Starting phenix.real_space_refine on Sun Jul 5 08:06:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7x7n_33042/07_2026/7x7n_33042.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x7n_33042/07_2026/7x7n_33042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x7n_33042/07_2026/7x7n_33042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x7n_33042/07_2026/7x7n_33042.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7x7n_33042/07_2026/7x7n_33042.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7x7n_33042/07_2026/7x7n_33042.cif" model { file = "/net/cci-nas-00/data/ceres_data/7x7n_33042/07_2026/7x7n_33042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x7n_33042/07_2026/7x7n_33042.cif" } resolution = 4.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 128 5.16 5 C 16909 2.51 5 N 4328 2.21 5 O 5128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26493 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 8031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8031 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 51, 'TRANS': 981} Chain breaks: 7 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 8033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8033 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 51, 'TRANS': 981} Chain breaks: 7 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "A" Number of atoms: 7981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 7981 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 51, 'TRANS': 974} Chain breaks: 7 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 3, 'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 164 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 153 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'DAL:plan-1': 1, 'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 164 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 153 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'DAL:plan-1': 1, 'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 164 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 153 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'DAL:plan-1': 1, 'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "I" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 164 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 153 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'DAL:plan-1': 1, 'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "F" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 164 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 153 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'DAL:plan-1': 1, 'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 164 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 153 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'DAL:plan-1': 1, 'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 5.94, per 1000 atoms: 0.22 Number of scatterers: 26493 At special positions: 0 Unit cell: (145.08, 211.77, 147.42, 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 128 16.00 O 5128 8.00 N 4328 7.00 C 16909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.01 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 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=2.04 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=2.04 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 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A1098 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 61 " " NAG A1310 " - " ASN A 234 " " NAG A1311 " - " ASN A 603 " " NAG A1312 " - " ASN A 165 " " NAG A1313 " - " ASN A 343 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B1098 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B 61 " " NAG B1310 " - " ASN B 234 " " NAG B1311 " - " ASN B 603 " " NAG B1312 " - " ASN B 165 " " NAG B1313 " - " ASN B 343 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C1098 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C 61 " " NAG C1310 " - " ASN C 234 " " NAG C1311 " - " ASN C 603 " " NAG C1312 " - " ASN C 165 " " NAG C1313 " - " ASN C 343 " TRANS " DAL D 20 " - " LEU D 19 " " DAL E 20 " - " LEU E 19 " " DAL F 20 " - " LEU F 19 " " DAL G 20 " - " LEU G 19 " " DAL H 20 " - " LEU H 19 " " DAL I 20 " - " LEU I 19 " Time building additional restraints: 4.53 Conformation dependent library (CDL) restraints added in 1.1 seconds 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL D 20 " pdb=" CB DAL E 20 " pdb=" CB DAL H 20 " pdb=" CB DAL I 20 " pdb=" CB DAL F 20 " pdb=" CB DAL G 20 " Number of C-beta restraints generated: 6236 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 46 sheets defined 27.6% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'B' and resid 294 through 302 removed outlier: 4.029A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.082A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.483A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 619 through 623 removed outlier: 4.125A pdb=" N VAL B 622 " --> pdb=" O GLU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.604A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.886A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL B 772 " --> pdb=" O THR B 768 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.850A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 removed outlier: 4.158A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 879 " --> pdb=" O SER B 875 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.601A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.315A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 934 removed outlier: 4.034A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN B 926 " --> pdb=" O LEU B 922 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 935 through 937 No H-bonds generated for 'chain 'B' and resid 935 through 937' Processing helix chain 'B' and resid 946 through 951 Processing helix chain 'B' and resid 952 through 961 Processing helix chain 'B' and resid 962 through 967 removed outlier: 3.509A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.630A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1035 removed outlier: 3.525A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG B1014 " --> pdb=" O GLN B1010 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA B1015 " --> pdb=" O GLN B1011 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA B1025 " --> pdb=" O SER B1021 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY B1035 " --> pdb=" O GLU B1031 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.898A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.906A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 370 removed outlier: 3.817A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.605A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.841A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 624 removed outlier: 3.533A pdb=" N ILE C 624 " --> pdb=" O VAL C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.019A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 782 removed outlier: 4.163A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.702A pdb=" N THR C 874 " --> pdb=" O ILE C 870 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.589A pdb=" N GLN C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE C 906 " --> pdb=" O MET C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 4.141A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 938 removed outlier: 