Starting phenix.real_space_refine on Sun Jan 26 11:43:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zb4_11144/01_2025/6zb4_11144.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zb4_11144/01_2025/6zb4_11144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zb4_11144/01_2025/6zb4_11144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zb4_11144/01_2025/6zb4_11144.map" model { file = "/net/cci-nas-00/data/ceres_data/6zb4_11144/01_2025/6zb4_11144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zb4_11144/01_2025/6zb4_11144.cif" } resolution = 3.03 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= 0.010 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 114 5.16 5 C 15856 2.51 5 N 4094 2.21 5 O 4777 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 24841 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 8056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8056 Classifications: {'peptide': 1035} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 47, 'TRANS': 987} Chain breaks: 11 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 8189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 8189 Classifications: {'peptide': 1050} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 47, 'TRANS': 1002} Chain breaks: 10 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 8158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8158 Classifications: {'peptide': 1048} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 48, 'TRANS': 999} Chain breaks: 11 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 104 Unusual residues: {'EIC': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 160 Unusual residues: {'EIC': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 146 Unusual residues: {'EIC': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 13.92, per 1000 atoms: 0.56 Number of scatterers: 24841 At special positions: 0 Unit cell: (143.85, 151.2, 161.7, 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 114 16.00 O 4777 8.00 N 4094 7.00 C 15856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C 837 " - pdb=" SG CYS C 848 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B 837 " - pdb=" SG CYS B 848 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A 837 " - pdb=" SG CYS A 848 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " 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 Atom "HETATM24659 O5 NAG B1309 .*. O " rejected from bonding due to valence issues. Atom "HETATM24443 O5 NAG C1401 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A2102 " - " ASN A 714 " " NAG A2104 " - " ASN A 343 " " NAG B1309 " - " ASN B 234 " " NAG C1403 " - " ASN C 616 " " NAG C1406 " - " ASN C 234 " " NAG D 1 " - " ASN C 714 " Time building additional restraints: 6.23 Conformation dependent library (CDL) restraints added in 3.3 seconds 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5852 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 50 sheets defined 23.1% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.52 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.525A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.754A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.529A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.586A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.031A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.501A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 744 through 751 removed outlier: 3.943A pdb=" N ASN C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 780 removed outlier: 3.599A pdb=" N LEU C 760 " --> pdb=" O PHE C 756 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS C 773 " --> pdb=" O VAL C 769 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 821 Processing helix chain 'C' and resid 833 through 838 removed outlier: 3.748A pdb=" N CYS C 837 " --> pdb=" O GLN C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 887 removed outlier: 3.924A pdb=" N GLY C 886 " --> pdb=" O TRP C 883 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 887 " --> pdb=" O THR C 884 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 883 through 887' Processing helix chain 'C' and resid 894 through 906 removed outlier: 3.693A pdb=" N ALA C 900 " --> pdb=" O ALA C 896 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR C 901 " --> pdb=" O MET C 897 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE C 906 " --> pdb=" O ARG C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 916 Processing helix chain 'C' and resid 916 through 936 Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.516A pdb=" N GLN C 946 " --> pdb=" O LEU C 942 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU C 956 " --> pdb=" O ASN C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 978 Processing helix chain 'C' and resid 986 through 1029 removed outlier: 3.838A pdb=" N ARG C 992 " --> pdb=" O VAL C 988 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA C1013 " --> pdb=" O LEU C1009 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU C1014 " --> pdb=" O ILE C1010 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C1015 " --> pdb=" O ARG C1011 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER C1027 " --> pdb=" O ALA C1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.018A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.593A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.967A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.673A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 750 removed outlier: 3.637A pdb=" N SER B 747 " --> pdb=" O SER B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 753 No H-bonds generated for 'chain 'B' and resid 751 