Starting phenix.real_space_refine on Mon Dec 30 14:52:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8afh_15398/12_2024/8afh_15398.cif Found real_map, /net/cci-nas-00/data/ceres_data/8afh_15398/12_2024/8afh_15398.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8afh_15398/12_2024/8afh_15398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8afh_15398/12_2024/8afh_15398.map" model { file = "/net/cci-nas-00/data/ceres_data/8afh_15398/12_2024/8afh_15398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8afh_15398/12_2024/8afh_15398.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 8248 2.51 5 N 2564 2.21 5 O 2712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13570 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 739 Classifications: {'peptide': 96} Link IDs: {'TRANS': 95} Chain: "B" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 747 Classifications: {'peptide': 97} Link IDs: {'TRANS': 96} Chain: "D" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "C" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 600 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Chain: "F" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 600 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Chain: "G" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 333 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "H" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 299 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "I" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 860 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain breaks: 1 Chain: "J" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "K" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 739 Classifications: {'peptide': 96} Link IDs: {'TRANS': 95} Chain: "L" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 747 Classifications: {'peptide': 97} Link IDs: {'TRANS': 96} Chain: "N" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "M" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "O" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 600 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Chain: "P" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 600 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Chain: "Q" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 333 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "R" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 299 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "S" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 860 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain breaks: 1 Chain: "T" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Time building chain proxies: 8.05, per 1000 atoms: 0.59 Number of scatterers: 13570 At special positions: 0 Unit cell: (99.375, 271.625, 88.775, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 2712 8.00 N 2564 7.00 C 8248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS D 795 " - pdb=" SG CYS D 868 " distance=2.03 Simple disulfide: pdb=" SG CYS C 795 " - pdb=" SG CYS C 868 " distance=2.03 Simple disulfide: pdb=" SG CYS I 795 " - pdb=" SG CYS I 868 " distance=2.03 Simple disulfide: pdb=" SG CYS J 795 " - pdb=" SG CYS J 868 " distance=2.03 Simple disulfide: pdb=" SG CYS N 795 " - pdb=" SG CYS N 868 " distance=2.03 Simple disulfide: pdb=" SG CYS M 795 " - pdb=" SG CYS M 868 " distance=2.03 Simple disulfide: pdb=" SG CYS S 795 " - pdb=" SG CYS S 868 " distance=2.03 Simple disulfide: pdb=" SG CYS T 795 " - pdb=" SG CYS T 868 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 1.7 seconds 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3296 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 26 sheets defined 50.3% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 350 through 357 removed outlier: 3.961A pdb=" N ASP A 354 " --> pdb=" O HIS A 350 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 357 " --> pdb=" O VAL A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 441 removed outlier: 3.646A pdb=" N GLU A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 432 removed outlier: 3.876A pdb=" N ALA B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL B 372 " --> pdb=" O ALA B 368 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU B 383 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG B 404 " --> pdb=" O ASP B 400 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 429 " --> pdb=" O SER B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 442 Processing helix chain 'B' and resid 443 through 446 Processing helix chain 'D' and resid 859 through 863 removed outlier: 3.554A pdb=" N THR D 863 " --> pdb=" O PRO D 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 863 removed outlier: 3.891A pdb=" N THR C 863 " --> pdb=" O PRO C 860 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 163 removed outlier: 3.828A pdb=" N LEU E 115 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 163 removed outlier: 3.592A pdb=" N ALA F 92 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 439 removed outlier: 3.796A pdb=" N ALA G 411 " --> pdb=" O ALA G 407 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS G 412 " --> pdb=" O THR G 408 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA G 418 " --> pdb=" O ALA G 414 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU G 426 " --> pdb=" O ARG G 422 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA G 427 " --> pdb=" O LEU G 423 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU G 429 " --> pdb=" O SER G 425 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA G 433 " --> pdb=" O LEU G 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 444 Processing helix chain 'H' and resid 405 through 431 removed outlier: 3.649A pdb=" N HIS H 409 " --> pdb=" O ASP H 405 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU H 410 " --> pdb=" O SER H 406 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE H 420 " --> pdb=" O LEU H 416 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU H 421 " --> pdb=" O GLN H 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 432 through 441 removed outlier: 3.588A pdb=" N ASP H 440 " --> pdb=" O ALA H 436 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG H 441 " --> pdb=" O ALA H 437 " (cutoff:3.500A) Processing helix chain 'I' and resid 859 through 863 removed outlier: 3.603A pdb=" N THR I 863 " --> pdb=" O PRO I 860 " (cutoff:3.500A) Processing helix chain 'J' and resid 859 through 863 removed outlier: 3.819A pdb=" N THR J 863 " --> pdb=" O PRO J 860 " (cutoff:3.500A) Processing helix chain 'K' and resid 351 through 357 removed outlier: 3.571A pdb=" N THR K 355 " --> pdb=" O ALA K 351 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG K 357 " --> pdb=" O VAL K 353 " (cutoff:3.500A) Processing helix chain 'K' and resid 357 through 441 removed outlier: 3.647A pdb=" N GLU K 362 " --> pdb=" O ALA K 358 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG K 363 " --> pdb=" O THR K 359 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA K 364 " --> pdb=" O ALA K 360 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA K 368 " --> pdb=" O ALA K 364 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS K 369 " --> pdb=" O ASP K 365 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL K 372 " --> pdb=" O ALA K 368 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER K 425 " --> pdb=" O GLU K 421 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU K 426 " --> pdb=" O ARG K 422 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG K 441 " --> pdb=" O ALA K 437 " (cutoff:3.500A) Processing helix chain 'L' and resid 352 through 432 removed outlier: 3.876A pdb=" N ALA L 356 " --> pdb=" O GLY L 352 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU L 362 " --> pdb=" O ALA L 358 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU L 367 " --> pdb=" O ARG L 363 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA L 371 " --> pdb=" O LEU L 367 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL L 372 " --> pdb=" O ALA L 368 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU L 383 " --> pdb=" O LYS L 379 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG L 404 " --> pdb=" O ASP L 400 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE L 420 " --> pdb=" O LEU L 416 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU L 429 " --> pdb=" O SER L 425 " (cutoff:3.500A) Processing helix chain 'L' and resid 432 through 442 Processing helix chain 'L' and resid 443 through 446 Processing helix chain 'N' and resid 859 through 863 removed outlier: 3.554A pdb=" N THR N 863 " --> pdb=" O PRO N 860 " (cutoff:3.500A) Processing helix chain 'M' and resid 859 through 863 removed outlier: 3.892A pdb=" N THR M 863 " --> pdb=" O PRO M 860 " (cutoff:3.500A) Processing helix chain 'O' and resid 86 through 163 removed outlier: 3.828A pdb=" N LEU O 115 " --> pdb=" O VAL O 111 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA O 116 " --> pdb=" O SER O 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 163 removed outlier: 3.592A pdb=" N ALA P 92 " --> pdb=" O ILE P 88 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN P 93 " --> pdb=" O ALA P 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 404 through 439 removed outlier: 3.796A pdb=" N ALA Q 411 " --> pdb=" O ALA Q 407 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS Q 412 " --> pdb=" O THR Q 408 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA Q 418 " --> pdb=" O ALA Q 414 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU Q 426 " --> pdb=" O ARG Q 422 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA Q 427 " --> pdb=" O LEU Q 423 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA Q 433 " --> pdb=" O LEU Q 429 " (cutoff:3.500A) Processing helix chain 'Q' and resid 440 through 444 Processing helix chain 'R' and resid 405 through 431 removed outlier: 3.648A pdb=" N HIS R 409 " --> pdb=" O ASP R 405 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU R 410 " --> pdb=" O SER R 406 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE R 420 " --> pdb=" O LEU R 416 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU R 421 " --> pdb=" O GLN R 417 " (cutoff:3.500A) Processing helix chain 'R' and resid 432 through 441 removed outlier: 3.588A pdb=" N ASP R 440 " --> pdb=" O ALA R 436 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG R 441 " --> pdb=" O ALA R 437 " (cutoff:3.500A) Processing helix chain 'S' and resid 859 through 863 removed outlier: 3.602A pdb=" N THR S 863 " --> pdb=" O PRO S 860 " (cutoff:3.500A) Processing helix chain 'T' and resid 859 through 863 removed outlier: 3.819A pdb=" N THR T 863 " --> pdb=" O PRO T 860 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 6 through 7 removed outlier: 3.710A pdb=" N VAL D 851 " --> pdb=" O CYS D 795 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 850 " --> pdb=" O ASP D 845 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.212A pdb=" N GLY D 10 " --> pdb=" O THR D 885 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N MET D 807 " --> pdb=" O VAL D 823 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL D 823 " --> pdb=" O MET D 807 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP D 809 " --> pdb=" O VAL D 821 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 870 through 872 Processing sheet with id=AA4, first strand: chain 'C' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.550A pdb=" N VAL C 12 " --> pdb=" O THR C 885 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 830 through 832 removed outlier: 7.030A pdb=" N TRP C 809 " --> pdb=" O VAL C 821 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VAL C 823 " --> pdb=" O MET C 807 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N MET C 807 " --> pdb=" O VAL C 823 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.613A pdb=" N VAL I 851 " --> pdb=" O CYS I 795 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.808A pdb=" N MET I 807 " --> pdb=" O VAL I 823 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL I 823 " --> pdb=" O MET I 807 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP I 809 " --> pdb=" O VAL I 821 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 870 through 872 removed outlier: 3.572A pdb=" N TYR I 872 " --> pdb=" O SER I 875 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AB2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.544A pdb=" N GLY J 10 " --> pdb=" O THR J 885 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.544A pdb=" N GLY J 10 " --> pdb=" O THR J 885 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 792 through 793 Processing sheet with id=AB5, first strand: chain 'N' and resid 6 through 7 removed outlier: 3.711A pdb=" N VAL N 851 " --> pdb=" O CYS N 795 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR N 850 " --> pdb=" O ASP N 845 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.212A pdb=" N GLY N 10 " --> pdb=" O THR N 885 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N MET N 807 " --> pdb=" O VAL N 823 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL N 823 " --> pdb=" O MET N 807 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP N 809 " --> pdb=" O VAL N 821 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 870 through 872 Processing sheet with id=AB8, first strand: chain 'M' and resid 5 through 7 Processing sheet with id=AB9, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.551A pdb=" N VAL M 