4.337A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.531A pdb=" N ASP C 950 " --> pdb=" O GLY C 946 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.673A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 991 removed outlier: 6.003A pdb=" N GLU C 990 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 1033 removed outlier: 3.724A pdb=" N THR C 998 " --> pdb=" O ASP C 994 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG C1014 " --> pdb=" O GLN C1010 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1148 removed outlier: 4.359A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 removed outlier: 4.317A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 365 through 372 removed outlier: 3.970A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.911A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.548A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 423 removed outlier: 4.144A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 601 through 605 Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.811A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 779 removed outlier: 3.683A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA A 766 " --> pdb=" O GLN A 762 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.733A pdb=" N ASP A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 883 removed outlier: 3.600A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.661A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.940A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 938 removed outlier: 3.533A pdb=" N ALA A 924 " --> pdb=" O GLN A 920 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.976A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN A 953 " --> pdb=" O GLN A 949 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA A 958 " --> pdb=" O GLN A 954 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 983 Processing helix chain 'A' and resid 985 through 989 removed outlier: 3.567A pdb=" N GLU A 988 " --> pdb=" O ASP A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1033 removed outlier: 3.501A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR A1009 " --> pdb=" O GLN A1005 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A1014 " --> pdb=" O GLN A1010 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR A1027 " --> pdb=" O ASN A1023 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.667A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 20 Processing helix chain 'D' and resid 23 through 38 Processing helix chain 'E' and resid 2 through 19 Processing helix chain 'E' and resid 21 through 38 Processing helix chain 'H' and resid 2 through 18 Processing helix chain 'H' and resid 23 through 38 Processing helix chain 'I' and resid 2 through 20 Processing helix chain 'I' and resid 21 through 37 removed outlier: 3.850A pdb=" N LYS I 37 " --> pdb=" O TYR I 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 20 Processing helix chain 'F' and resid 22 through 37 Processing helix chain 'G' and resid 2 through 20 Processing helix chain 'G' and resid 21 through 38 Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.837A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.472A pdb=" N PHE B 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 49 removed outlier: 3.585A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR B 279 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 52 through 55 Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.685A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.827A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER B 205 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 317 through 319 removed outlier: 3.970A pdb=" N PHE B 318 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA B 609 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 378 through 379 Processing sheet with id=AA9, first strand: chain 'B' and resid 398 through 403 removed outlier: 3.692A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 448 through 454 removed outlier: 7.258A pdb=" N TYR B 495 " --> pdb=" O ASN B 450 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU B 452 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLN B 493 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 539 through 540 removed outlier: 3.775A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.561A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 713 through 721 removed outlier: 6.548A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA B1070 " --> pdb=" O ASN B 717 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 713 through 721 removed outlier: 6.548A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA B1070 " --> pdb=" O ASN B 717 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE B1052 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B1065 " --> pdb=" O MET B1050 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1120 through 1121 removed outlier: 4.038A pdb=" N HIS B1083 " --> pdb=" O LYS B1086 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 3.540A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 28 through 31 Processing sheet with id=AB9, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.829A pdb=" N PHE C 43 " --> pdb=" O ARG A 567 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.880A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 83 through 84 removed outlier: 3.529A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 192 through 194 removed outlier: 3.680A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 188 through 190 removed outlier: 3.942A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.832A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE C 651 " --> pdb=" O VAL C 610 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 376 through 378 Processing sheet with id=AC7, first strand: chain 'C' and resid 376 through 378 removed outlier: 3.618A pdb=" N TYR C 508 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 670 through 674 Processing sheet with id=AC9, first strand: chain 'C' and resid 711 through 714 removed outlier: 3.804A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.718A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C1070 " --> pdb=" O ASN C 717 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C1060 " --> pdb=" O LEU C 727 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.615A pdb=" N PHE C1089 " --> pdb=" O PHE C1121 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1095 through 1097 Processing sheet with id=AD5, first strand: chain 'A' and resid 28 through 31 removed outlier: 4.021A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.950A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AD8, first strand: chain 'A' and resid 224 through 230 removed outlier: 3.510A pdb=" N LEU A 226 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR A 91 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY A 268 " --> pdb=" O TYR A 91 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 118 through 121 removed outlier: 3.774A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.568A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.568A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 398 through 403 removed outlier: 4.075A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 452 through 453 removed outlier: 4.454A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 665 through 667 removed outlier: 6.564A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS A 671 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 711 through 714 removed outlier: 3.885A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.628A pdb=" N HIS A1064 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A1065 " --> pdb=" O MET A1050 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 1082 through 1083 Processing sheet with id=AE9, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AF1, first strand: chain 'A' and resid 1094 through 1096 removed outlier: 3.686A pdb=" N VAL A1096 " --> pdb=" O PHE A1103 " (cutoff:3.500A) 764 hydrogen bonds defined for protein. 