through 753' Processing helix chain 'B' and resid 756 through 780 removed outlier: 3.850A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 773 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR B 775 " --> pdb=" O GLN B 771 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B 778 " --> pdb=" O ASN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 821 Processing helix chain 'B' and resid 847 through 852 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 887 Processing helix chain 'B' and resid 894 through 905 removed outlier: 3.756A pdb=" N TYR B 901 " --> pdb=" O MET B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 915 Processing helix chain 'B' and resid 916 through 936 Processing helix chain 'B' and resid 942 through 962 removed outlier: 4.439A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B 956 " --> pdb=" O ASN B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 removed outlier: 3.628A pdb=" N ARG B 980 " --> pdb=" O ASP B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1029 removed outlier: 3.987A pdb=" N GLU B 987 " --> pdb=" O LYS B 983 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL B 988 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 993 " --> pdb=" O GLN B 989 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA B1013 " --> pdb=" O LEU B1009 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER B1027 " --> pdb=" O ALA B1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.019A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.657A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.906A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.562A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 744 through 751 Processing helix chain 'A' and resid 756 through 780 removed outlier: 3.772A pdb=" N ALA A 763 " --> pdb=" O GLN A 759 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 773 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 778 " --> pdb=" O ASN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 821 Processing helix chain 'A' and resid 833 through 838 Processing helix chain 'A' and resid 863 through 881 Processing helix chain 'A' and resid 894 through 905 removed outlier: 3.771A pdb=" N TYR A 901 " --> pdb=" O MET A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 915 Processing helix chain 'A' and resid 916 through 937 removed outlier: 4.121A pdb=" N SER A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 962 removed outlier: 4.302A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 956 " --> pdb=" O ASN A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1030 removed outlier: 3.706A pdb=" N VAL A 988 " --> pdb=" O VAL A 984 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG A 992 " --> pdb=" O VAL A 988 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A1013 " --> pdb=" O LEU A1009 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU A1014 " --> pdb=" O ILE A1010 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.250A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR C 91 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.072A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.123A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 83 through 85 removed outlier: 13.309A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.561A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.711A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.688A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.452A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.525A pdb=" N ILE C 587 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.245A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.384A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 708 through 710 removed outlier: 3.907A pdb=" N THR C1073 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 715 through 725 removed outlier: 3.592A pdb=" N ALA C1053 " --> pdb=" O GLY C1056 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 731 through 733 Processing sheet with id=AB6, first strand: chain 'C' and resid 1083 through 1086 removed outlier: 4.105A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 29 removed outlier: 3.751A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.541A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.643A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.884A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.638A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 11.015A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 10.288A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 140 " --> pdb=" O ARG B 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.749A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 224 through 230 removed outlier: 6.154A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.707A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 539 through 543 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.369A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 709 through 710 Processing sheet with id=AD2, first strand: chain 'B' and resid 715 through 725 removed outlier: 3.577A pdb=" N SER B 718 " --> pdb=" O THR B1063 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 731 through 733 Processing sheet with id=AD4, first strand: chain 'B' and resid 786 through 787 Processing sheet with id=AD5, first strand: chain 'B' and resid 1118 through 1122 removed outlier: 4.849A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1091 through 1094 removed outlier: 4.644A pdb=" N GLN B1103 " --> pdb=" O GLU B1108 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLU B1108 " --> pdb=" O GLN B1103 