue: 0.1355 time to fit residues: 60.4735 Evaluate side-chains 352 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 297 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 423 LEU Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain D residue 797 SER Chi-restraints excluded: chain D residue 824 VAL 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 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 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 851 VAL Chi-restraints excluded: chain J residue 823 VAL 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 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 423 LEU Chi-restraints excluded: chain L residue 429 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 790 SER Chi-restraints excluded: chain N residue 835 SER Chi-restraints excluded: chain N residue 839 ARG Chi-restraints excluded: chain N residue 845 ASP Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 13 TYR Chi-restraints excluded: chain M residue 794 SER Chi-restraints excluded: chain M residue 821 VAL Chi-restraints excluded: chain M residue 825 THR Chi-restraints excluded: chain M residue 851 VAL Chi-restraints excluded: chain O residue 103 LEU Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 124 GLU 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 835 SER Chi-restraints excluded: chain S residue 886 VAL Chi-restraints excluded: chain T residue 824 VAL Chi-restraints excluded: chain T residue 855 MET Chi-restraints excluded: chain T residue 875 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 39 optimal weight: 0.0170 chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 122 optimal weight: 0.2980 chunk 92 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 69 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 82 optimal weight: 0.0170 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 854 GLN L 374 GLN M 854 GLN ** R 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 831 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.181647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.170364 restraints weight = 18540.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.173031 restraints weight = 10973.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.174810 restraints weight = 7263.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.176016 restraints weight = 5191.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.176837 restraints weight = 3909.550| |-----------------------------------------------------------------------------| r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6315 moved from start: 0.6063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13690 Z= 0.114 Angle : 0.519 10.475 18434 Z= 0.276 Chirality : 0.038 0.146 2082 Planarity : 0.003 0.044 2438 Dihedral : 4.077 27.127 1962 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.01 % Allowed : 22.71 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.21), residues: 1704 helix: 3.15 (0.17), residues: 784 sheet: -1.09 (0.23), residues: 456 loop : 0.59 (0.32), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 404 TYR 0.015 0.001 TYR C 810 PHE 0.005 0.001 PHE S 840 TRP 0.025 0.001 TRP N 878 HIS 0.002 0.001 HIS K 350 Details of bonding type rmsd covalent geometry : bond 0.00237 (13682) covalent geometry : angle 0.51870 (18418) SS BOND : bond 0.00098 ( 8) SS BOND : angle 0.52688 ( 16) hydrogen bonds : bond 0.03678 ( 918) hydrogen bonds : angle 4.21431 ( 2586) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2038.00 seconds wall clock time: 35 minutes 50.85 seconds (2150.85 seconds total)