12 " --> pdb=" O THR M 885 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 830 through 832 removed outlier: 7.030A pdb=" N TRP M 809 " --> pdb=" O VAL M 821 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VAL M 823 " --> pdb=" O MET M 807 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N MET M 807 " --> pdb=" O VAL M 823 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'S' and resid 5 through 6 removed outlier: 3.613A pdb=" N VAL S 851 " --> pdb=" O CYS S 795 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.810A pdb=" N MET S 807 " --> pdb=" O VAL S 823 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL S 823 " --> pdb=" O MET S 807 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP S 809 " --> pdb=" O VAL S 821 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'S' and resid 870 through 872 removed outlier: 3.571A pdb=" N TYR S 872 " --> pdb=" O SER S 875 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'T' and resid 4 through 6 Processing sheet with id=AC6, first strand: chain 'T' and resid 10 through 12 removed outlier: 6.545A pdb=" N GLY T 10 " --> pdb=" O THR T 885 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'T' and resid 10 through 12 removed outlier: 6.545A pdb=" N GLY T 10 " --> pdb=" O THR T 885 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'T' and resid 792 through 793 926 hydrogen bonds defined for protein. 2586 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.01 Time building geometry restraints manager: 3.57 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: 0.00 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: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 30.370 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.270 ------------------------------------------------------------------------------- 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 13682 Z= 0.378 Angle : 0.699 5.869 18418 Z= 0.430 Chirality : 0.044 0.201 2082 Planarity : 0.004 0.086 2438 Dihedral : 14.167 86.270 5146 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.20), residues: 1704 helix: -0.24 (0.18), residues: 758 sheet: -2.06 (0.22), residues: 478 loop : 0.03 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 827 HIS 0.005 0.002 HIS K 350 PHE 0.006 0.001 PHE I 840 TYR 0.018 0.002 TYR T 13 ARG 0.013 0.001 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 1.626 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: 0.3763 time to fit residues: 162.8202 Evaluate side-chains 305 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.4980 chunk 125 optimal weight: 0.6980 chunk 69 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 150 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN D 869 ASN C 831 ASN E 93 ASN J 805 ASN ** N 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 856 ASN N 869 ASN M 854 GLN P 98 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13682 Z= 0.241 Angle : 0.603 7.527 18418 Z= 0.335 Chirality : 0.041 0.178 2082 Planarity : 0.006 0.103 2438 Dihedral : 4.811 21.591 1962 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.36 % Allowed : 11.46 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.21), residues: 1704 helix: 1.38 (0.18), residues: 762 sheet: -1.73 (0.22), residues: 476 loop : 0.31 (0.32), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 827 HIS 0.003 0.001 HIS A 350 PHE 0.006 0.002 PHE M 840 TYR 0.022 0.002 TYR T 810 ARG 0.009 0.001 ARG N 844 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 311 time to evaluate : 1.583 Fit side-chains revert: symmetry clash REVERT: B 379 LYS cc_start: 0.8388 (tmtt) cc_final: 0.7859 (tmmt) REVERT: B 384 ARG cc_start: 0.7063 (mtp180) cc_final: 0.6726 (mtp-110) REVERT: G 419 THR cc_start: 0.7490 (t) cc_final: 0.7181 (p) REVERT: I 807 MET cc_start: 0.6965 (mpp) cc_final: 0.6763 (mpp) REVERT: I 817 GLN cc_start: 0.5811 (mp10) cc_final: 0.5489 (mp10) REVERT: I 829 SER cc_start: 0.8506 (t) cc_final: 0.8090 (p) REVERT: I 872 TYR cc_start: 0.7460 (t80) cc_final: 0.7183 (t80) REVERT: J 858 LEU cc_start: 0.6186 (mt) cc_final: 0.5669 (tt) REVERT: L 395 MET cc_start: 0.5547 (ttm) cc_final: 0.5212 (mmm) REVERT: N 810 TYR cc_start: 0.8058 (m-80) cc_final: 0.7797 (m-10) REVERT: M 13 TYR cc_start: 0.5363 (m-80) cc_final: 0.5068 (m-80) REVERT: M 820 MET cc_start: 0.7987 (ttp) cc_final: 0.7637 (ttp) REVERT: O 107 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6878 (tm-30) REVERT: P 107 GLU cc_start: 0.7495 (tt0) cc_final: 0.6798 (tt0) REVERT: Q 416 LEU cc_start: 0.7307 (mt) cc_final: 0.7074 (mt) REVERT: R 413 ILE cc_start: 0.7755 (mm) cc_final: 0.7385 (mm) REVERT: R 426 GLU cc_start: 0.6622 (mt-10) cc_final: 0.6150 (mt-10) REVERT: S 807 MET cc_start: 0.7099 (mpp) cc_final: 0.6823 (mpp) REVERT: T 7 SER cc_start: 0.6844 (m) cc_final: 0.6434 (t) REVERT: T 820 MET cc_start: 0.7258 (mmm) cc_final: 0.7035 (mmm) REVERT: T 871 ILE cc_start: 0.7972 (mp) cc_final: 0.7735 (mt) outliers start: 33 outliers final: 19 residues processed: 327 average time/residue: 0.3127 time to fit residues: 140.8908 Evaluate side-chains 316 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 297 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 835 SER Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain J residue 824 VAL Chi-restraints excluded: chain K residue 425 SER Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 824 VAL Chi-restraints excluded: chain N residue 835 SER Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain O residue 163 SER Chi-restraints excluded: chain P residue 98 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 125 optimal weight: 0.0470 chunk 102 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 149 optimal weight: 0.5980 chunk 51 optimal weight: 0.0970 chunk 121 optimal weight: 0.