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AD8, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.172A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 65 through 66 removed outlier: 5.957A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.926A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.235A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.630A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.717A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.797A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AE4, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.318A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.571A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.509A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.097A pdb=" N GLU A 654 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N THR A 693 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 708 through 712 Processing sheet with id=AF2, first strand: chain 'A' and resid 715 through 725 removed outlier: 3.625A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 731 through 733 Processing sheet with id=AF4, first strand: chain 'A' and resid 1078 through 1079 removed outlier: 4.202A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 1091 through 1094 863 hydrogen bonds defined for protein. 2313 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: 11.04 Time building geometry restraints manager: 7.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4043 1.31 - 1.44: 7056 1.44 - 1.57: 14142 1.57 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 25379 Sorted by residual: bond pdb=" C7 NAG B1306 " pdb=" N2 NAG B1306 " ideal model delta sigma weight residual 1.346 1.472 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" C7 NAG B1302 " pdb=" N2 NAG B1302 " ideal model delta sigma weight residual 1.346 1.471 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C7 NAG B1307 " pdb=" N2 NAG B1307 " ideal model delta sigma weight residual 1.346 1.471 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C7 NAG B1303 " pdb=" N2 NAG B1303 " ideal model delta sigma weight residual 1.346 1.471 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C7 NAG C1401 " pdb=" N2 NAG C1401 " ideal model delta sigma weight residual 1.346 1.471 -0.125 2.00e-02 2.50e+03 3.89e+01 ... (remaining 25374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 33417 1.72 - 3.43: 902 3.43 - 5.15: 141 5.15 - 6.87: 22 6.87 - 8.59: 1 Bond angle restraints: 34483 Sorted by residual: angle pdb=" N ILE B 847 " pdb=" CA ILE B 847 " pdb=" C ILE B 847 " ideal model delta sigma weight residual 112.96 108.66 4.30 1.00e+00 1.00e+00 1.85e+01 angle pdb=" N MET C1047 " pdb=" CA MET C1047 " pdb=" C MET C1047 " ideal model delta sigma weight residual 107.73 113.36 -5.63 1.34e+00 5.57e-01 1.76e+01 angle pdb=" N ALA C 703 " pdb=" CA ALA C 703 " pdb=" C ALA C 703 " ideal model delta sigma weight residual 110.97 115.07 -4.10 1.09e+00 8.42e-01 1.41e+01 angle pdb=" CA TYR B 37 " pdb=" CB TYR B 37 " pdb=" CG TYR B 37 " ideal model delta sigma weight residual 113.90 120.42 -6.52 1.80e+00 3.09e-01 1.31e+01 angle pdb=" N GLY C 697 " pdb=" CA GLY C 697 " pdb=" C GLY C 697 " ideal model delta sigma weight residual 113.18 121.77 -8.59 2.37e+00 1.78e-01 1.31e+01 ... (remaining 34478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.79: 14507 26.79 - 53.58: 758 53.58 - 80.38: 114 80.38 - 107.17: 16 107.17 - 133.96: 2 Dihedral angle restraints: 15397 sinusoidal: 6309 harmonic: 9088 Sorted by residual: dihedral pdb=" CA ARG C1088 " pdb=" C ARG C1088 " pdb=" N GLU C1089 " pdb=" CA GLU C1089 " ideal model delta harmonic sigma weight residual 180.00 154.12 25.88 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA ASP A 88 " pdb=" C ASP A 88 " pdb=" N GLY A 89 " pdb=" CA GLY A 89 " ideal model delta harmonic sigma weight residual -180.00 -155.79 -24.21 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA TYR A 753 " pdb=" C TYR A 753 " pdb=" N GLY A 754 " pdb=" CA GLY A 754 " ideal model delta harmonic sigma weight residual 180.00 155.94 24.06 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 15394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.258: 3970 0.258 - 0.516: 2 0.516 - 0.773: 1 0.773 - 1.031: 0 1.031 - 1.289: 1 Chirality restraints: 3974 Sorted by residual: chirality pdb=" C1 NAG B1309 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B1309 " pdb=" O5 NAG B1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.11 -1.29 2.00e-01 2.50e+01 4.15e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN C 714 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.68e+00 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.35 -0.05 2.00e-02 2.50e+03 5.15e+00 ... (remaining 3971 not shown) Planarity restraints: 4425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " 0.495 2.00e-02 2.50e+03 5.08e-01 3.23e+03 pdb=" CG ASN B 234 " -0.178 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " -0.126 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " -0.796 2.00e-02 2.50e+03 pdb=" C1 NAG B1309 " 0.605 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1402 " 0.303 2.00e-02 2.50e+03 2.54e-01 8.09e+02 pdb=" C7 NAG C1402 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C1402 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG C1402 " -0.435 2.00e-02 2.50e+03 pdb=" O7 NAG C1402 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1304 " -0.299 2.00e-02 2.50e+03 2.52e-01 7.95e+02 pdb=" C7 NAG B1304 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG B1304 " -0.185 2.00e-02 2.50e+03 pdb=" N2 NAG B1304 " 0.433 2.00e-02 2.50e+03 pdb=" O7 NAG B1304 " -0.026 2.00e-02 2.50e+03 ... (remaining 4422 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 