2091 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: 6.31 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.57: 26882 1.57 - 1.93: 176 1.93 - 2.29: 0 2.29 - 2.64: 0 2.64 - 3.00: 1 Bond restraints: 27059 Sorted by residual: bond pdb=" C GLN A 675 " pdb=" N GLN A 690 " ideal model delta sigma weight residual 1.335 2.999 -1.664 1.34e-02 5.57e+03 1.54e+04 bond pdb=" CA GLN C 913 " pdb=" C GLN C 913 " ideal model delta sigma weight residual 1.523 1.448 0.075 1.80e-02 3.09e+03 1.75e+01 bond pdb=" C1 NAG B1309 " pdb=" O5 NAG B1309 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" N THR B 333 " pdb=" CA THR B 333 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.29e-02 6.01e+03 1.15e+01 bond pdb=" C ILE A 664 " pdb=" N PRO A 665 " ideal model delta sigma weight residual 1.333 1.293 0.040 1.20e-02 6.94e+03 1.14e+01 ... (remaining 27054 not shown) Histogram of bond angle deviations from ideal: 0.00 - 16.17: 36773 16.17 - 32.34: 2 32.34 - 48.51: 0 48.51 - 64.68: 0 64.68 - 80.85: 1 Bond angle restraints: 36776 Sorted by residual: angle pdb=" O GLN A 675 " pdb=" C GLN A 675 " pdb=" N GLN A 690 " ideal model delta sigma weight residual 121.76 40.91 80.85 1.15e+00 7.56e-01 4.94e+03 angle pdb=" CA GLN A 675 " pdb=" C GLN A 675 " pdb=" N GLN A 690 " ideal model delta sigma weight residual 118.24 144.57 -26.33 1.18e+00 7.18e-01 4.98e+02 angle pdb=" C GLN A 675 " pdb=" N GLN A 690 " pdb=" CA GLN A 690 " ideal model delta sigma weight residual 120.28 139.65 -19.37 1.44e+00 4.82e-01 1.81e+02 angle pdb=" N ASN B 334 " pdb=" CA ASN B 334 " pdb=" C ASN B 334 " ideal model delta sigma weight residual 110.97 102.83 8.14 1.09e+00 8.42e-01 5.57e+01 angle pdb=" N VAL A 130 " pdb=" CA VAL A 130 " pdb=" C VAL A 130 " ideal model delta sigma weight residual 111.91 105.78 6.13 8.90e-01 1.26e+00 4.74e+01 ... (remaining 36771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 14086 17.73 - 35.46: 1470 35.46 - 53.19: 244 53.19 - 70.92: 33 70.92 - 88.65: 28 Dihedral angle restraints: 15861 sinusoidal: 6191 harmonic: 9670 Sorted by residual: dihedral pdb=" CA GLN A 675 " pdb=" C GLN A 675 " pdb=" N GLN A 690 " pdb=" CA GLN A 690 " ideal model delta harmonic sigma weight residual 180.00 130.16 49.84 0 5.00e+00 4.00e-02 9.94e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -1.99 -84.01 1 1.00e+01 1.00e-02 8.60e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -10.49 -75.51 1 1.00e+01 1.00e-02 7.20e+01 ... (remaining 15858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 4100 0.109 - 0.218: 173 0.218 - 0.327: 8 0.327 - 0.436: 6 0.436 - 0.545: 4 Chirality restraints: 4291 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.44e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.85e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.84e+00 ... (remaining 4288 not shown) Planarity restraints: 4734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 675 " -0.267 2.00e-02 2.50e+03 2.43e-01 5.92e+02 pdb=" C GLN A 675 " 0.387 2.00e-02 2.50e+03 pdb=" O GLN A 675 " 0.006 2.00e-02 2.50e+03 pdb=" N GLN A 690 " -0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 811 " 0.042 5.00e-02 4.00e+02 6.41e-02 6.58e+00 pdb=" N PRO B 812 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 812 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 812 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 490 " 0.039 5.00e-02 4.00e+02 5.92e-02 5.61e+00 pdb=" N PRO B 491 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 491 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 491 " 0.032 5.00e-02 4.00e+02 ... (remaining 4731 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 491 2.55 - 3.13: 25006 3.13 - 3.72: 40827 3.72 - 4.31: 54986 4.31 - 4.90: 83810 Nonbonded interactions: 205120 Sorted by model distance: nonbonded pdb=" O CYS A1032 " pdb=" OG SER A1051 " model vdw 1.956 3.040 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.015 3.040 nonbonded pdb=" O VAL A 308 " pdb=" OG1 THR A 602 " model vdw 2.044 3.040 nonbonded pdb=" OG SER B 746 " pdb=" OE2 GLU B 748 " model vdw 2.046 3.040 nonbonded pdb=" O GLN B 580 " pdb=" O6 NAG B1301 " model vdw 2.065 3.040 ... (remaining 205115 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 26 through 675 or resid 691 through 1313)) selection = (chain 'B' and (resid 26 through 480 or (resid 481 and (name N or name CA or nam \ e C or name O or name CB )) or resid 489 through 675 or resid 691 through 1313)) \ selection = (chain 'C' and (resid 26 through 480 or (resid 481 and (name N or name CA or nam \ e C or name O or name CB )) or resid 489 through 675 or resid 691 through 1313)) \ } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 27.220 Find NCS groups from input model: 0.760 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: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 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 : 0.013 1.664 27142 Z= 0.856 Angle : 1.109 80.851 36987 Z= 0.652 Chirality : 0.057 0.545 4291 Planarity : 0.006 0.243 4689 Dihedral : 14.554 88.645 9493 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 28.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 19.61 % Favored : 80.27 % Rotamer: Outliers : 0.52 % Allowed : 9.67 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.63 (0.11), residues: 3228 helix: -3.39 (0.13), residues: 708 sheet: -3.47 (0.19), residues: 496 loop : -4.19 (0.11), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 577 TYR 0.031 0.003 TYR A 421 PHE 0.032 0.003 PHE A 759 TRP 0.025 0.002 TRP A 353 HIS 0.012 0.002 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.01330 / 0.86 (27059) covalent geometry : angle 1.05400 / 0.64 (36776) SS BOND : bond 0.00859 / 0.55 ( 38) SS BOND : angle 2.57637 / 1.70 ( 76) hydrogen bonds : bond 0.30088 / 20.02 ( 749) hydrogen bonds : angle 11.05451 / 7.51 ( 2091) link_NAG-ASN : bond 0.01153 / 0.73 ( 39) link_NAG-ASN : angle 5.95565 / 3.87 ( 117) link_TRANS : bond 0.00228 / 0.13 ( 6) link_TRANS : angle 0.92522 / 0.55 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6456 Ramachandran restraints generated. 