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN D 3 GLN E 93 ASN L 374 GLN ** N 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6146 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13682 Z= 0.190 Angle : 0.524 5.493 18418 Z= 0.290 Chirality : 0.039 0.150 2082 Planarity : 0.004 0.059 2438 Dihedral : 4.389 18.870 1962 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.01 % Allowed : 15.04 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.21), residues: 1704 helix: 2.07 (0.18), residues: 766 sheet: -1.47 (0.22), residues: 474 loop : 0.50 (0.32), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 809 HIS 0.002 0.001 HIS K 350 PHE 0.012 0.002 PHE N 840 TYR 0.022 0.001 TYR M 866 ARG 0.007 0.001 ARG Q 422 *********************** 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 348 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 306 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 423 LEU cc_start: 0.7923 (tp) cc_final: 0.7682 (tp) REVERT: C 820 MET cc_start: 0.8364 (tmm) cc_final: 0.8136 (ttp) REVERT: C 855 MET cc_start: 0.7166 (mtm) cc_final: 0.6753 (mtp) REVERT: G 419 THR cc_start: 0.7577 (t) cc_final: 0.7343 (p) REVERT: H 426 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: I 817 GLN cc_start: 0.5990 (mp10) cc_final: 0.5695 (mp10) REVERT: I 829 SER cc_start: 0.8469 (t) cc_final: 0.8056 (p) REVERT: I 872 TYR cc_start: 0.7487 (t80) cc_final: 0.7145 (t80) REVERT: J 858 LEU cc_start: 0.6423 (mt) cc_final: 0.5780 (tt) REVERT: L 363 ARG cc_start: 0.7392 (mmm-85) cc_final: 0.7081 (mmm-85) REVERT: L 416 LEU cc_start: 0.8048 (mt) cc_final: 0.7710 (mp) REVERT: N 877 TYR cc_start: 0.7945 (m-10) cc_final: 0.7664 (m-80) REVERT: M 820 MET cc_start: 0.8007 (ttp) cc_final: 0.7428 (ttp) REVERT: M 825 THR cc_start: 0.7057 (OUTLIER) cc_final: 0.6743 (p) REVERT: O 107 GLU cc_start: 0.6913 (tm-30) cc_final: 0.6632 (tm-30) REVERT: O 156 LYS cc_start: 0.7411 (mttt) cc_final: 0.7054 (mttt) REVERT: P 107 GLU cc_start: 0.7795 (tt0) cc_final: 0.6794 (tt0) REVERT: Q 423 LEU cc_start: 0.7166 (tp) cc_final: 0.6887 (tp) REVERT: R 413 ILE cc_start: 0.7771 (mm) cc_final: 0.7334 (mm) REVERT: R 421 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6381 (mp0) REVERT: R 426 GLU cc_start: 0.6520 (mt-10) cc_final: 0.6253 (mt-10) REVERT: S 872 TYR cc_start: 0.7187 (t80) cc_final: 0.6829 (t80) REVERT: T 7 SER cc_start: 0.6992 (m) cc_final: 0.6546 (t) REVERT: T 886 VAL cc_start: 0.7597 (m) cc_final: 0.7370 (p) outliers start: 42 outliers final: 30 residues processed: 322 average time/residue: 0.3127 time to fit residues: 138.7600 Evaluate side-chains 330 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 298 time to evaluate : 1.323 ------------------------------------------------------------------------------- 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 797 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 131 THR 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 434 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 L residue 355 THR 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 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 143 ILE Chi-restraints excluded: chain R residue 416 LEU Chi-restraints excluded: chain S residue 869 ASN Chi-restraints excluded: chain T residue 820 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 143 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN B 409 HIS C 5 GLN E 93 ASN E 139 ASN ** H 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 350 HIS L 374 GLN ** N 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 417 GLN S 805 ASN T 805 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6263 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13682 Z= 0.281 Angle : 0.582 9.687 18418 Z= 0.318 Chirality : 0.041 0.153 2082 Planarity : 0.004 0.055 2438 Dihedral : 4.635 21.153 1962 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.01 % Allowed : 16.40 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.20), residues: 1704 helix: 2.04 (0.17), residues: 764 sheet: -1.49 (0.22), residues: 474 loop : 0.45 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 827 HIS 0.004 0.001 HIS K 350 PHE 0.006 0.001 PHE N 840 TYR 0.019 0.002 TYR D 832 ARG 0.008 0.001 ARG M 792 *********************** 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 381 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 311 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 HIS cc_start: 0.1425 (OUTLIER) cc_final: 0.1159 (p-80) REVERT: A 422 ARG cc_start: 0.7084 (tpt90) cc_final: 0.6684 (tpp-160) REVERT: B 416 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8077 (mp) REVERT: D 789 ASP cc_start: 0.6740 (m-30) cc_final: 0.6531 (m-30) REVERT: C 6 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6581 (mm-30) REVERT: C 809 TRP cc_start: 0.8459 (m100) cc_final: 0.8126 (m100) REVERT: C 855 MET cc_start: 0.7393 (mtm) cc_final: 0.6731 (mtp) REVERT: H 426 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6992 (mp0) REVERT: I 817 GLN cc_start: 0.6043 (mp10) cc_final: 0.5723 (mp10) REVERT: K 412 LYS cc_start: 0.7531 (ttmm) cc_final: 0.7226 (ttmm) REVERT: L 363 ARG cc_start: 0.7573 (mmm-85) cc_final: 0.7179 (mmm-85) REVERT: L 416 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7799 (mp) REVERT: L 438 ARG cc_start: 0.6523 (mtp180) cc_final: 0.6148 (mtp180) REVERT: N 810 TYR cc_start: 0.7856 (m-80) cc_final: 0.7568 (m-80) REVERT: N 829 SER cc_start: 0.8025 (p) cc_final: 0.7803 (p) REVERT: M 13 TYR cc_start: 0.6119 (OUTLIER) cc_final: 0.5254 (t80) REVERT: M 820 MET cc_start: 0.7911 (ttp) cc_final: 0.7427 (ttp) REVERT: O 107 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6629 (tm-30) REVERT: P 107 GLU cc_start: 0.7707 (tt0) cc_final: 0.6553 (tt0) REVERT: R 413 ILE cc_start: 0.7943 (mm) cc_final: 0.7532 (mm) REVERT: S 824 VAL cc_start: 0.8460 (p) cc_final: 0.8231 (p) REVERT: T 7 SER cc_start: 0.7399 (m) cc_final: 0.7027 (t) REVERT: T 809 TRP cc_start: 0.7546 (m100) cc_final: 0.7345 (m100) REVERT: T 855 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7770 (mtt) REVERT: T 886 VAL cc_start: 0.7616 (m) cc_final: 0.7364 (p) outliers start: 70 outliers final: 41 residues processed: 346 average time/residue: 0.3344 time to fit residues: 157.0655 Evaluate side-chains 350 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 303 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 HIS 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 7 SER Chi-restraints excluded: chain C residue 816 LYS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain G residue 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 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 K residue 425 SER Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 416 LEU Chi-restraints excluded: chain L residue 423 LEU Chi-restraints excluded: chain L residue 429 LEU 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 N residue 876 GLU 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 O residue 163 SER Chi-restraints excluded: chain P residue 98 GLN Chi-restraints excluded: chain P residue 131 THR 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 821 VAL Chi-restraints excluded: chain S residue 869 ASN Chi-restraints excluded: chain T residue 805 ASN Chi-restraints excluded: chain T residue 823 VAL Chi-restraints excluded: chain T residue 855 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 136 optimal weight: 0.1980 chunk 110 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 144 optimal weight: 0.0670 chunk 40 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN C 854 GLN E 93 ASN ** H 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 374 GLN L 409 HIS P 98 GLN S 805 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13682 Z= 0.215 Angle : 0.522 6.492 18418 Z= 0.286 Chirality : 0.039 0.148 2082 Planarity : 0.004 0.050 2438 Dihedral : 4.373 18.765 1962 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.87 % Allowed : 18.48 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.21), residues: 1704 helix: 2.40 (0.17), residues: 766 sheet: -1.39 (0.22), residues: 474 loop : 0.50 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 827 HIS 0.003 0.001 HIS K 350 PHE 0.004 0.001 PHE N 840 TYR 0.018 0.002 TYR M 866 ARG 0.006 0.001 ARG F 145 *********************** 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 378 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 310 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 416 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8320 (mp) REVERT: C 6 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6691 (mm-30) REVERT: C 809 TRP cc_start: 0.8444 (m100) cc_final: 0.8098 (m100) REVERT: C 855 MET cc_start: 0.7358 (mtm) cc_final: 0.6652 (mtp) REVERT: F 115 LEU cc_start: 0.6458 (tp) cc_final: 0.5981 (tp) REVERT: G 423 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6914 (mt) REVERT: H 426 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7043 (mp0) REVERT: H 435 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7577 (mt-10) REVERT: I 817 GLN cc_start: 0.6094 (mp10) cc_final: 0.5796 (mp10) REVERT: I 829 SER cc_start: 0.8216 (t) cc_final: 0.7594 (p) REVERT: J 855 MET cc_start: 0.7821 (mmm) cc_final: 0.7484 (mmm) REVERT: K 412 LYS cc_start: 0.7550 (ttmm) cc_final: 0.7184 (ttmm) REVERT: L 416 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7752 (mp) REVERT: N 792 ARG cc_start: 0.7786 (ttt-90) cc_final: 0.7509 (ttp80) REVERT: N 810 TYR cc_start: 0.7882 (m-80) cc_final: 0.7644 (m-80) REVERT: N 839 ARG cc_start: 0.6580 (OUTLIER) cc_final: 0.6367 (ttp80) REVERT: M 13 TYR cc_start: 0.5714 (OUTLIER) cc_final: 0.4996 (t80) REVERT: M 820 MET cc_start: 0.7911 (ttp) cc_final: 0.7457 (ttp) REVERT: O 107 GLU cc_start: 0.7115 (tm-30) cc_final: 0.6768 (tm-30) REVERT: O 156 LYS cc_start: 0.7358 (mttt) cc_final: 0.7054 (mttt) REVERT: P 107 GLU cc_start: 0.7706 (tt0) cc_final: 0.6568 (tt0) REVERT: P 146 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6942 (tp) REVERT: R 426 GLU cc_start: 0.6575 (mt-10) cc_final: 0.6027 (mt-10) REVERT: T 7 SER cc_start: 0.7573 (m) cc_final: 0.7086 (t) REVERT: T 809 TRP cc_start: 0.7501 (m100) cc_final: 0.7254 (m100) REVERT: T 886 VAL cc_start: 0.7429 (OUTLIER) cc_final: 0.7159 (p) outliers start: 68 outliers final: 45 residues processed: 346 average time/residue: 0.3248 time to fit residues: 153.2696 Evaluate side-chains 356 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 303 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain D residue 800 SER Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain C residue 816 LYS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain G residue 412 LYS Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain I residue 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 831 ASN Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 409 HIS Chi-restraints excluded: chain L residue 416 LEU Chi-restraints excluded: chain 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 O residue 163 SER Chi-restraints excluded: chain P residue 98 GLN 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 821 VAL Chi-restraints excluded: chain S residue 851 VAL Chi-restraints excluded: chain S residue 869 ASN Chi-restraints excluded: chain T residue 823 VAL Chi-restraints excluded: chain T residue 855 MET Chi-restraints excluded: chain T residue 886 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 0.6980 chunk 144 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 74 optimal weight: 0.0000 chunk 13 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 154 optimal weight: 0.5980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 ASN L 374 GLN M 854 GLN P 98 GLN S 805 ASN T 805 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6255 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13682 Z= 0.216 Angle : 0.523 8.796 18418 Z= 0.284 Chirality : 0.039 0.201 2082 Planarity : 0.003 0.048 2438 Dihedral : 4.301 19.636 1962 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.58 % Allowed : 20.13 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.20), residues: 1704 helix: 2.57 (0.17), residues: 766 sheet: -1.37 (0.24), residues: 408 loop : 0.17 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 827 HIS 0.004 0.001 HIS K 350 PHE 0.003 0.001 PHE N 840 TYR 0.015 0.001 TYR C 810 ARG 0.004 0.000 ARG C 818 *********************** 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 366 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 302 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 ARG cc_start: 0.7031 (tpt90) cc_final: 0.6718 (tpp-160) REVERT: B 384 ARG cc_start: 0.7182 (mtp180) cc_final: 0.6640 (mtp-110) REVERT: B 416 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8358 (mp) REVERT: C 6 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6663 (mm-30) REVERT: C 809 TRP cc_start: 0.8435 (m100) cc_final: 0.8086 (m100) REVERT: C 855 MET cc_start: 0.7174 (mtm) cc_final: 0.6613 (mtp) REVERT: G 423 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6883 (mt) REVERT: H 426 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: H 435 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7506 (mt-10) REVERT: I 817 GLN cc_start: 0.6142 (mp10) cc_final: 0.5827 (mp10) REVERT: J 855 MET cc_start: 0.7894 (mmm) cc_final: 0.7514 (mmm) REVERT: L 384 ARG cc_start: 0.6666 (mtp180) cc_final: 0.6445 (mpp-170) REVERT: L 416 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7682 (mp) REVERT: N 792 ARG cc_start: 0.7780 (ttt-90) cc_final: 0.7517 (ttt-90) REVERT: N 855 MET cc_start: 0.7561 (mmm) cc_final: 0.7226 (mmm) REVERT: M 13 TYR cc_start: 0.5799 (OUTLIER) cc_final: 0.5162 (t80) REVERT: O 156 LYS cc_start: 0.7346 (mttt) cc_final: 0.7028 (mttt) REVERT: P 107 GLU cc_start: 0.7752 (tt0) cc_final: 0.7336 (tt0) REVERT: R 426 GLU cc_start: 0.6539 (mt-10) cc_final: 0.5986 (mt-10) REVERT: T 7 SER cc_start: 0.7543 (m) cc_final: 0.7063 (t) REVERT: T 809 TRP cc_start: 0.7448 (m100) cc_final: 0.7221 (m100) outliers start: 64 outliers final: 47 residues processed: 333 average time/residue: 0.3127 time to fit residues: 142.2334 Evaluate side-chains 350 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 298 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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 366 GLN Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 443 ARG Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 816 LYS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain I residue 820 MET Chi-restraints excluded: chain I residue 861 GLU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 824 VAL Chi-restraints excluded: chain J residue 825 THR Chi-restraints excluded: chain J residue 831 ASN Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 416 LEU Chi-restraints excluded: chain L residue 423 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 790 SER Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain N residue 876 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 13 TYR Chi-restraints excluded: chain M residue 794 SER Chi-restraints excluded: chain M residue 821 VAL Chi-restraints excluded: chain P residue 143 ILE 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 851 VAL Chi-restraints excluded: chain S residue 869 ASN Chi-restraints excluded: chain T residue 805 ASN 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 18 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 117 optimal weight: 0.4980 chunk 90 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 159 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 ASN L 374 GLN M 854 GLN ** R 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 805 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6269 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13682 Z= 0.228 Angle : 0.536 8.825 18418 Z= 0.290 Chirality : 0.040 0.161 2082 Planarity : 0.003 0.047 2438 Dihedral : 4.342 22.441 1962 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 5.59 % Allowed : 19.91 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.20), residues: 1704 helix: 2.62 (0.17), residues: 766 sheet: -1.33 (0.25), residues: 408 loop : 0.20 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 827 HIS 0.004 0.001 HIS K 350 PHE 0.004 0.001 PHE N 840 TYR 0.017 0.002 TYR M 866 ARG 0.004 0.000 ARG D 799 *********************** 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 374 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 296 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 ARG cc_start: 0.6991 (tpt90) cc_final: 0.6595 (tpp-160) REVERT: B 384 ARG cc_start: 0.7199 (mtp180) cc_final: 0.6631 (mtp-110) REVERT: C 6 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6962 (mm-30) REVERT: C 809 TRP cc_start: 0.8411 (m100) cc_final: 0.8152 (m100) REVERT: C 855 MET cc_start: 0.7135 (mtm) cc_final: 0.6624 (mtp) REVERT: G 416 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7894 (mp) REVERT: G 423 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6885 (mt) REVERT: H 426 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: H 435 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7448 (mt-10) REVERT: I 817 GLN cc_start: 0.6204 (mp10) cc_final: 0.5881 (mp10) REVERT: J 855 MET cc_start: 0.7870 (mmm) cc_final: 0.7566 (mmm) REVERT: J 862 ASP cc_start: 0.6720 (m-30) cc_final: 0.6469 (m-30) REVERT: N 839 ARG cc_start: 0.6523 (OUTLIER) cc_final: 0.6274 (ttp80) REVERT: N 855 MET cc_start: 0.7521 (mmm) cc_final: 0.7022 (mtp) REVERT: N 865 VAL cc_start: 0.8798 (OUTLIER) cc_final: 0.8550 (t) REVERT: M 13 TYR cc_start: 0.5792 (OUTLIER) cc_final: 0.5304 (t80) REVERT: M 832 TYR cc_start: 0.7617 (m-80) cc_final: 0.7032 (m-80) REVERT: O 156 LYS cc_start: 0.7347 (mttt) cc_final: 0.7033 (mttt) REVERT: R 426 GLU cc_start: 0.6624 (mt-10) cc_final: 0.6009 (mt-10) REVERT: T 7 SER cc_start: 0.7631 (m) cc_final: 0.7043 (t) REVERT: T 809 TRP cc_start: 0.7412 (m100) cc_final: 0.7109 (m100) outliers start: 78 outliers final: 60 residues processed: 338 average time/residue: 0.3099 time to fit residues: 143.2991 Evaluate side-chains 361 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 295 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 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 D residue 829 SER Chi-restraints excluded: chain D residue 834 ASP Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 816 LYS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain I residue 820 MET Chi-restraints excluded: chain I residue 861 GLU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 824 VAL Chi-restraints excluded: chain J residue 825 THR Chi-restraints excluded: chain J residue 831 ASN Chi-restraints excluded: chain J residue 886 VAL Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 416 LEU Chi-restraints excluded: chain L residue 423 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 790 SER Chi-restraints excluded: chain N residue 806 ILE 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 N residue 876 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 13 TYR Chi-restraints excluded: chain M residue 794 SER Chi-restraints excluded: chain M residue 821 VAL Chi-restraints excluded: chain M residue 851 VAL Chi-restraints excluded: chain M residue 855 MET Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain Q residue 405 ASP Chi-restraints excluded: chain R residue 416 LEU Chi-restraints excluded: chain R residue 422 ARG Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 820 MET Chi-restraints excluded: chain S residue 821 VAL Chi-restraints excluded: chain S residue 851 VAL Chi-restraints excluded: chain S residue 868 CYS Chi-restraints excluded: chain S residue 869 ASN Chi-restraints excluded: chain T residue 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 63 optimal weight: 0.2980 chunk 95 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 101 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 ASN L 374 GLN ** R 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 805 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13682 Z= 0.199 Angle : 0.526 9.061 18418 Z= 0.284 Chirality : 0.039 0.174 2082 Planarity : 0.003 0.045 2438 Dihedral : 4.303 26.144 1962 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.58 % Allowed : 21.20 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.21), residues: 1704 helix: 2.74 (0.17), residues: 772 sheet: -1.31 (0.24), residues: 408 loop : 0.30 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 827 HIS 0.004 0.001 HIS K 350 PHE 0.004 0.001 PHE I 840 TYR 0.016 0.001 TYR C 810 ARG 0.006 0.000 ARG L 391 *********************** 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 358 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 294 time to evaluate : 1.369 Fit side-chains revert: symmetry clash REVERT: B 384 ARG cc_start: 0.7184 (mtp180) cc_final: 0.6609 (mtp-110) REVERT: C 6 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6449 (mm-30) REVERT: C 809 TRP cc_start: 0.8369 (m100) cc_final: 0.7586 (m100) REVERT: C 855 MET cc_start: 0.7124 (mtm) cc_final: 0.6434 (mtp) REVERT: G 416 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7838 (mp) REVERT: H 426 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: H 435 