88 2.43 - 3.05: 15250 3.05 - 3.67: 31943 3.67 - 4.28: 51449 4.28 - 4.90: 90927 Nonbonded interactions: 189657 Sorted by model distance: nonbonded pdb=" O GLY A 339 " pdb=" OD1 ASN A 343 " model vdw 1.814 3.040 nonbonded pdb=" O ASN C 975 " pdb=" OG SER C 979 " model vdw 1.949 3.040 nonbonded pdb=" ND2 ASN C 343 " pdb=" O5 NAG C1401 " model vdw 1.966 3.120 nonbonded pdb=" O3 NAG B1310 " pdb=" O7 NAG B1310 " model vdw 2.051 3.040 nonbonded pdb=" O ASN A 975 " pdb=" OG SER A 979 " model vdw 2.072 3.040 ... (remaining 189652 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' and (resid 15 through 67 or resid 81 through 96 or (resid 97 and (nam \ e N or name CA or name C or name O or name CB )) or resid 98 through 142 or (res \ id 143 and (name N or name CA or name C or name O or name CB )) or resid 157 thr \ ough 172 or (resid 187 and (name N or name CA or name C or name O or name CB )) \ or resid 188 through 210 or resid 216 through 245 or resid 255 or resid 257 thro \ ugh 675 or resid 686 through 808 or resid 810 through 825 or resid 829 through 8 \ 40 or resid 845 through 931 or (resid 932 and (name N or name CA or name C or na \ me O or name CB )) or resid 933 through 1136 or resid 2101 through 2106)) selection = (chain 'B' and (resid 15 through 67 or resid 81 through 96 or (resid 97 and (nam \ e N or name CA or name C or name O or name CB )) or resid 98 through 172 or (res \ id 187 and (name N or name CA or name C or name O or name CB )) or resid 188 thr \ ough 210 or resid 216 through 255 or resid 257 through 675 or resid 686 through \ 807 or (resid 808 and (name N or name CA or name C or name O or name CB )) or re \ sid 810 through 840 or resid 845 through 931 or (resid 932 and (name N or name C \ A or name C or name O or name CB )) or resid 933 through 936 or (resid 937 and ( \ name N or name CA or name C or name O or name CB )) or resid 941 through 1136 or \ resid 1301 through 1306)) selection = (chain 'C' and (resid 15 through 18 or resid 25 through 67 or resid 81 through 1 \ 42 or (resid 143 and (name N or name CA or name C or name O or name CB )) or res \ id 157 through 245 or resid 256 through 808 or resid 810 through 936 or (resid 9 \ 37 through 941 and (name N or name CA or name C or name O or name CB )) or resid \ 942 through 1136 or resid 1401 through 1406)) } 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 individual isotropic 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 55.930 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 : 0.007 0.126 25379 Z= 0.441 Angle : 0.691 8.586 34483 Z= 0.366 Chirality : 0.051 1.289 3974 Planarity : 0.009 0.254 4419 Dihedral : 16.161 133.959 9452 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.19 % Favored : 91.74 % Rotamer: Outliers : 3.84 % Allowed : 16.85 % Favored : 79.31 % 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: -4.11 (0.12), residues: 3063 helix: -1.95 (0.17), residues: 659 sheet: -1.71 (0.18), residues: 689 loop : -3.65 (0.11), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.003 0.001 HIS B1061 PHE 0.014 0.001 PHE C 592 TYR 0.020 0.001 TYR A 37 ARG 0.003 0.000 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 317 time to evaluate : 2.886 Fit side-chains REVERT: C 88 ASP cc_start: 0.7440 (t70) cc_final: 0.6995 (t0) REVERT: C 702 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7968 (m) REVERT: C 773 LYS cc_start: 0.8658 (ttpp) cc_final: 0.8437 (ttpt) REVERT: C 820 PHE cc_start: 0.7956 (t80) cc_final: 0.7279 (m-80) REVERT: C 983 LYS cc_start: 0.7815 (tptm) cc_final: 0.7485 (mmtm) REVERT: C 1078 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7908 (mt) REVERT: C 1104 ARG cc_start: 0.7361 (mtt90) cc_final: 0.7105 (mpt180) REVERT: C 1112 ILE cc_start: 0.8548 (mt) cc_final: 0.8326 (mt) REVERT: B 115 GLN cc_start: 0.8737 (mt0) cc_final: 0.8448 (mt0) REVERT: B 661 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6588 (mm-30) REVERT: B 675 GLN cc_start: 0.7150 (mm110) cc_final: 0.6890 (mm-40) REVERT: B 1088 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6987 (ptm-80) REVERT: B 1133 THR cc_start: 0.7329 (OUTLIER) cc_final: 0.7071 (p) REVERT: A 309 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6303 (mp0) REVERT: A 1070 LYS cc_start: 0.7680 (mtpp) cc_final: 0.7257 (mmtp) outliers start: 104 outliers final: 60 residues processed: 398 average time/residue: 0.3548 time to fit residues: 225.9844 Evaluate side-chains 306 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 240 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1088 ARG Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1034 SER Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1136 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.9980 chunk 236 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 182 optimal weight: 9.9990 chunk 283 optimal weight: 20.0000 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 ASN C 481 ASN C 487 ASN C 613 GLN C 752 GLN C 798 ASN C 952 ASN C1007 GLN C1045 HIS B 409 GLN B 487 ASN B 613 GLN B 655 HIS B 798 ASN B 952 ASN A 606 ASN A 616 ASN A 898 GLN A 952 ASN A 989 GLN A1068 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.149757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.127163 restraints weight = 29588.714| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.48 r_work: 0.3119 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25379 Z= 0.189 Angle : 0.609 9.379 34483 Z= 0.319 Chirality : 0.047 0.537 3974 Planarity : 0.005 0.059 4419 Dihedral : 8.957 82.224 4051 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 3.44 % Allowed : 17.33 % Favored : 79.24 % 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: -2.81 (0.13), residues: 3063 helix: -0.38 (0.20), residues: 654 sheet: -0.94 (0.19), residues: 686 loop : -3.01 (0.12), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 64 HIS 0.003 0.001 HIS B1085 PHE 0.013 0.001 PHE A 342 TYR 0.031 0.001 TYR B 170 ARG 0.005 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 248 time to evaluate : 2.661 Fit side-chains REVERT: C 88 ASP cc_start: 0.8054 (t70) cc_final: 0.7613 (t0) REVERT: C 102 ARG cc_start: 0.8533 (mmt180) cc_final: 0.8176 (mmt90) REVERT: C 228 ASP cc_start: 0.7403 (t0) cc_final: 0.7109 (m-30) REVERT: C 290 ASP cc_start: 0.8725 (t0) cc_final: 0.8497 (t0) REVERT: C 613 GLN cc_start: 0.8329 (mt0) cc_final: 0.7235 (tt0) REVERT: C 636 TYR cc_start: 0.7870 (m-10) cc_final: 0.7635 (m-10) REVERT: C 702 VAL cc_start: 0.8125 (p) cc_final: 0.7882 (m) REVERT: C 820 PHE cc_start: 0.8259 (t80) cc_final: 0.7373 (m-80) REVERT: C 1104 ARG cc_start: 0.8041 (mtt90) cc_final: 0.7780 (mpt180) REVERT: B 62 VAL cc_start: 0.7924 (t) cc_final: 0.7704 (t) REVERT: B 115 GLN cc_start: 0.8951 (mt0) cc_final: 0.8642 (mt0) REVERT: B 567 ARG cc_start: 0.8266 (tpp80) cc_final: 0.7737 (mmm-85) REVERT: B 613 GLN cc_start: 0.8755 (mt0) cc_final: 0.8520 (mt0) REVERT: B 787 LYS cc_start: 0.8627 (mttm) cc_final: 0.8322 (mttm) REVERT: B 1035 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8167 (mmtm) REVERT: B 1133 THR cc_start: 0.7797 (OUTLIER) cc_final: 0.7514 (p) REVERT: A 207 HIS cc_start: 0.8033 (t-90) cc_final: 0.7602 (m-70) REVERT: A 309 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: A 613 GLN cc_start: 0.8311 (mp10) cc_final: 0.7564 (tt0) REVERT: A 699 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7808 (tt0) REVERT: A 1070 LYS cc_start: 0.7951 (mtpp) cc_final: 0.7357 (mmtp) REVERT: A 1115 ASP cc_start: 0.8088 (p0) cc_final: 0.7859 (p0) outliers start: 93 outliers final: 54 residues processed: 323 average time/residue: 0.3478 time to fit residues: 181.9242 Evaluate side-chains 281 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 223 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1124 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 933 ASP Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1127 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 0.9990 chunk 247 optimal weight: 0.4980 chunk 178 optimal weight: 1.9990 chunk 237 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 220 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 196 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 243 optimal weight: 6.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 798 ASN C 898 GLN B 606 ASN B 801 GLN A 81 ASN A 487 ASN A 606 ASN A 917 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.144867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.120054 restraints weight = 29872.679| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.44 r_work: 0.3037 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25379 Z= 0.223 Angle : 0.597 9.807 34483 Z= 0.314 Chirality : 0.046 0.247 3974 Planarity : 0.005 0.065 4419 Dihedral : 8.163 79.049 3989 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 3.51 % Allowed : 17.55 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.31 (0.14), residues: 3063 helix: -0.00 (0.20), residues: 665 sheet: -0.55 (0.20), residues: 688 loop : -2.73 (0.12), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS B1061 PHE 0.014 0.001 PHE A 377 TYR 0.024 0.002 TYR A 37 ARG 0.005 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 235 time to evaluate : 2.609 Fit side-chains REVERT: C 88 ASP cc_start: 0.8169 (t70) cc_final: 0.7514 (t0) REVERT: C 102 ARG cc_start: 0.8542 (mmt180) cc_final: 0.8188 (mmt90) REVERT: C 290 ASP cc_start: 0.8840 (t0) cc_final: 0.8557 (t0) REVERT: C 568 ASP cc_start: 0.7463 (t0) cc_final: 0.7134 (t0) REVERT: C 606 ASN cc_start: 0.7639 (m110) cc_final: 0.7367 (t0) REVERT: C 613 GLN cc_start: 0.8295 (mt0) cc_final: 0.7180 (tt0) REVERT: C 820 PHE cc_start: 0.8252 (t80) cc_final: 0.7320 (m-80) REVERT: C 983 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8159 (tmtm) REVERT: B 62 VAL cc_start: 0.7919 (OUTLIER) cc_final: 0.7700 (t) REVERT: B 158 ARG cc_start: 0.7432 (mtt180) cc_final: 0.7102 (mtt180) REVERT: B 567 ARG cc_start: 0.8265 (tpp80) cc_final: 0.7653 (mmm-85) REVERT: B 787 LYS cc_start: 0.8592 (mttm) cc_final: 0.8222 (mttm) REVERT: B 999 GLN cc_start: 0.8293 (tt0) cc_final: 0.7731 (pt0) REVERT: B 1035 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8237 (mmtp) REVERT: A 207 HIS cc_start: 0.8046 (t-90) cc_final: 0.7495 (m-70) REVERT: A 500 THR cc_start: 0.8222 (p) cc_final: 0.7850 (t) REVERT: A 699 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7713 (tt0) REVERT: A 947 ASP cc_start: 0.8297 (m-30) cc_final: 0.8094 (m-30) REVERT: A 1070 LYS cc_start: 0.7986 (mtpp) cc_final: 0.7363 (mmtp) outliers start: 95 outliers final: 67 residues processed: 309 average time/residue: 0.3630 time to fit residues: 180.3265 Evaluate side-chains 295 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 224 time to evaluate : 4.