3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 335 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 LEU cc_start: 0.8197 (mm) cc_final: 0.7730 (mm) REVERT: B 319 ARG cc_start: 0.7525 (mpp-170) cc_final: 0.6645 (ptt90) REVERT: B 486 PHE cc_start: 0.6829 (p90) cc_final: 0.6446 (m-80) REVERT: B 740 MET cc_start: 0.8195 (mmm) cc_final: 0.7990 (mmm) REVERT: C 160 TYR cc_start: 0.6208 (m-10) cc_final: 0.5856 (m-80) REVERT: C 280 ASN cc_start: 0.6946 (p0) cc_final: 0.6391 (p0) REVERT: C 454 ARG cc_start: 0.5139 (tpm170) cc_final: 0.4355 (ttm-80) REVERT: C 528 LYS cc_start: 0.6023 (OUTLIER) cc_final: 0.4970 (mmtp) REVERT: C 904 TYR cc_start: 0.7794 (t80) cc_final: 0.7436 (t80) REVERT: A 226 LEU cc_start: 0.8254 (mt) cc_final: 0.8000 (mp) REVERT: A 517 LEU cc_start: 0.7212 (tp) cc_final: 0.6912 (pp) REVERT: A 869 MET cc_start: 0.8614 (ttp) cc_final: 0.8168 (ttp) REVERT: A 900 MET cc_start: 0.8686 (ppp) cc_final: 0.7908 (ppp) REVERT: A 984 LEU cc_start: 0.8173 (tt) cc_final: 0.7515 (mt) REVERT: A 1019 ARG cc_start: 0.8424 (tmm160) cc_final: 0.8123 (tpt170) REVERT: D 9 ILE cc_start: 0.8565 (mt) cc_final: 0.8296 (tp) REVERT: D 23 GLU cc_start: 0.5436 (tp30) cc_final: 0.5209 (tp30) REVERT: D 35 PHE cc_start: 0.6923 (t80) cc_final: 0.6616 (t80) REVERT: E 36 MET cc_start: 0.1105 (tpt) cc_final: 0.0540 (ttt) REVERT: H 4 TRP cc_start: 0.5871 (m-90) cc_final: 0.5222 (m-10) REVERT: H 8 LYS cc_start: 0.8883 (mttt) cc_final: 0.8145 (mmmt) REVERT: I 11 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8043 (mm-30) REVERT: I 13 MET cc_start: 0.7962 (tpt) cc_final: 0.7558 (tpt) REVERT: F 34 GLU cc_start: 0.5974 (mt-10) cc_final: 0.5717 (mm-30) REVERT: G 26 MET cc_start: -0.4374 (mtt) cc_final: -0.4786 (tpp) outliers start: 15 outliers final: 2 residues processed: 345 average time/residue: 0.1893 time to fit residues: 102.0859 Evaluate side-chains 175 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 172 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 121 ASN B 439 ASN B 450 ASN B 644 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 134 GLN C 388 ASN C 460 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 HIS C 641 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1064 HIS ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 493 GLN A 690 GLN A 751 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1048 HIS A1054 GLN A1142 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.090717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.071137 restraints weight = 110636.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.070451 restraints weight = 124017.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.070985 restraints weight = 121525.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.070735 restraints weight = 86316.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.070930 restraints weight = 85407.856| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27142 Z= 0.170 Angle : 0.838 21.115 36987 Z= 0.413 Chirality : 0.051 0.379 4291 Planarity : 0.005 0.064 4689 Dihedral : 6.433 53.828 3545 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.03 % Favored : 89.91 % Rotamer: Outliers : 0.28 % Allowed : 8.41 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.35 (0.13), residues: 3230 helix: -1.92 (0.16), residues: 786 sheet: -2.88 (0.21), residues: 483 loop : -3.49 (0.12), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 357 TYR 0.023 0.002 TYR B 380 PHE 0.027 0.002 PHE A 275 TRP 0.022 0.002 TRP G 4 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (27059) covalent geometry : angle 0.77364 / 0.40 (36776) SS BOND : bond 0.00526 / 0.35 ( 38) SS BOND : angle 1.91958 / 1.27 ( 76) hydrogen bonds : bond 0.05760 / 3.81 ( 749) hydrogen bonds : angle 7.17183 / 4.86 ( 2091) link_NAG-ASN : bond 0.00803 / 0.48 ( 39) link_NAG-ASN : angle 5.58554 / 3.61 ( 117) link_TRANS : bond 0.00156 / 0.11 ( 6) link_TRANS : angle 0.90446 / 0.55 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 279 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 TYR cc_start: 0.7515 (m-10) cc_final: 0.7024 (m-10) REVERT: B 54 LEU cc_start: 0.6745 (tp) cc_final: 0.6165 (tt) REVERT: B 153 MET cc_start: 0.5202 (ptt) cc_final: 0.2622 (mpt) REVERT: B 207 HIS cc_start: 0.7863 (p90) cc_final: 0.7628 (p90) REVERT: B 319 ARG cc_start: 0.7270 (mpp-170) cc_final: 0.6538 (ptt90) REVERT: B 560 LEU cc_start: 0.7692 (mt) cc_final: 0.7252 (mp) REVERT: B 819 GLU cc_start: 0.8265 (pt0) cc_final: 0.7962 (pt0) REVERT: B 1029 MET cc_start: 0.8788 (tmm) cc_final: 0.8486 (tmm) REVERT: C 160 TYR cc_start: 0.6179 (m-10) cc_final: 0.5844 (m-80) REVERT: C 900 MET cc_start: 0.8269 (mmt) cc_final: 0.8045 (mmt) REVERT: A 193 VAL cc_start: 0.8974 (t) cc_final: 0.8761 (p) REVERT: A 353 TRP cc_start: 0.4076 (p-90) cc_final: 0.3743 (p-90) REVERT: A 466 ARG cc_start: 0.4643 (mtt180) cc_final: 0.2766 (mtm180) REVERT: A 954 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7802 (pt0) REVERT: A 984 LEU cc_start: 0.7962 (tt) cc_final: 0.7273 (mt) REVERT: A 1119 ASN cc_start: 0.8556 (p0) cc_final: 0.8102 (m-40) REVERT: D 8 LYS cc_start: 0.7493 (tptp) cc_final: 0.7218 (tppt) REVERT: D 9 ILE cc_start: 0.8357 (mt) cc_final: 0.8132 (mt) REVERT: D 10 TYR cc_start: 0.7301 (t80) cc_final: 0.6936 (t80) REVERT: D 12 ILE cc_start: 0.8043 (mt) cc_final: 0.7797 (mt) REVERT: D 14 ARG cc_start: 0.8044 (ptm-80) cc_final: 0.7505 (ttp-110) REVERT: D 26 MET cc_start: 0.7451 (tpt) cc_final: 0.7193 (tpt) REVERT: E 36 MET cc_start: 0.1249 (tpt) cc_final: 0.0781 (ttt) REVERT: H 4 TRP cc_start: 0.5608 (m-90) cc_final: 0.5098 (m-10) REVERT: H 8 LYS cc_start: 0.8771 (mttt) cc_final: 0.7839 (mmmt) REVERT: H 23 GLU cc_start: 0.7706 (pm20) cc_final: 0.6822 (pm20) REVERT: F 4 TRP cc_start: 0.3927 (t-100) cc_final: 0.3670 (t60) REVERT: G 10 TYR cc_start: 0.5235 (t80) cc_final: 0.4996 (t80) REVERT: G 14 ARG cc_start: 0.6104 (mmt-90) cc_final: 0.5318 (ppt170) REVERT: G 15 LEU cc_start: 0.6628 (tt) cc_final: 0.5519 (tt) REVERT: G 26 MET cc_start: -0.4187 (mtt) cc_final: -0.4631 (tpp) outliers start: 8 outliers final: 3 residues processed: 287 average time/residue: 0.1778 time to fit residues: 81.5057 Evaluate side-chains 173 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 169 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 219 optimal weight: 9.9990 chunk 59 optimal weight: 0.4980 chunk 192 optimal weight: 1.9990 chunk 309 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 281 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 259 optimal weight: 0.9990 chunk 221 optimal weight: 6.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.091205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.071452 restraints weight = 110156.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.070807 restraints weight = 123185.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.071395 restraints weight = 121102.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.071321 restraints weight = 84482.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.071464 restraints weight = 83155.458| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27142 Z= 0.159 Angle : 0.787 20.961 36987 Z= 0.382 Chirality : 0.050 0.660 4291 Planarity : 0.005 0.076 4689 Dihedral : 5.971 44.159 3545 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.06 % Favored : 89.91 % Rotamer: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.80 (0.13), residues: 3230 helix: -1.36 (0.17), residues: 788 sheet: -2.43 (0.21), residues: 502 loop : -3.21 (0.12), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 577 TYR 0.031 0.002 TYR I 10 PHE 0.020 0.002 PHE C 377 TRP 0.020 0.002 TRP G 4 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (27059) covalent geometry : angle 0.71586 / 0.37 (36776) SS BOND : bond 0.00620 / 0.38 ( 38) SS BOND : angle 1.79575 / 1.17 ( 76) hydrogen bonds : bond 0.04973 / 3.31 ( 749) hydrogen bonds : angle 6.49070 / 4.41 ( 2091) link_NAG-ASN : bond 0.00991 / 0.55 ( 39) link_NAG-ASN : angle 5.70367 / 3.96 ( 117) link_TRANS : bond 0.00116 / 0.07 ( 6) link_TRANS : angle 0.73497 / 0.44 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 LEU cc_start: 0.6843 (tp) cc_final: 0.6448 (tt) REVERT: B 102 ARG cc_start: 0.3539 (ptt180) cc_final: 0.3048 (ptt90) REVERT: B 153 MET cc_start: 0.5346 (ptt) cc_final: 0.2800 (mpt) REVERT: B 319 ARG cc_start: 0.7263 (mpp-170) cc_final: 0.6415 (ptt90) REVERT: B 560 LEU cc_start: 0.7664 (mt) cc_final: 0.7207 (mp) REVERT: B 819 GLU cc_start: 0.8195 (pt0) cc_final: 0.7947 (pt0) REVERT: B 936 ASP cc_start: 0.6674 (t0) cc_final: 0.6411 (t0) REVERT: B 1029 MET cc_start: 0.8779 (tmm) cc_final: 0.8370 (tmm) REVERT: C 38 TYR cc_start: 0.8603 (m-10) cc_final: 0.8280 (m-10) REVERT: C 160 TYR cc_start: 0.6198 (m-10) cc_final: 0.5926 (m-80) REVERT: C 353 TRP cc_start: 0.3314 (p-90) cc_final: 0.3100 (p-90) REVERT: C 454 ARG cc_start: 0.5109 (tpm170) cc_final: 0.4284 (ttm-80) REVERT: A 517 LEU cc_start: 0.7278 (tp) cc_final: 0.6772 (pt) REVERT: A 811 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7552 (mmmt) REVERT: A 900 MET cc_start: 0.8309 (ppp) cc_final: 0.7186 (ppp) REVERT: A 984 LEU cc_start: 0.7844 (tt) cc_final: 0.7141 (mt) REVERT: A 1119 ASN cc_start: 0.8528 (p0) cc_final: 0.8150 (m-40) REVERT: D 8 LYS cc_start: 0.7313 (tptp) cc_final: 0.7107 (tppt) REVERT: D 10 TYR cc_start: 0.7298 (t80) cc_final: 0.7096 (t80) REVERT: D 12 ILE cc_start: 0.8049 (mt) cc_final: 0.7813 (mt) REVERT: D 14 ARG cc_start: 0.8144 (ptm-80) cc_final: 0.7575 (ttp-110) REVERT: E 7 GLN cc_start: 0.7526 (pm20) cc_final: 0.7068 (pm20) REVERT: H 4 TRP cc_start: 0.5478 (m-90) cc_final: 0.5033 (m-10) REVERT: H 8 LYS cc_start: 0.8731 (mttt) cc_final: 0.7902 (mmmt) REVERT: H 23 GLU cc_start: 0.7692 (pm20) cc_final: 0.7299 (pm20) REVERT: H 26 MET cc_start: 0.7730 (ttt) cc_final: 0.7439 (ttm) REVERT: F 3 GLU cc_start: 0.3802 (tp30) cc_final: 0.1568 (pm20) REVERT: G 26 MET cc_start: -0.4241 (mtt) cc_final: -0.4655 (tpp) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.1776 time to fit residues: 73.7134 Evaluate side-chains 171 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 98 optimal weight: 7.9990 chunk 252 optimal weight: 7.9990 chunk 316 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 305 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 192 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 249 optimal weight: 8.9990 chunk 101 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 HIS C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN C1064 HIS ** C1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 935 GLN A1048 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.087876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.067666 restraints weight = 110689.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.066764 restraints weight = 139768.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.067354 restraints weight = 117979.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.067530 restraints weight = 95703.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.067788 restraints weight = 85957.496| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 27142 Z= 0.251 Angle : 0.870 20.602 36987 Z= 0.423 Chirality : 0.053 0.801 4291 Planarity : 0.005 0.068 4689 Dihedral : 6.203 54.368 3545 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.04 % Favored : 87.93 % Rotamer: Outliers : 0.03 % Allowed : 6.95 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.75 (0.13), residues: 3230 helix: -1.35 (0.17), residues: 798 sheet: -2.43 (0.21), residues: 519 loop : -3.17 (0.13), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 403 TYR 0.026 0.002 TYR C1067 PHE 0.032 0.002 PHE A 759 TRP 0.015 0.002 TRP G 4 HIS 0.010 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.25 (27059) covalent geometry : angle 0.80459 / 0.41 (36776) SS BOND : bond 0.00910 / 0.61 ( 38) SS BOND : angle 2.08700 / 1.42 ( 76) hydrogen bonds : bond 0.05056 / 3.33 ( 749) hydrogen bonds : angle 6.34827 / 4.31 ( 2091) link_NAG-ASN : bond 0.00906 / 0.53 ( 39) link_NAG-ASN : angle 5.74758 / 3.93 ( 117) link_TRANS : bond 0.00170 / 0.11 ( 6) link_TRANS : angle 0.77209 / 0.45 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 TYR cc_start: 0.7807 (m-10) cc_final: 0.7578 (m-10) REVERT: B 319 ARG cc_start: 0.7163 (mpp-170) cc_final: 0.6369 (ptt90) REVERT: B 560 LEU cc_start: 0.7893 (mt) cc_final: 0.7467 (mp) REVERT: B 740 MET cc_start: 0.7991 (mmm) cc_final: 0.7776 (mmm) REVERT: B 900 MET cc_start: 0.9127 (mmm) cc_final: 0.8782 (tpp) REVERT: B 936 ASP cc_start: 0.6771 (t0) cc_final: 0.6536 (t0) REVERT: B 1029 MET cc_start: 0.8397 (tmm) cc_final: 0.8018 (tmm) REVERT: C 900 MET cc_start: 0.8201 (mmt) cc_final: 0.7893 (mmt) REVERT: A 517 LEU cc_start: 0.7424 (tp) cc_final: 0.7004 (pp) REVERT: A 900 MET cc_start: 0.8245 (ppp) cc_final: 0.7195 (ppp) REVERT: A 984 LEU cc_start: 0.8051 (tt) cc_final: 0.7290 (mt) REVERT: D 8 LYS cc_start: 0.7393 (tptp) cc_final: 0.7179 (tppt) REVERT: D 12 ILE cc_start: 0.8137 (mt) cc_final: 0.7882 (mt) REVERT: D 36 MET cc_start: 0.6635 (mtp) cc_final: 0.6314 (mtp) REVERT: E 7 GLN cc_start: 0.7364 (pm20) cc_final: 0.6941 (pm20) REVERT: H 4 TRP cc_start: 0.5670 (m-90) cc_final: 0.5280 (m100) REVERT: H 8 LYS cc_start: 0.8801 (mttt) cc_final: 0.7969 (mmmt) REVERT: H 26 MET cc_start: 0.8088 (ttt) cc_final: 0.7728 (ttm) REVERT: I 7 GLN cc_start: 0.7800 (tm-30) cc_final: 0.7594 (pt0) REVERT: I 14 ARG cc_start: 0.8075 (mmt180) cc_final: 0.7804 (mtt180) outliers start: 1 outliers final: 1 residues processed: 225 average time/residue: 0.1728 time to fit residues: 62.7002 Evaluate side-chains 158 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 15 optimal weight: 0.5980 chunk 151 optimal weight: 9.9990 chunk 212 optimal weight: 6.9990 chunk 188 optimal weight: 0.7980 chunk 180 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 234 optimal weight: 6.9990 chunk 279 optimal weight: 0.0470 chunk 270 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 247 optimal weight: 4.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 448 ASN B 774 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 935 GLN A1048 HIS A1054 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.091310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.070477 restraints weight = 109615.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.069772 restraints weight = 136863.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.070201 restraints weight = 115834.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.070494 restraints weight = 96290.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.070845 restraints weight = 85133.498| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 27142 Z= 0.131 Angle : 0.762 20.264 36987 Z= 0.364 Chirality : 0.049 0.595 4291 Planarity : 0.005 0.067 4689 Dihedral : 5.771 56.901 3545 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.13), residues: 3230 helix: -0.89 (0.18), residues: 785 sheet: -2.06 (0.20), residues: 529 loop : -2.94 (0.13), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 509 TYR 0.030 0.002 TYR D 33 PHE 0.020 0.001 PHE C 456 TRP 0.030 0.002 TRP C 353 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (27059) covalent geometry : angle 0.68858 / 0.35 (36776) SS BOND : bond 0.00496 / 0.32 ( 38) SS BOND : angle 2.02227 / 1.32 ( 76) hydrogen bonds : bond 0.04237 / 2.78 ( 749) hydrogen bonds : angle 5.85765 / 3.98 ( 2091) link_NAG-ASN : bond 0.00962 / 0.57 ( 39) link_NAG-ASN : angle 5.64874 / 3.82 ( 117) link_TRANS : bond 0.00114 / 0.07 ( 6) link_TRANS : angle 0.72345 / 0.43 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 191 GLU cc_start: 0.6669 (mm-30) cc_final: 0.6279 (mm-30) REVERT: B 319 ARG cc_start: 0.7110 (mpp-170) cc_final: 0.6528 (ptt90) REVERT: B 360 ASN cc_start: 0.7256 (m110) cc_final: 0.6662 (p0) REVERT: B 456 PHE cc_start: 0.4306 (m-80) cc_final: 0.4015 (m-80) REVERT: B 560 LEU cc_start: 0.7697 (mt) cc_final: 0.7234 (mp) REVERT: B 563 GLN cc_start: 0.8346 (mp10) cc_final: 0.8055 (mm-40) REVERT: B 707 TYR cc_start: 0.8389 (t80) cc_final: 0.8030 (t80) REVERT: B 740 MET cc_start: 0.7829 (mmm) cc_final: 0.7592 (mmm) REVERT: B 936 ASP cc_start: 0.6804 (t0) cc_final: 0.6522 (t0) REVERT: B 1029 MET cc_start: 0.8588 (tmm) cc_final: 0.8385 (tmm) REVERT: B 1050 MET cc_start: 0.8817 (ptm) cc_final: 0.8557 (ptm) REVERT: C 160 TYR cc_start: 0.6606 (m-10) cc_final: 0.6293 (m-80) REVERT: C 900 MET cc_start: 0.8242 (mmt) cc_final: 0.7938 (mmt) REVERT: A 238 PHE cc_start: 0.7951 (p90) cc_final: 0.7404 (p90) REVERT: A 366 SER cc_start: 0.7554 (m) cc_final: 0.7345 (p) REVERT: A 517 LEU cc_start: 0.7403 (tp) cc_final: 0.7036 (pp) REVERT: A 811 LYS cc_start: 0.8240 (mmtt) cc_final: 0.7592 (mmmt) REVERT: A 900 MET cc_start: 0.8032 (ppp) cc_final: 0.7092 (ppp) REVERT: A 984 LEU cc_start: 0.7996 (tt) cc_final: 0.7153 (mt) REVERT: A 1119 ASN cc_start: 0.8598 (p0) cc_final: 0.8089 (m-40) REVERT: D 12 ILE cc_start: 0.8109 (mt) cc_final: 0.7872 (mt) REVERT: D 14 ARG cc_start: 0.8068 (ptm-80) cc_final: 0.7868 (ttp-110) REVERT: E 14 ARG cc_start: 0.8586 (mtt180) cc_final: 0.8044 (mtm110) REVERT: H 4 TRP cc_start: 0.5792 (m-90) cc_final: 0.5159 (m100) REVERT: H 8 LYS cc_start: 0.8808 (mttt) cc_final: 0.7973 (mmmt) REVERT: H 26 MET cc_start: 0.7772 (ttt) cc_final: 0.7380 (ttm) REVERT: I 7 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7318 (pt0) REVERT: I 8 LYS cc_start: 0.7598 (mppt) cc_final: 0.7357 (mmtp) REVERT: F 38 LYS cc_start: 0.7008 (mtmm) cc_final: 0.6173 (mttt) REVERT: G 26 MET cc_start: -0.3938 (mtt) cc_final: -0.4972 (tpp) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.1784 time to fit residues: 73.9457 Evaluate side-chains 171 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 184 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 209 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 239 optimal weight: 0.6980 chunk 241 optimal weight: 0.9980 chunk 126 optimal weight: 0.5980 chunk 142 optimal weight: 8.9990 chunk 295 optimal weight: 2.9990 chunk 253 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 HIS ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 935 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.090648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.069849 restraints weight = 109413.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.069152 restraints weight = 131277.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.069540 restraints weight = 112683.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.069864 restraints weight = 94864.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.070054 restraints weight = 83623.105| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27142 Z= 0.142 Angle : 0.744 20.278 36987 Z= 0.355 Chirality : 0.048 0.420 4291 Planarity : 0.005 0.066 4689 Dihedral : 5.595 58.732 3545 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.14), residues: 3230 helix: -0.65 (0.18), residues: 779 sheet: -1.90 (0.21), residues: 537 loop : -2.83 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 815 TYR 0.032 0.002 TYR A 495 PHE 0.040 0.002 PHE C 823 TRP 0.036 0.002 TRP C 353 HIS 0.010 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (27059) covalent geometry : angle 0.67811 / 0.34 (36776) SS BOND : bond 0.00440 / 0.27 ( 38) SS BOND : angle 1.85891 / 1.24 ( 76) hydrogen bonds : bond 0.04023 / 2.65 ( 749) hydrogen bonds : angle 5.68043 / 3.87 ( 2091) link_NAG-ASN : bond 0.00934 / 0.55 ( 39) link_NAG-ASN : angle 5.32020 / 3.41 ( 117) link_TRANS : bond 0.00120 / 0.08 ( 6) link_TRANS : angle 0.63267 / 0.37 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 LEU cc_start: 0.6653 (tp) cc_final: 0.6212 (tt) REVERT: B 191 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6448 (mm-30) REVERT: B 319 ARG cc_start: 0.7025 (mpp-170) cc_final: 0.6566 (ptt90) REVERT: B 360 ASN cc_start: 0.7317 (m110) cc_final: 0.6704 (p0) REVERT: B 456 PHE cc_start: 0.4211 (m-80) cc_final: 0.3764 (m-80) REVERT: B 560 LEU cc_start: 0.7724 (mt) cc_final: 0.7287 (mp) REVERT: B 707 TYR cc_start: 0.8462 (t80) cc_final: 0.8171 (t80) REVERT: B 740 MET cc_start: 0.7688 (mmm) cc_final: 0.7401 (mmm) REVERT: B 895 GLN cc_start: 0.9041 (pm20) cc_final: 0.8725 (pm20) REVERT: B 936 ASP cc_start: 0.6827 (t0) cc_final: 0.6590 (t0) REVERT: B 1050 MET cc_start: 0.8964 (ptm) cc_final: 0.8743 (ptm) REVERT: C 38 TYR cc_start: 0.8755 (m-80) cc_final: 0.8501 (m-10) REVERT: C 160 TYR cc_start: 0.6632 (m-10) cc_final: 0.6339 (m-80) REVERT: C 900 MET cc_start: 0.8254 (mmt) cc_final: 0.7969 (mmt) REVERT: A 238 PHE cc_start: 0.7982 (p90) cc_final: 0.7451 (p90) REVERT: A 366 SER cc_start: 0.7530 (m) cc_final: 0.7287 (p) REVERT: A 663 ASP cc_start: 0.8885 (p0) cc_final: 0.8030 (t0) REVERT: A 984 LEU cc_start: 0.7986 (tt) cc_final: 0.7145 (mt) REVERT: A 985 ASP cc_start: 0.7723 (t0) cc_final: 0.7509 (t70) REVERT: D 14 ARG cc_start: 0.8188 (ptm-80) cc_final: 0.7860 (ttp-110) REVERT: D 26 MET cc_start: 0.7718 (mmm) cc_final: 0.7508 (mmm) REVERT: E 12 ILE cc_start: 0.8919 (mt) cc_final: 0.8667 (mt) REVERT: E 14 ARG cc_start: 0.8668 (mtt180) cc_final: 0.8180 (mtm110) REVERT: H 4 TRP cc_start: 0.5793 (m-90) cc_final: 0.5152 (m100) REVERT: H 8 LYS cc_start: 0.8776 (mttt) cc_final: 0.7958 (mmmt) REVERT: I 7 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7453 (pt0) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.1732 time to fit residues: 65.9552 Evaluate side-chains 164 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 57 optimal weight: 8.9990 chunk 157 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 300 optimal weight: 2.9990 chunk 204 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 chunk 249 optimal weight: 8.9990 chunk 28 optimal weight: 30.0000 chunk 88 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 197 optimal weight: 0.0770 overall best weight: 0.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 ASN B 563 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 935 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.092320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.072537 restraints weight = 108863.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.071659 restraints weight = 145728.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.072068 restraints weight = 139499.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.072120 restraints weight = 93199.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.072318 restraints weight = 87309.761| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27142 Z= 0.120 Angle : 0.725 20.000 36987 Z= 0.346 Chirality : 0.047 0.418 4291 Planarity : 0.004 0.065 4689 Dihedral : 5.379 59.491 3545 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.03 % Allowed : 1.92 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.14), residues: 3230 helix: -0.28 (0.19), residues: 768 sheet: -1.69 (0.21), residues: 552 loop : -2.68 (0.13), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 403 TYR 0.028 0.001 TYR D 33 PHE 0.023 0.001 PHE C 329 TRP 0.036 0.002 TRP B 104 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (27059) covalent geometry : angle 0.66058 / 0.33 (36776) SS BOND : bond 0.00361 / 0.24 ( 38) SS BOND : angle 1.69993 / 1.09 ( 76) hydrogen bonds : bond 0.03830 / 2.54 ( 749) hydrogen bonds : angle 5.50249 / 3.75 ( 2091) link_NAG-ASN : bond 0.00924 / 0.54 ( 39) link_NAG-ASN : angle 5.18427 / 3.32 ( 117) link_TRANS : bond 0.00121 / 0.07 ( 6) link_TRANS : angle 0.58606 / 0.34 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 243 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 LEU cc_start: 0.6616 (tp) cc_final: 0.6200 (tt) REVERT: B 104 TRP cc_start: 0.7218 (m-90) cc_final: 0.6891 (m-90) REVERT: B 191 GLU cc_start: 0.6795 (mm-30) cc_final: 0.6337 (mm-30) REVERT: B 319 ARG cc_start: 0.7003 (mpp-170) cc_final: 0.6537 (ptt90) REVERT: B 663 ASP cc_start: 0.6905 (p0) cc_final: 0.6487 (t70) REVERT: B 707 TYR cc_start: 0.8447 (t80) cc_final: 0.8162 (t80) REVERT: B 740 MET cc_start: 0.7685 (mmm) cc_final: 0.7371 (mmm) REVERT: B 895 GLN cc_start: 0.9033 (pm20) cc_final: 0.8789 (pm20) REVERT: B 936 ASP cc_start: 0.6825 (t0) cc_final: 0.6557 (t0) REVERT: C 160 TYR cc_start: 0.6566 (m-10) cc_final: 0.6325 (m-80) REVERT: C 434 ILE cc_start: 0.6884 (mp) cc_final: 0.5878 (mp) REVERT: C 900 MET cc_start: 0.8284 (mmt) cc_final: 0.8035 (mmt) REVERT: A 238 PHE cc_start: 0.7777 (p90) cc_final: 0.7473 (p90) REVERT: A 366 SER cc_start: 0.7528 (m) cc_final: 0.7328 (p) REVERT: A 392 PHE cc_start: 0.6753 (m-10) cc_final: 0.6423 (m-80) REVERT: A 663 ASP cc_start: 0.8800 (p0) cc_final: 0.8089 (t70) REVERT: A 811 LYS cc_start: 0.8259 (mmtt) cc_final: 0.7647 (mmmt) REVERT: A 984 LEU cc_start: 0.7707 (tt) cc_final: 0.6949 (mt) REVERT: D 14 ARG cc_start: 0.8023 (ptm-80) cc_final: 0.7398 (tpp-160) REVERT: E 10 TYR cc_start: 0.6439 (t80) cc_final: 0.6230 (t80) REVERT: E 14 ARG cc_start: 0.8718 (mtt180) cc_final: 0.8223 (mtm110) REVERT: H 4 TRP cc_start: 0.5283 (m-90) cc_final: 0.4800 (m100) REVERT: H 8 LYS cc_start: 0.8718 (mttt) cc_final: 0.7850 (mmmt) REVERT: I 7 GLN cc_start: 0.7899 (tm-30) cc_final: 0.7455 (pt0) REVERT: F 3 GLU cc_start: 0.3387 (tp30) cc_final: 0.1146 (pm20) REVERT: F 4 TRP cc_start: 0.4614 (t-100) cc_final: 0.4387 (t60) REVERT: F 36 MET cc_start: 0.6671 (ppp) cc_final: 0.5521 (ppp) REVERT: G 26 MET cc_start: -0.3821 (mtt) cc_final: -0.4831 (tpp) outliers start: 1 outliers final: 0 residues processed: 244 average time/residue: 0.1706 time to fit residues: 67.3198 Evaluate side-chains 164 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 55 optimal weight: 5.9990 chunk 310 optimal weight: 20.0000 chunk 54 optimal weight: 0.0270 chunk 24 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 204 optimal weight: 0.0670 chunk 45 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 208 optimal weight: 5.9990 overall best weight: 1.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 49 HIS ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 935 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.091265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.070305 restraints weight = 109569.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.068873 restraints weight = 120983.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.068818 restraints weight = 118286.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.069276 restraints weight = 97604.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.069414 restraints weight = 85427.630| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27142 Z= 0.135 Angle : 0.718 20.029 36987 Z= 0.344 Chirality : 0.047 0.433 4291 Planarity : 0.005 0.064 4689 Dihedral : 5.367 57.718 3545 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.03 % Allowed : 1.22 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.14), residues: 3230 helix: -0.18 (0.19), residues: 773 sheet: -1.60 (0.21), residues: 526 loop : -2.62 (0.13), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 509 TYR 0.025 0.002 TYR A 421 PHE 0.020 0.001 PHE A 400 TRP 0.026 0.002 TRP C 353 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (27059) covalent geometry : angle 0.65525 / 0.33 (36776) SS BOND : bond 0.00486 / 0.27 ( 38) SS BOND : angle 1.79445 / 1.16 ( 76) hydrogen bonds : bond 0.03773 / 2.50 ( 749) hydrogen bonds : angle 5.44055 / 3.71 ( 2091) link_NAG-ASN : bond 0.00886 / 0.52 ( 39) link_NAG-ASN : angle 5.10775 / 3.26 ( 117) link_TRANS : bond 0.00103 / 0.07 ( 6) link_TRANS : angle 0.55842 / 0.32 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 LEU cc_start: 0.6736 (tp) cc_final: 0.6263 (tt) REVERT: B 319 ARG cc_start: 0.7134 (mpp-170) cc_final: 0.6566 (ptt90) REVERT: B 456 PHE cc_start: 0.4079 (m-80) cc_final: 0.3535 (m-80) REVERT: B 707 TYR cc_start: 0.8492 (t80) cc_final: 0.8157 (t80) REVERT: B 740 MET cc_start: 0.7595 (mmm) cc_final: 0.7331 (mmm) REVERT: B 895 GLN cc_start: 0.8936 (pm20) cc_final: 0.8615 (pm20) REVERT: C 160 TYR cc_start: 0.6753 (m-10) cc_final: 0.6468 (m-80) REVERT: C 900 MET cc_start: 0.8279 (mmt) cc_final: 0.8013 (mmt) REVERT: A 238 PHE cc_start: 0.7923 (p90) cc_final: 0.7484 (p90) REVERT: A 366 SER cc_start: 0.7589 (m) cc_final: 0.7370 (p) REVERT: A 392 PHE cc_start: 0.6692 (m-10) cc_final: 0.6489 (m-80) REVERT: A 663 ASP cc_start: 0.8784 (p0) cc_final: 0.8100 (t70) REVERT: A 811 LYS cc_start: 0.8277 (mmtt) cc_final: 0.7714 (mmmt) REVERT: D 14 ARG cc_start: 0.8114 (ptm-80) cc_final: 0.7841 (ttp-110) REVERT: D 26 MET cc_start: 0.7600 (mmm) cc_final: 0.7281 (mmm) REVERT: E 14 ARG cc_start: 0.8666 (mtt180) cc_final: 0.8248 (mtm110) REVERT: H 4 TRP cc_start: 0.5840 (m-90) cc_final: 0.5123 (m100) REVERT: H 8 LYS cc_start: 0.8742 (mttt) cc_final: 0.7943 (mmmt) REVERT: H 35 PHE cc_start: 0.6119 (t80) cc_final: 0.5839 (t80) REVERT: I 7 GLN cc_start: 0.8240 (tm-30) cc_final: 0.7573 (pt0) REVERT: F 4 TRP cc_start: 0.5040 (t-100) cc_final: 0.4565 (t60) REVERT: G 10 TYR cc_start: 0.5348 (t80) cc_final: 0.4408 (t80) REVERT: G 14 ARG cc_start: 0.5674 (mmt-90) cc_final: 0.4989 (ppt170) outliers start: 1 outliers final: 0 residues processed: 230 average time/residue: 0.1687 time to fit residues: 63.8860 Evaluate side-chains 163 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 108 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 127 optimal weight: 7.9990 chunk 233 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 264 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1011 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 935 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.089554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.068957 restraints weight = 110116.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.068015 restraints weight = 142223.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.068573 restraints weight = 118622.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.068819 restraints weight = 97657.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.069157 restraints weight = 86678.717| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 27142 Z= 0.198 Angle : 0.777 20.033 36987 Z= 0.375 Chirality : 0.049 0.429 4291 Planarity : 0.005 0.065 4689 Dihedral : 5.569 55.028 3545 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.14), residues: 3230 helix: -0.40 (0.18), residues: 782 sheet: -1.62 (0.21), residues: 535 loop : -2.67 (0.13), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 509 TYR 0.022 0.002 TYR C1067 PHE 0.038 0.002 PHE A1109 TRP 0.028 0.002 TRP C 353 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (27059) covalent geometry : angle 0.71813 / 0.36 (36776) SS BOND : bond 0.00450 / 0.25 ( 38) SS BOND : angle 1.96198 / 1.29 ( 76) hydrogen bonds : bond 0.04157 / 2.76 ( 749) hydrogen bonds : angle 5.60359 / 3.80 ( 2091) link_NAG-ASN : bond 0.00852 / 0.51 ( 39) link_NAG-ASN : angle 5.11299 / 3.24 ( 117) link_TRANS : bond 0.00144 / 0.09 ( 6) link_TRANS : angle 0.59387 / 0.34 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 ARG cc_start: 0.7207 (mpp-170) cc_final: 0.6579 (ptt90) REVERT: B 740 MET cc_start: 0.7606 (mmm) cc_final: 0.7346 (mmm) REVERT: C 160 TYR cc_start: 0.6711 (m-10) cc_final: 0.6470 (m-80) REVERT: C 406 GLU cc_start: 0.6398 (tt0) cc_final: 0.6098 (tt0) REVERT: C 784 GLN cc_start: 0.8823 (mp10) cc_final: 0.8617 (mp10) REVERT: A 303 LEU cc_start: 0.9387 (tp) cc_final: 0.8765 (tt) REVERT: A 366 SER cc_start: 0.7516 (m) cc_final: 0.7310 (p) REVERT: A 663 ASP cc_start: 0.8777 (p0) cc_final: 0.7994 (t0) REVERT: A 900 MET cc_start: 0.7989 (ppp) cc_final: 0.7022 (ppp) REVERT: A 984 LEU cc_start: 0.8050 (tt) cc_final: 0.7367 (mt) REVERT: A 985 ASP cc_start: 0.7920 (t0) cc_final: 0.7671 (t0) REVERT: D 14 ARG cc_start: 0.8105 (ptm-80) cc_final: 0.7454 (tpp-160) REVERT: D 26 MET cc_start: 0.7330 (mmm) cc_final: 0.7039 (mmm) REVERT: E 10 TYR cc_start: 0.6736 (t80) cc_final: 0.6516 (t80) REVERT: E 14 ARG cc_start: 0.8755 (mtt180) cc_final: 0.8328 (mtm110) REVERT: H 4 TRP cc_start: 0.5588 (m-90) cc_final: 0.4991 (m100) REVERT: H 8 LYS cc_start: 0.8769 (mttt) cc_final: 0.7990 (mmmt) REVERT: I 7 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7450 (pt0) REVERT: I 13 MET cc_start: 0.7549 (mmp) cc_final: 0.7138 (mmm) REVERT: F 4 TRP cc_start: 0.4782 (t-100) cc_final: 0.4377 (t60) REVERT: F 26 MET cc_start: -0.0617 (mmt) cc_final: -0.0850 (mmt) REVERT: G 10 TYR cc_start: 0.5391 (t80) cc_final: 0.4365 (t80) REVERT: G 14 ARG cc_start: 0.5823 (mmt-90) cc_final: 0.5102 (ppt170) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.1711 time to fit residues: 59.3779 Evaluate side-chains 154 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 156 optimal weight: 6.9990 chunk 231 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 37 optimal weight: 0.0670 chunk 306 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 245 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 45 optimal weight: 0.0970 chunk 60 optimal weight: 10.0000 overall best weight: 1.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 935 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.091523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.070687 restraints weight = 109156.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.068886 restraints weight = 104872.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.069102 restraints weight = 104761.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.069250 restraints weight = 94131.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.069419 restraints weight = 85243.501| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27142 Z= 0.124 Angle : 0.737 19.702 36987 Z= 0.349 Chirality : 0.049 0.790 4291 Planarity : 0.005 0.065 4689 Dihedral : 5.359 55.650 3545 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.14), residues: 3230 helix: -0.12 (0.19), residues: 786 sheet: -1.56 (0.21), residues: 549 loop : -2.59 (0.13), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 815 TYR 0.027 0.001 TYR C 873 PHE 0.040 0.001 PHE B 823 TRP 0.025 0.001 TRP C 353 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (27059) covalent geometry : angle 0.67521 / 0.33 (36776) SS BOND : bond 0.00471 / 0.29 ( 38) SS BOND : angle 1.82443 / 1.23 ( 76) hydrogen bonds : bond 0.03769 / 2.50 ( 749) hydrogen bonds : angle 5.42271 / 3.70 ( 2091) link_NAG-ASN : bond 0.00877 / 0.51 ( 39) link_NAG-ASN : angle 5.11668 / 3.26 ( 117) link_TRANS : bond 0.00100 / 0.06 ( 6) link_TRANS : angle 0.54625 / 0.32 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6460 Ramachandran restraints generated. 3230 Oldfield, 0 Emsley, 3230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 ARG cc_start: 0.7292 (mpp-170) cc_final: 0.6459 (ptt90) REVERT: B 707 TYR cc_start: 0.8506 (t80) cc_final: 0.8175 (t80) REVERT: B 740 MET cc_start: 0.7605 (mmm) cc_final: 0.7320 (mmm) REVERT: B 819 GLU cc_start: 0.8456 (pt0) cc_final: 0.8228 (pt0) REVERT: B 1029 MET cc_start: 0.8448 (tmm) cc_final: 0.8239 (tmm) REVERT: B 1050 MET cc_start: 0.8709 (ptm) cc_final: 0.8380 (ptm) REVERT: C 406 GLU cc_start: 0.6719 (tt0) cc_final: 0.6240 (tt0) REVERT: A 238 PHE cc_start: 0.7857 (p90) cc_final: 0.7480 (p90) REVERT: A 303 LEU cc_start: 0.9374 (tp) cc_final: 0.8741 (tt) REVERT: A 663 ASP cc_start: 0.8741 (p0) cc_final: 0.7799 (t70) REVERT: A 984 LEU cc_start: 0.7999 (tt) cc_final: 0.7318 (mt) REVERT: A 985 ASP cc_start: 0.7918 (t0) cc_final: 0.7657 (t0) REVERT: D 14 ARG cc_start: 0.8098 (ptm-80) cc_final: 0.7501 (tpp-160) REVERT: D 26 MET cc_start: 0.7527 (mmm) cc_final: 0.7215 (mmm) REVERT: E 10 TYR cc_start: 0.6814 (t80) cc_final: 0.6595 (t80) REVERT: E 14 ARG cc_start: 0.8737 (mtt180) cc_final: 0.8322 (mtm110) REVERT: H 4 TRP cc_start: 0.5884 (m-90) cc_final: 0.5163 (m100) REVERT: H 8 LYS cc_start: 0.8705 (mttt) cc_final: 0.7961 (mmmt) REVERT: I 11 GLU cc_start: 0.8362 (pp20) cc_final: 0.8148 (mm-30) REVERT: I 13 MET cc_start: 0.7805 (mmp) cc_final: 0.7305 (mmm) REVERT: F 4 TRP cc_start: 0.5062 (t-100) cc_final: 0.4582 (t60) REVERT: F 26 MET cc_start: -0.0817 (mmt) cc_final: -0.1019 (mmt) REVERT: G 7 GLN cc_start: 0.6794 (tp-100) cc_final: 0.6466 (mm110) REVERT: G 10 TYR cc_start: 0.5153 (t80) cc_final: 0.4111 (t80) REVERT: G 14 ARG cc_start: 0.5931 (mmt-90) cc_final: 0.5257 (ppt170) REVERT: G 15 LEU cc_start: 0.6618 (tt) cc_final: 0.5656 (tt) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.1733 time to fit residues: 64.2658 Evaluate side-chains 158 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 50 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 26 optimal weight: 0.0370 chunk 61 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 215 optimal weight: 20.0000 chunk 266 optimal weight: 1.9990 chunk 207 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 HIS ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.090518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.069837 restraints weight = 108851.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.069260 restraints weight = 117004.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.068832 restraints weight = 105801.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.068441 restraints weight = 100807.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.068865 restraints weight = 87713.283| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27142 Z= 0.151 Angle : 0.747 19.719 36987 Z= 0.356 Chirality : 0.049 0.519 4291 Planarity : 0.005 0.065 4689 Dihedral : 5.405 54.816 3545 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.14), residues: 3230 helix: -0.18 (0.19), residues: 791 sheet: -1.48 (0.21), residues: 560 loop : -2.63 (0.13), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 454 TYR 0.030 0.002 TYR C 873 PHE 0.033 0.002 PHE B 823 TRP 0.025 0.001 TRP C 353 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (27059) covalent geometry : angle 0.68942 / 0.34 (36776) SS BOND : bond 0.00371 / 0.21 ( 38) SS BOND : angle 1.82593 / 1.23 ( 76) hydrogen bonds : bond 0.03926 / 2.63 ( 749) hydrogen bonds : angle 5.47487 / 3.73 ( 2091) link_NAG-ASN : bond 0.00852 / 0.50 ( 39) link_NAG-ASN : angle 4.98649 / 3.17 ( 117) link_TRANS : bond 0.00102 / 0.07 ( 6) link_TRANS : angle 0.55181 / 0.32 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3617.19 seconds wall clock time: 64 minutes 30.05 seconds (3870.05 seconds total)