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7619 (mt-10) REVERT: I 817 GLN cc_start: 0.6290 (mp10) cc_final: 0.5930 (mp10) REVERT: J 855 MET cc_start: 0.7892 (mmm) cc_final: 0.7509 (mmm) REVERT: L 391 ARG cc_start: 0.7129 (mtp-110) cc_final: 0.6889 (ttp80) REVERT: L 416 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7695 (mp) REVERT: N 839 ARG cc_start: 0.6473 (OUTLIER) cc_final: 0.6220 (ttp80) REVERT: N 855 MET cc_start: 0.7512 (mmm) cc_final: 0.7057 (mtp) REVERT: N 865 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8548 (t) REVERT: M 13 TYR cc_start: 0.5770 (OUTLIER) cc_final: 0.5295 (t80) REVERT: M 832 TYR cc_start: 0.7637 (m-80) cc_final: 0.7035 (m-80) REVERT: O 156 LYS cc_start: 0.7296 (mttt) cc_final: 0.6985 (mttt) REVERT: R 426 GLU cc_start: 0.6673 (mt-10) cc_final: 0.5970 (mt-10) REVERT: T 7 SER cc_start: 0.7676 (m) cc_final: 0.7137 (t) REVERT: T 809 TRP cc_start: 0.7326 (m100) cc_final: 0.7054 (m100) outliers start: 64 outliers final: 52 residues processed: 323 average time/residue: 0.3085 time to fit residues: 137.1272 Evaluate side-chains 351 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 293 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 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 D residue 829 SER Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 816 LYS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain I residue 820 MET Chi-restraints excluded: chain I residue 861 GLU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 824 VAL Chi-restraints excluded: chain J residue 825 THR Chi-restraints excluded: chain J residue 831 ASN Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 416 LEU Chi-restraints excluded: chain L residue 423 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 790 SER Chi-restraints excluded: chain N residue 806 ILE 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 N residue 876 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 13 TYR Chi-restraints excluded: chain M residue 794 SER Chi-restraints excluded: chain M residue 821 VAL Chi-restraints excluded: chain M residue 851 VAL Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 143 ILE Chi-restraints excluded: chain Q residue 405 ASP Chi-restraints excluded: chain R residue 416 LEU Chi-restraints excluded: chain R residue 422 ARG Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 821 VAL Chi-restraints excluded: chain S residue 851 VAL Chi-restraints excluded: chain S residue 869 ASN Chi-restraints excluded: chain T residue 823 VAL Chi-restraints excluded: chain T residue 855 MET Chi-restraints excluded: chain T residue 886 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 117 optimal weight: 0.2980 chunk 45 optimal weight: 0.6980 chunk 134 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN L 374 GLN L 409 HIS ** R 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 805 ASN T 805 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.5788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13682 Z= 0.268 Angle : 0.581 8.908 18418 Z= 0.313 Chirality : 0.041 0.192 2082 Planarity : 0.004 0.046 2438 Dihedral : 4.556 29.620 1962 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 5.16 % Allowed : 20.63 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.21), residues: 1704 helix: 2.54 (0.17), residues: 768 sheet: -1.29 (0.23), residues: 450 loop : 0.38 (0.31), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP S 827 HIS 0.004 0.001 HIS K 350 PHE 0.005 0.001 PHE N 840 TYR 0.023 0.002 TYR C 810 ARG 0.007 0.001 ARG B 404 *********************** 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 376 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 304 time to evaluate : 1.539 Fit side-chains revert: symmetry clash REVERT: B 384 ARG cc_start: 0.7213 (mtp180) cc_final: 0.6628 (mtp-110) REVERT: C 6 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6775 (mp0) REVERT: C 809 TRP cc_start: 0.8337 (m100) cc_final: 0.7867 (m100) REVERT: C 855 MET cc_start: 0.7070 (mtm) cc_final: 0.6477 (mtp) REVERT: G 426 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6590 (mt-10) REVERT: H 426 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7142 (mp0) REVERT: H 435 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7634 (mt-10) REVERT: I 817 GLN cc_start: 0.6456 (mp10) cc_final: 0.6112 (mp10) REVERT: J 862 ASP cc_start: 0.6774 (m-30) cc_final: 0.6170 (t0) REVERT: J 875 SER cc_start: 0.8262 (t) cc_final: 0.7833 (m) REVERT: N 818 ARG cc_start: 0.7796 (ptp-170) cc_final: 0.7515 (ptp-170) REVERT: N 855 MET cc_start: 0.7587 (mmm) cc_final: 0.7053 (mtt) REVERT: N 865 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8579 (t) REVERT: M 13 TYR cc_start: 0.5690 (OUTLIER) cc_final: 0.5374 (t80) REVERT: O 156 LYS cc_start: 0.7302 (mttt) cc_final: 0.7005 (mttt) REVERT: R 413 ILE cc_start: 0.7730 (mm) cc_final: 0.7353 (mm) REVERT: R 426 GLU cc_start: 0.6534 (mt-10) cc_final: 0.5898 (mt-10) REVERT: T 7 SER cc_start: 0.7737 (m) cc_final: 0.7158 (t) REVERT: T 809 TRP cc_start: 0.7338 (m100) cc_final: 0.7066 (m100) outliers start: 72 outliers final: 56 residues processed: 339 average time/residue: 0.3275 time to fit residues: 157.2503 Evaluate side-chains 361 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 302 time to evaluate : 1.860 ------------------------------------------------------------------------------- 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 443 ARG Chi-restraints excluded: chain D residue 797 SER Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 829 SER Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 816 LYS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP 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 425 SER Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain I residue 820 MET Chi-restraints excluded: chain 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 L residue 355 THR Chi-restraints excluded: chain L residue 409 HIS Chi-restraints excluded: chain L residue 416 LEU Chi-restraints excluded: chain L residue 423 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 790 SER Chi-restraints excluded: chain N residue 806 ILE Chi-restraints excluded: chain N residue 835 SER Chi-restraints excluded: chain N residue 845 ASP Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain N residue 868 CYS Chi-restraints excluded: chain N residue 876 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 13 TYR Chi-restraints excluded: chain M residue 794 SER Chi-restraints excluded: chain M residue 821 VAL Chi-restraints excluded: chain M residue 851 VAL Chi-restraints excluded: chain M residue 855 MET Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain Q residue 405 ASP Chi-restraints excluded: chain R residue 416 LEU Chi-restraints excluded: chain R residue 422 ARG Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 821 VAL Chi-restraints excluded: chain S residue 835 SER Chi-restraints excluded: chain S residue 851 VAL Chi-restraints excluded: chain S residue 869 ASN Chi-restraints excluded: chain T residue 805 ASN Chi-restraints excluded: chain T residue 823 VAL Chi-restraints excluded: chain T residue 824 VAL Chi-restraints excluded: chain T residue 855 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 165 optimal weight: 0.6980 chunk 152 optimal weight: 0.7980 chunk 131 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 80 optimal weight: 0.0170 chunk 104 optimal weight: 0.9980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 374 GLN ** N 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 805 ASN O 139 ASN ** R 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 805 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.5868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13682 Z= 0.230 Angle : 0.576 10.729 18418 Z= 0.308 Chirality : 0.041 0.163 2082 Planarity : 0.004 0.045 2438 Dihedral : 4.501 28.897 1962 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.87 % Allowed : 21.20 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.21), residues: 1704 helix: 2.64 (0.17), residues: 768 sheet: -1.33 (0.23), residues: 450 loop : 0.37 (0.31), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP S 827 HIS 0.009 0.001 HIS L 409 PHE 0.004 0.001 PHE I 840 TYR 0.021 0.002 TYR C 810 ARG 0.012 0.001 ARG B 404 ********************** 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 372 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 304 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 384 ARG cc_start: 0.7206 (mtp180) cc_final: 0.6623 (mtp-110) REVERT: C 6 GLU cc_start: 0.7264 (mm-30) cc_final: 0.6768 (mp0) REVERT: C 855 MET cc_start: 0.7050 (mtm) cc_final: 0.6579 (mtp) REVERT: E 128 ARG cc_start: 0.6088 (tpm170) cc_final: 0.5469 (tpm170) REVERT: G 426 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6764 (mt-10) REVERT: H 426 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: H 435 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7450 (mt-10) REVERT: I 817 GLN cc_start: 0.6435 (mp10) cc_final: 0.6132 (mp10) REVERT: L 416 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7755 (mp) REVERT: N 855 MET cc_start: 0.7581 (mmm) cc_final: 0.7058 (mtp) REVERT: N 865 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8563 (t) REVERT: M 13 TYR cc_start: 0.5741 (OUTLIER) cc_final: 0.5402 (t80) REVERT: M 832 TYR cc_start: 0.7676 (m-80) cc_final: 0.7110 (m-80) REVERT: O 156 LYS cc_start: 0.7248 (mttt) cc_final: 0.6959 (mttt) REVERT: Q 443 ARG cc_start: 0.5777 (mtt180) cc_final: 0.5048 (mmt90) REVERT: R 413 ILE cc_start: 0.7725 (mm) cc_final: 0.7362 (mm) REVERT: R 426 GLU cc_start: 0.6584 (mt-10) cc_final: 0.5944 (mt-10) REVERT: S 855 MET cc_start: 0.6787 (mtm) cc_final: 0.6528 (mtt) REVERT: T 7 SER cc_start: 0.7806 (m) cc_final: 0.7217 (t) REVERT: T 809 TRP cc_start: 0.7349 (m100) cc_final: 0.7093 (m100) REVERT: T 820 MET cc_start: 0.6730 (ttm) cc_final: 0.6366 (ttm) outliers start: 68 outliers final: 57 residues processed: 335 average time/residue: 0.3053 time to fit residues: 140.9826 Evaluate side-chains 361 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 300 time to evaluate : 1.561 ------------------------------------------------------------------------------- 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 D residue 829 SER Chi-restraints excluded: chain D residue 834 ASP Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 816 LYS Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 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 425 SER Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain I residue 797 SER Chi-restraints excluded: chain I residue 820 MET Chi-restraints excluded: chain 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 855 MET Chi-restraints excluded: chain L residue 355 THR Chi-restraints excluded: chain L residue 416 LEU Chi-restraints excluded: chain L residue 423 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 790 SER Chi-restraints excluded: chain N residue 806 ILE Chi-restraints excluded: chain N residue 835 SER Chi-restraints excluded: chain N residue 845 ASP Chi-restraints excluded: chain N residue 865 VAL Chi-restraints excluded: chain N residue 868 CYS Chi-restraints excluded: chain N residue 876 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 13 TYR Chi-restraints excluded: chain M residue 794 SER Chi-restraints excluded: chain M residue 821 VAL Chi-restraints excluded: chain M residue 851 VAL Chi-restraints excluded: chain M residue 855 MET Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 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 851 VAL Chi-restraints excluded: chain S residue 869 ASN Chi-restraints excluded: chain T residue 823 VAL Chi-restraints excluded: chain T residue 824 VAL Chi-restraints excluded: chain T residue 855 MET Chi-restraints excluded: chain T residue 886 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.0670 chunk 40 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 19 optimal weight: 0.0040 chunk 36 optimal weight: 0.7980 chunk 131 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 135 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 0.3980 chunk 115 optimal weight: 0.5980 overall best weight: 0.3330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 350 HIS C 817 GLN L 374 GLN ** N 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4280 r_free = 0.4280 target = 0.180556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.169315 restraints weight = 18295.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.171956 restraints weight = 10873.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.173733 restraints weight = 7184.077| |-----------------------------------------------------------------------------| r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.6006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13682 Z= 0.169 Angle : 0.534 10.591 18418 Z= 0.286 Chirality : 0.039 0.146 2082 Planarity : 0.003 0.044 2438 Dihedral : 4.248 27.302 1962 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.15 % Allowed : 21.92 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.21), residues: 1704 helix: 2.86 (0.17), residues: 780 sheet: -1.25 (0.23), residues: 456 loop : 0.48 (0.32), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP N 878 HIS 0.003 0.001 HIS K 350 PHE 0.005 0.001 PHE I 840 TYR 0.019 0.001 TYR C 810 ARG 0.010 0.001 ARG B 404 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3235.09 seconds wall clock time: 60 minutes 36.93 seconds (3636.93 seconds total)