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 898 GLN Chi-restraints excluded: chain C residue 983 LYS Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1130 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 191 optimal weight: 10.0000 chunk 70 optimal weight: 0.3980 chunk 159 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 305 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 290 optimal weight: 3.9990 chunk 167 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 798 ASN C 850 GLN C 898 GLN B 606 ASN ** B 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 801 GLN B1080 HIS A 69 HIS A 81 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.148324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.125510 restraints weight = 29956.175| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.39 r_work: 0.3131 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25379 Z= 0.167 Angle : 0.549 9.402 34483 Z= 0.289 Chirality : 0.044 0.187 3974 Planarity : 0.004 0.064 4419 Dihedral : 7.697 75.542 3981 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 3.32 % Allowed : 17.92 % Favored : 78.76 % 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: -1.94 (0.14), residues: 3063 helix: 0.37 (0.21), residues: 659 sheet: -0.30 (0.20), residues: 680 loop : -2.52 (0.13), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 64 HIS 0.002 0.001 HIS B1085 PHE 0.016 0.001 PHE A 377 TYR 0.021 0.001 TYR A 37 ARG 0.007 0.000 ARG C1104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 243 time to evaluate : 2.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 32 PHE cc_start: 0.7261 (m-80) cc_final: 0.6998 (m-80) REVERT: C 88 ASP cc_start: 0.8089 (t70) cc_final: 0.7417 (t0) REVERT: C 102 ARG cc_start: 0.8490 (mmt180) cc_final: 0.8149 (mmt90) REVERT: C 290 ASP cc_start: 0.8773 (t0) cc_final: 0.8518 (t0) REVERT: C 568 ASP cc_start: 0.7535 (t0) cc_final: 0.7174 (t0) REVERT: C 606 ASN cc_start: 0.7533 (m110) cc_final: 0.7323 (t0) REVERT: C 613 GLN cc_start: 0.8267 (mt0) cc_final: 0.7235 (tt0) REVERT: C 820 PHE cc_start: 0.8388 (t80) cc_final: 0.7413 (m-80) REVERT: C 983 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8151 (tmtm) REVERT: C 1104 ARG cc_start: 0.8049 (mtt90) cc_final: 0.7842 (mpt180) REVERT: B 62 VAL cc_start: 0.7926 (OUTLIER) cc_final: 0.7724 (t) REVERT: B 158 ARG cc_start: 0.7457 (mtt180) cc_final: 0.7139 (mtt180) REVERT: B 567 ARG cc_start: 0.8226 (tpp80) cc_final: 0.7665 (mmm-85) REVERT: B 661 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7116 (mm-30) REVERT: B 801 GLN cc_start: 0.8312 (mt0) cc_final: 0.8088 (mt0) REVERT: B 891 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8610 (mt) REVERT: B 999 GLN cc_start: 0.8281 (tt0) cc_final: 0.8051 (tp-100) REVERT: B 1035 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8181 (mmtm) REVERT: B 1132 ASN cc_start: 0.7672 (t0) cc_final: 0.7394 (t0) REVERT: A 207 HIS cc_start: 0.7971 (t-90) cc_final: 0.7523 (m170) REVERT: A 309 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: A 500 THR cc_start: 0.8203 (p) cc_final: 0.7900 (t) REVERT: A 932 GLN cc_start: 0.7860 (tt0) cc_final: 0.7531 (tt0) REVERT: A 947 ASP cc_start: 0.8312 (m-30) cc_final: 0.8105 (m-30) REVERT: A 1070 LYS cc_start: 0.8023 (mtpp) cc_final: 0.7398 (mmtp) outliers start: 90 outliers final: 65 residues processed: 315 average time/residue: 0.3676 time to fit residues: 186.3415 Evaluate side-chains 297 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 226 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 898 GLN Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 983 LYS Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1124 ASP Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1130 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 93 optimal weight: 8.9990 chunk 282 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 276 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 163 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 24 optimal weight: 0.3980 chunk 90 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 798 ASN C 898 GLN ** B 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN A 898 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.136759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.111006 restraints weight = 30979.415| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.67 r_work: 0.2954 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 25379 Z= 0.420 Angle : 0.715 10.000 34483 Z= 0.377 Chirality : 0.050 0.258 3974 Planarity : 0.005 0.079 4419 Dihedral : 8.216 74.280 3979 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 4.17 % Allowed : 17.99 % Favored : 77.84 % 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: -2.17 (0.14), residues: 3063 helix: -0.18 (0.20), residues: 672 sheet: -0.32 (0.20), residues: 685 loop : -2.58 (0.13), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 353 HIS 0.006 0.001 HIS B1061 PHE 0.021 0.002 PHE C 541 TYR 0.038 0.002 TYR B 37 ARG 0.006 0.001 ARG C1104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 236 time to evaluate : 2.633 Fit side-chains revert: symmetry clash REVERT: C 32 PHE cc_start: 0.7337 (m-80) cc_final: 0.6991 (m-80) REVERT: C 88 ASP cc_start: 0.8269 (t70) cc_final: 0.7294 (t0) REVERT: C 290 ASP cc_start: 0.9050 (t0) cc_final: 0.8792 (t0) REVERT: C 568 ASP cc_start: 0.7705 (t0) cc_final: 0.7307 (t0) REVERT: C 606 ASN cc_start: 0.7682 (m110) cc_final: 0.7354 (t0) REVERT: C 820 PHE cc_start: 0.8246 (t80) cc_final: 0.7241 (m-80) REVERT: C 915 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: C 983 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8299 (tmtm) REVERT: C 1104 ARG cc_start: 0.8213 (mtt90) cc_final: 0.7983 (mpt180) REVERT: B 62 VAL cc_start: 0.7996 (OUTLIER) cc_final: 0.7790 (t) REVERT: B 158 ARG cc_start: 0.7361 (mtt180) cc_final: 0.7061 (mtt180) REVERT: B 606 ASN cc_start: 0.7949 (t160) cc_final: 0.7717 (t0) REVERT: B 787 LYS cc_start: 0.8598 (mttm) cc_final: 0.8396 (mttm) REVERT: A 207 HIS cc_start: 0.8098 (t-90) cc_final: 0.7533 (m-70) REVERT: A 244 LEU cc_start: 0.6273 (OUTLIER) cc_final: 0.5413 (mt) REVERT: A 309 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7492 (mp0) REVERT: A 613 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7865 (mt0) REVERT: A 776 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8213 (tp40) REVERT: A 932 GLN cc_start: 0.7919 (tt0) cc_final: 0.7678 (tt0) REVERT: A 1070 LYS cc_start: 0.8094 (mtpp) cc_final: 0.7392 (mmtp) outliers start: 113 outliers final: 83 residues processed: 320 average time/residue: 0.3623 time to fit residues: 185.9842 Evaluate side-chains 313 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 223 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 915 GLU Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 983 LYS Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1130 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 41 optimal weight: 8.9990 chunk 170 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 230 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 233 optimal weight: 5.9990 chunk 284 optimal weight: 3.9990 chunk 289 optimal weight: 0.9980 chunk 167 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 798 ASN C 898 GLN ** B 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.139341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.113296 restraints weight = 30606.299| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.67 r_work: 0.2974 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25379 Z= 0.229 Angle : 0.593 9.134 34483 Z= 0.315 Chirality : 0.046 0.281 3974 Planarity : 0.005 0.072 4419 Dihedral : 7.636 69.750 3975 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 4.10 % Allowed : 18.51 % Favored : 77.39 % 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: -1.92 (0.14), residues: 3063 helix: 0.14 (0.20), residues: 666 sheet: -0.19 (0.20), residues: 685 loop : -2.45 (0.13), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 64 HIS 0.003 0.001 HIS A1061 PHE 0.015 0.001 PHE C 592 TYR 0.024 0.002 TYR A 37 ARG 0.006 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 238 time to evaluate : 2.544 Fit side-chains REVERT: C 32 PHE cc_start: 0.7285 (m-80) cc_final: 0.6958 (m-80) REVERT: C 88 ASP cc_start: 0.8301 (t70) cc_final: 0.7353 (t0) REVERT: C 102 ARG cc_start: 0.8531 (mmt180) cc_final: 0.8127 (mmt90) REVERT: C 290 ASP cc_start: 0.8989 (t0) cc_final: 0.8706 (t0) REVERT: C 568 ASP cc_start: 0.7761 (t0) cc_final: 0.7471 (t0) REVERT: C 606 ASN cc_start: 0.7793 (m110) cc_final: 0.7491 (t0) REVERT: C 613 GLN cc_start: 0.8421 (mt0) cc_final: 0.7217 (tt0) REVERT: C 820 PHE cc_start: 0.8290 (t80) cc_final: 0.7257 (m-80) REVERT: C 983 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8368 (tmtm) REVERT: B 62 VAL cc_start: 0.7882 (OUTLIER) cc_final: 0.7679 (t) REVERT: B 158 ARG cc_start: 0.7331 (mtt180) cc_final: 0.7030 (mtt180) REVERT: B 606 ASN cc_start: 0.7892 (OUTLIER) cc_final: 0.7426 (t0) REVERT: B 661 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7318 (mm-30) REVERT: B 787 LYS cc_start: 0.8562 (mttm) cc_final: 0.8346 (mttm) REVERT: B 1035 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8298 (mmtp) REVERT: A 207 HIS cc_start: 0.8103 (t-90) cc_final: 0.7491 (m-70) REVERT: A 244 LEU cc_start: 0.6113 (OUTLIER) cc_final: 0.5266 (mt) REVERT: A 309 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: A 500 THR cc_start: 0.8244 (p) cc_final: 0.7894 (t) REVERT: A 613 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7843 (mt0) REVERT: A 776 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8178 (tp40) REVERT: A 932 GLN cc_start: 0.7973 (tt0) cc_final: 0.7663 (tt0) REVERT: A 947 ASP cc_start: 0.8408 (m-30) cc_final: 0.8189 (m-30) REVERT: A 1070 LYS cc_start: 0.8062 (mtpp) cc_final: 0.7363 (mmtp) REVERT: A 1125 VAL cc_start: 0.6955 (OUTLIER) cc_final: 0.6548 (p) outliers start: 111 outliers final: 81 residues processed: 322 average time/residue: 0.3601 time to fit residues: 186.6328 Evaluate side-chains 325 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 234 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 983 LYS Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1124 ASP Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1130 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 193 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 201 optimal weight: 9.9990 chunk 230 optimal weight: 9.9990 chunk 302 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 260 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 chunk 146 optimal weight: 4.9990 chunk 236 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 798 ASN C 898 GLN B 798 ASN A 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.141811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.116425 restraints weight = 30559.287| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.56 r_work: 0.3031 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25379 Z= 0.192 Angle : 0.560 8.769 34483 Z= 0.298 Chirality : 0.045 0.195 3974 Planarity : 0.004 0.069 4419 Dihedral : 7.321 63.958 3975 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 4.03 % Allowed : 18.62 % Favored : 77.36 % 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: -1.74 (0.14), residues: 3063 helix: 0.35 (0.20), residues: 666 sheet: -0.08 (0.20), residues: 682 loop : -2.35 (0.13), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 64 HIS 0.003 0.001 HIS B1061 PHE 0.014 0.001 PHE C 797 TYR 0.022 0.001 TYR A 37 ARG 0.006 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 242 time to evaluate : 2.587 Fit side-chains revert: symmetry clash REVERT: C 32 PHE cc_start: 0.7270 (m-80) cc_final: 0.6997 (m-80) REVERT: C 88 ASP cc_start: 0.8240 (t70) cc_final: 0.7451 (t0) REVERT: C 102 ARG cc_start: 0.8571 (mmt180) cc_final: 0.8166 (mmt90) REVERT: C 290 ASP cc_start: 0.8949 (t0) cc_final: 0.8686 (t0) REVERT: C 606 ASN cc_start: 0.7728 (m110) cc_final: 0.7487 (t0) REVERT: C 613 GLN cc_start: 0.8303 (mt0) cc_final: 0.7186 (tt0) REVERT: C 820 PHE cc_start: 0.8338 (t80) cc_final: 0.7305 (m-80) REVERT: C 983 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8243 (tmtm) REVERT: B 129 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7600 (mtmt) REVERT: B 158 ARG cc_start: 0.7389 (mtt180) cc_final: 0.7089 (mtt180) REVERT: B 445 VAL cc_start: 0.6672 (OUTLIER) cc_final: 0.6443 (t) REVERT: B 606 ASN cc_start: 0.7830 (OUTLIER) cc_final: 0.7377 (t0) REVERT: B 661 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7541 (mm-30) REVERT: B 801 GLN cc_start: 0.8364 (mt0) cc_final: 0.8107 (mt0) REVERT: B 999 GLN cc_start: 0.8358 (tt0) cc_final: 0.8137 (tp-100) REVERT: B 1035 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8254 (mmtt) REVERT: A 207 HIS cc_start: 0.8072 (t-90) cc_final: 0.7525 (m-70) REVERT: A 244 LEU cc_start: 0.6132 (OUTLIER) cc_final: 0.5317 (mt) REVERT: A 309 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: A 500 THR cc_start: 0.8262 (p) cc_final: 0.7943 (t) REVERT: A 613 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: A 932 GLN cc_start: 0.7927 (tt0) cc_final: 0.7673 (tt0) REVERT: A 947 ASP cc_start: 0.8350 (m-30) cc_final: 0.8136 (m-30) REVERT: A 1070 LYS cc_start: 0.8052 (mtpp) cc_final: 0.7417 (mmtp) REVERT: A 1125 VAL cc_start: 0.6981 (OUTLIER) cc_final: 0.6546 (p) outliers start: 109 outliers final: 82 residues processed: 327 average time/residue: 0.3635 time to fit residues: 190.0204 Evaluate side-chains 326 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 234 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 898 GLN Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 983 LYS Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1124 ASP Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1130 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 12 optimal weight: 0.0030 chunk 193 optimal weight: 7.9990 chunk 151 optimal weight: 0.0010 chunk 295 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 243 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 278 optimal weight: 0.0470 chunk 246 optimal weight: 10.0000 overall best weight: 0.3694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 GLN C 798 ASN B 474 GLN B 613 GLN ** B 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN A 239 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.145201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.119349 restraints weight = 30617.008| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.61 r_work: 0.3063 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 25379 Z= 0.123 Angle : 0.503 8.574 34483 Z= 0.268 Chirality : 0.043 0.157 3974 Planarity : 0.004 0.061 4419 Dihedral : 6.770 61.289 3975 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.73 % Allowed : 19.80 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.15), residues: 3063 helix: 0.81 (0.21), residues: 671 sheet: 0.06 (0.20), residues: 685 loop : -2.18 (0.13), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 64 HIS 0.002 0.000 HIS C1080 PHE 0.032 0.001 PHE B 799 TYR 0.019 0.001 TYR B 901 ARG 0.006 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 255 time to evaluate : 3.148 Fit side-chains revert: symmetry clash REVERT: C 32 PHE cc_start: 0.7140 (m-80) cc_final: 0.6920 (m-80) REVERT: C 88 ASP cc_start: 0.8182 (t70) cc_final: 0.7460 (t0) REVERT: C 290 ASP cc_start: 0.8908 (t0) cc_final: 0.8637 (t0) REVERT: C 474 GLN cc_start: 0.7510 (tm-30) cc_final: 0.6717 (mt0) REVERT: C 606 ASN cc_start: 0.7469 (m110) cc_final: 0.7258 (t0) REVERT: C 613 GLN cc_start: 0.8217 (mt0) cc_final: 0.7151 (tt0) REVERT: C 820 PHE cc_start: 0.8326 (t80) cc_final: 0.7281 (m-80) REVERT: B 129 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7586 (mtmt) REVERT: B 158 ARG cc_start: 0.7249 (mtt180) cc_final: 0.6970 (mtt180) REVERT: B 271 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7862 (mt0) REVERT: B 567 ARG cc_start: 0.8174 (tpp80) cc_final: 0.7461 (mmm-85) REVERT: B 606 ASN cc_start: 0.7735 (OUTLIER) cc_final: 0.7293 (t0) REVERT: B 613 GLN cc_start: 0.8787 (mt0) cc_final: 0.8480 (mt0) REVERT: B 661 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7344 (mm-30) REVERT: B 801 GLN cc_start: 0.8406 (mt0) cc_final: 0.8150 (mt0) REVERT: B 999 GLN cc_start: 0.8345 (tt0) cc_final: 0.8134 (tp-100) REVERT: B 1035 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8288 (mmtt) REVERT: B 1132 ASN cc_start: 0.7765 (t0) cc_final: 0.7478 (t0) REVERT: A 207 HIS cc_start: 0.7992 (t-90) cc_final: 0.7389 (m170) REVERT: A 244 LEU cc_start: 0.5868 (OUTLIER) cc_final: 0.5134 (mt) REVERT: A 309 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: A 500 THR cc_start: 0.8170 (p) cc_final: 0.7870 (t) REVERT: A 1070 LYS cc_start: 0.8055 (mtpp) cc_final: 0.7373 (mmtp) REVERT: A 1125 VAL cc_start: 0.6974 (OUTLIER) cc_final: 0.6557 (p) outliers start: 74 outliers final: 55 residues processed: 309 average time/residue: 0.3843 time to fit residues: 189.6620 Evaluate side-chains 301 residues out of total 2722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 238 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 798 ASN Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1091 VAL Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1124 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 1035 LYS Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 1035 LYS Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1127 ILE Chi-restraints excluded: chain A residue 1130 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 265 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 2 optimal weight: 0.0980 chunk 1 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 chunk 168 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: