Starting phenix.real_space_refine on Mon Jun 23 01:10:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x7n_33042/06_2025/7x7n_33042.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x7n_33042/06_2025/7x7n_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_33042/06_2025/7x7n_33042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x7n_33042/06_2025/7x7n_33042.map" model { file = "/net/cci-nas-00/data/ceres_data/7x7n_33042/06_2025/7x7n_33042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x7n_33042/06_2025/7x7n_33042.cif" } resolution = 4.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG: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: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG: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: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG: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} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 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} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 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} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 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} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 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} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 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} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 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 dihedrals: 39 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 dihedrals: 39 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 dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 16.04, per 1000 atoms: 0.61 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: 7.46 Conformation dependent library (CDL) restraints added in 3.5 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: 3.90 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: 11.69 Time building geometry restraints manager: 8.78 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 - 22.82: 15429 22.82 - 45.64: 1049 45.64 - 68.46: 140 68.46 - 91.28: 44 91.28 - 114.10: 18 Dihedral angle restraints: 16680 sinusoidal: 7010 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 16677 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 1149 or resid 1301 thr \ ough 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 1149 o \ r resid 1301 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 1149 o \ r resid 1301 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: 0.820 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: 1.180 Check model and map are aligned: 0.200 Set scattering table: 0.280 Process input model: 64.130 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.190 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 : 15.668 114.104 10312 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 29.11 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.025 0.002 TRP A 353 HIS 0.012 0.002 HIS C1064 PHE 0.032 0.003 PHE A 759 TYR 0.031 0.003 TYR A 421 ARG 0.010 0.001 ARG A 577 Details of bonding type rmsd link_TRANS : bond 0.00228 ( 6) link_TRANS : angle 0.92522 ( 18) link_NAG-ASN : bond 0.01153 ( 39) link_NAG-ASN : angle 5.95565 ( 117) hydrogen bonds : bond 0.30088 ( 749) hydrogen bonds : angle 11.05451 ( 2091) SS BOND : bond 0.00859 ( 38) SS BOND : angle 2.57637 ( 76) covalent geometry : bond 0.01330 (27059) covalent geometry : angle 1.05400 (36776) *********************** 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 : 2.952 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: 0.7526 (mpp-170) cc_final: 0.6644 (ptt90) REVERT: B 486 PHE cc_start: 0.6829 (p90) cc_final: 0.6447 (m-80) REVERT: B 489 TYR cc_start: 0.5872 (m-80) cc_final: 0.5649 (m-80) REVERT: B 740 MET cc_start: 0.8195 (mmm) cc_final: 0.7991 (mmm) REVERT: C 160 TYR cc_start: 0.6208 (m-10) cc_final: 0.5859 (m-80) REVERT: C 280 ASN cc_start: 0.6946 (p0) cc_final: 0.6390 (p0) REVERT: C 454 ARG cc_start: 0.5139 (tpm170) cc_final: 0.4356 (ttm-80) REVERT: C 528 LYS cc_start: 0.6022 (OUTLIER) cc_final: 0.4969 (mmtp) REVERT: C 904 TYR cc_start: 0.7794 (t80) cc_final: 0.7477 (t80) REVERT: A 226 LEU cc_start: 0.8254 (mt) cc_final: 0.8001 (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: 0.8167 (ttp) REVERT: A 900 MET cc_start: 0.8686 (ppp) cc_final: 0.7907 (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: 0.8121 (tpt170) REVERT: D 9 ILE cc_start: 0.8564 (mt) cc_final: 0.8297 (tp) REVERT: D 23 GLU cc_start: 0.5436 (tp30) cc_final: 0.5194 (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: 0.0541 (ttt) REVERT: H 4 TRP cc_start: 0.5871 (m-90) cc_final: 0.5221 (m-10) REVERT: H 8 LYS cc_start: 0.8883 (mttt) cc_final: 0.8144 (mmmt) REVERT: I 11 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7963 (mm-30) REVERT: I 13 MET cc_start: 0.7962 (tpt) cc_final: 0.7556 (tpt) REVERT: F 34 GLU cc_start: 0.5974 (mt-10) cc_final: 0.5718 (mm-30) REVERT: G 26 MET cc_start: -0.4374 (mtt) cc_final: -0.4787 (tpp) outliers start: 15 outliers final: 2 residues processed: 345 average time/residue: 0.4149 time to fit residues: 222.2295 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 : 3.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 0.6980 chunk 242 optimal weight: 30.0000 chunk 134 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 chunk 129 optimal weight: 20.0000 chunk 250 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 186 optimal weight: 0.9990 chunk 290 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B 439 ASN B 450 ASN B 644 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN B1064 HIS 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 H 7 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.090462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.070682 restraints weight = 110420.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.069694 restraints weight = 147412.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.070181 restraints weight = 128502.729| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2429 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= 0.175 Angle : 0.845 20.990 36987 Z= 0.415 Chirality : 0.051 0.399 4291 Planarity : 0.005 0.070 4689 Dihedral : 10.089 103.771 4364 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.12 % Favored : 89.81 % Rotamer: Outliers : 0.28 % Allowed : 8.20 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.37 (0.13), residues: 3230 helix: -1.94 (0.16), residues: 787 sheet: -2.84 (0.20), residues: 495 loop : -3.52 (0.12), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 4 HIS 0.006 0.001 HIS A 207 PHE 0.029 0.002 PHE C 329 TYR 0.021 0.002 TYR A 453 ARG 0.010 0.001 ARG B 357 Details of bonding type rmsd link_TRANS : bond 0.00166 ( 6) link_TRANS : angle 0.91873 ( 18) link_NAG-ASN : bond 0.00808 ( 39) link_NAG-ASN : angle 5.63212 ( 117) hydrogen bonds : bond 0.05810 ( 749) hydrogen bonds : angle 7.13066 ( 2091) SS BOND : bond 0.00556 ( 38) SS BOND : angle 2.08205 ( 76) covalent geometry : bond 0.00388 (27059) covalent geometry : angle 0.77967 (36776) *********************** 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 281 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 273 time to evaluate : 2.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 TYR cc_start: 0.7517 (m-10) cc_final: 0.7255 (m-10) REVERT: B 54 LEU cc_start: 0.6713 (tp) cc_final: 0.5927 (tt) REVERT: B 153 MET cc_start: 0.5300 (ptt) cc_final: 0.2779 (mpt) REVERT: B 207 HIS cc_start: 0.7941 (p90) cc_final: 0.7657 (p90) REVERT: B 319 ARG cc_start: 0.7282 (mpp-170) cc_final: 0.6523 (ptt90) REVERT: B 560 LEU cc_start: 0.7668 (mt) cc_final: 0.7217 (mp) REVERT: B 819 GLU cc_start: 0.8242 (pt0) cc_final: 0.7934 (pt0) REVERT: B 1029 MET cc_start: 0.8801 (tmm) cc_final: 0.8454 (tmm) REVERT: C 160 TYR cc_start: 0.6217 (m-10) cc_final: 0.5855 (m-80) REVERT: C 900 MET cc_start: 0.8264 (mmt) cc_final: 0.8044 (mmt) REVERT: A 353 TRP cc_start: 0.4125 (p-90) cc_final: 0.3711 (p-90) REVERT: A 466 ARG cc_start: 0.4589 (mtt180) cc_final: 0.2561 (mtm180) REVERT: A 811 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7580 (mmmt) REVERT: A 954 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7855 (pt0) REVERT: A 984 LEU cc_start: 0.7968 (tt) cc_final: 0.7281 (mt) REVERT: A 1119 ASN cc_start: 0.8583 (p0) cc_final: 0.8162 (m-40) REVERT: D 9 ILE cc_start: 0.8344 (mt) cc_final: 0.8131 (mt) REVERT: D 12 ILE cc_start: 0.8061 (mt) cc_final: 0.7841 (mt) REVERT: D 14 ARG cc_start: 0.8045 (ptm-80) cc_final: 0.7605 (ttp-110) REVERT: H 4 TRP cc_start: 0.5654 (m-90) cc_final: 0.5050 (m-10) REVERT: H 8 LYS cc_start: 0.8784 (mttt) cc_final: 0.7827 (mmmt) REVERT: H 23 GLU cc_start: 0.7697 (pm20) cc_final: 0.7116 (pm20) REVERT: H 32 ILE cc_start: 0.6992 (OUTLIER) cc_final: 0.6740 (tt) REVERT: F 4 TRP cc_start: 0.3921 (t-100) cc_final: 0.3660 (t60) REVERT: F 36 MET cc_start: 0.6120 (ppp) cc_final: 0.5015 (ttt) REVERT: G 26 MET cc_start: -0.4340 (mtt) cc_final: -0.4749 (tpp) outliers start: 8 outliers final: 3 residues processed: 281 average time/residue: 0.4121 time to fit residues: 186.0711 Evaluate side-chains 169 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 164 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 201 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 27 optimal weight: 30.0000 chunk 172 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 190 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B1002 GLN ** 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** C1054 GLN ** C1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.088602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.068222 restraints weight = 110063.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.067304 restraints weight = 134569.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.067920 restraints weight = 132594.036| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 27142 Z= 0.236 Angle : 0.857 21.462 36987 Z= 0.418 Chirality : 0.051 0.589 4291 Planarity : 0.005 0.080 4689 Dihedral : 9.199 99.099 4364 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.46 % Favored : 88.51 % Rotamer: Outliers : 0.10 % Allowed : 7.96 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.13), residues: 3230 helix: -1.48 (0.16), residues: 797 sheet: -2.52 (0.21), residues: 496 loop : -3.35 (0.12), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 4 HIS 0.009 0.001 HIS B1064 PHE 0.022 0.002 PHE A 759 TYR 0.030 0.002 TYR I 10 ARG 0.008 0.001 ARG A 577 Details of bonding type rmsd link_TRANS : bond 0.00147 ( 6) link_TRANS : angle 0.73386 ( 18) link_NAG-ASN : bond 0.00909 ( 39) link_NAG-ASN : angle 5.91187 ( 117) hydrogen bonds : bond 0.05317 ( 749) hydrogen bonds : angle 6.61864 ( 2091) SS BOND : bond 0.00574 ( 38) SS BOND : angle 1.80792 ( 76) covalent geometry : bond 0.00531 (27059) covalent geometry : angle 0.78734 (36776) *********************** 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 240 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 237 time to evaluate : 2.827 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: 0.7237 (mpp-170) cc_final: 0.6404 (ptt90) REVERT: B 560 LEU cc_start: 0.7843 (mt) cc_final: 0.7424 (mp) REVERT: B 936 ASP cc_start: 0.6860 (t0) cc_final: 0.6535 (t0) REVERT: B 1029 MET cc_start: 0.8821 (tmm) cc_final: 0.8452 (tmm) REVERT: C 38 TYR cc_start: 0.8764 (m-10) cc_final: 0.8519 (m-10) REVERT: C 160 TYR cc_start: 0.6035 (m-10) cc_final: 0.5801 (m-80) REVERT: C 353 TRP cc_start: 0.3420 (p-90) cc_final: 0.3209 (p-90) REVERT: A 517 LEU cc_start: 0.7344 (tp) cc_final: 0.6827 (pp) REVERT: A 900 MET cc_start: 0.8390 (ppp) cc_final: 0.7723 (ppp) REVERT: A 984 LEU cc_start: 0.7963 (tt) cc_final: 0.7237 (mt) REVERT: D 8 LYS cc_start: 0.7174 (tptt) cc_final: 0.6737 (tppt) REVERT: D 12 ILE cc_start: 0.8090 (mt) cc_final: 0.7869 (mt) REVERT: H 4 TRP cc_start: 0.5605 (m-90) cc_final: 0.5230 (m100) REVERT: H 8 LYS cc_start: 0.8726 (mttt) cc_final: 0.7880 (mmmt) REVERT: H 13 MET cc_start: 0.7665 (mtt) cc_final: 0.7338 (mmp) REVERT: H 26 MET cc_start: 0.7889 (ttt) cc_final: 0.7478 (ttt) REVERT: I 13 MET cc_start: 0.7139 (mmm) cc_final: 0.6873 (tpt) REVERT: I 26 MET cc_start: 0.4419 (ttt) cc_final: 0.3924 (ttt) outliers start: 3 outliers final: 0 residues processed: 238 average time/residue: 0.3836 time to fit residues: 148.0081 Evaluate side-chains 161 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 3.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 125 optimal weight: 3.9990 chunk 244 optimal weight: 9.9990 chunk 292 optimal weight: 4.9990 chunk 283 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 248 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 140 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 315 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** C1083 HIS ** 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 = 0.3613 r_free = 0.3613 target = 0.090648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.070162 restraints weight = 110567.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.069213 restraints weight = 136847.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.069755 restraints weight = 115570.173| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 27142 Z= 0.145 Angle : 0.775 20.835 36987 Z= 0.369 Chirality : 0.050 0.713 4291 Planarity : 0.005 0.068 4689 Dihedral : 8.474 101.253 4364 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.85 % Favored : 91.11 % Rotamer: Outliers : 0.07 % Allowed : 5.03 % Favored : 94.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.13), residues: 3230 helix: -1.01 (0.17), residues: 784 sheet: -2.16 (0.21), residues: 516 loop : -3.10 (0.12), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 104 HIS 0.004 0.001 HIS C1064 PHE 0.022 0.002 PHE B 490 TYR 0.022 0.002 TYR A 351 ARG 0.011 0.001 ARG B 454 Details of bonding type rmsd link_TRANS : bond 0.00131 ( 6) link_TRANS : angle 0.77625 ( 18) link_NAG-ASN : bond 0.01099 ( 39) link_NAG-ASN : angle 5.70698 ( 117) hydrogen bonds : bond 0.04390 ( 749) hydrogen bonds : angle 6.02575 ( 2091) SS BOND : bond 0.00375 ( 38) SS BOND : angle 1.96057 ( 76) covalent geometry : bond 0.00324 (27059) covalent geometry : angle 0.70106 (36776) *********************** 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 242 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 240 time to evaluate : 3.030 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 54 LEU cc_start: 0.6917 (tp) cc_final: 0.6413 (tt) REVERT: B 319 ARG cc_start: 0.7183 (mpp-170) cc_final: 0.6483 (ptt90) REVERT: B 560 LEU cc_start: 0.7758 (mt) cc_final: 0.7329 (mp) REVERT: B 562 PHE cc_start: 0.7226 (m-80) cc_final: 0.6992 (m-80) REVERT: B 936 ASP cc_start: 0.6918 (t0) cc_final: 0.6595 (t0) REVERT: B 1029 MET cc_start: 0.8621 (tmm) cc_final: 0.8233 (tmm) REVERT: C 160 TYR cc_start: 0.6469 (m-10) cc_final: 0.6235 (m-80) REVERT: C 781 VAL cc_start: 0.8001 (p) cc_final: 0.7620 (p) REVERT: C 900 MET cc_start: 0.8320 (mmt) cc_final: 0.8040 (mmt) REVERT: C 1050 MET cc_start: 0.6966 (mtm) cc_final: 0.6706 (mtm) REVERT: A 517 LEU cc_start: 0.7323 (tp) cc_final: 0.6935 (pp) REVERT: A 900 MET cc_start: 0.8302 (ppp) cc_final: 0.7238 (ppp) REVERT: A 917 TYR cc_start: 0.8929 (m-10) cc_final: 0.8726 (m-10) REVERT: A 984 LEU cc_start: 0.8177 (tt) cc_final: 0.7443 (mt) REVERT: D 12 ILE cc_start: 0.8101 (mt) cc_final: 0.7838 (mt) REVERT: D 14 ARG cc_start: 0.8068 (ptm-80) cc_final: 0.7756 (ttp-110) REVERT: H 4 TRP cc_start: 0.5827 (m-90) cc_final: 0.5368 (m100) REVERT: H 8 LYS cc_start: 0.8796 (mttt) cc_final: 0.7879 (mmmt) REVERT: H 23 GLU cc_start: 0.7891 (pm20) cc_final: 0.7303 (pm20) REVERT: H 26 MET cc_start: 0.7869 (ttt) cc_final: 0.7617 (ttm) REVERT: I 26 MET cc_start: 0.4560 (ttt) cc_final: 0.4128 (ttt) REVERT: G 26 MET cc_start: -0.3744 (mtt) cc_final: -0.4784 (tpp) outliers start: 2 outliers final: 1 residues processed: 242 average time/residue: 0.4790 time to fit residues: 192.2784 Evaluate side-chains 173 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 2.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 152 optimal weight: 10.0000 chunk 248 optimal weight: 0.4980 chunk 154 optimal weight: 5.9990 chunk 318 optimal weight: 4.9990 chunk 294 optimal weight: 0.9980 chunk 240 optimal weight: 7.9990 chunk 250 optimal weight: 20.0000 chunk 243 optimal weight: 0.5980 chunk 278 optimal weight: 0.0470 chunk 34 optimal weight: 8.9990 chunk 280 optimal weight: 1.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 ASN ** 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 644 GLN A 901 GLN A 935 GLN A1054 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.091941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.071647 restraints weight = 109031.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.070007 restraints weight = 131060.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.070181 restraints weight = 117991.769| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27142 Z= 0.124 Angle : 0.742 20.730 36987 Z= 0.352 Chirality : 0.048 0.647 4291 Planarity : 0.005 0.063 4689 Dihedral : 7.956 95.467 4364 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.14), residues: 3230 helix: -0.61 (0.18), residues: 778 sheet: -1.91 (0.21), residues: 521 loop : -2.86 (0.13), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 104 HIS 0.003 0.001 HIS A 207 PHE 0.018 0.001 PHE C 456 TYR 0.026 0.001 TYR A 495 ARG 0.008 0.000 ARG B 509 Details of bonding type rmsd link_TRANS : bond 0.00108 ( 6) link_TRANS : angle 0.67120 ( 18) link_NAG-ASN : bond 0.00993 ( 39) link_NAG-ASN : angle 5.74438 ( 117) hydrogen bonds : bond 0.03984 ( 749) hydrogen bonds : angle 5.71139 ( 2091) SS BOND : bond 0.00386 ( 38) SS BOND : angle 1.79453 ( 76) covalent geometry : bond 0.00277 (27059) covalent geometry : angle 0.66451 (36776) *********************** 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 265 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 2.748 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 54 LEU cc_start: 0.6831 (tp) cc_final: 0.6402 (tt) REVERT: B 319 ARG cc_start: 0.7083 (mpp-170) cc_final: 0.6527 (ptt90) REVERT: B 360 ASN cc_start: 0.7592 (m110) cc_final: 0.6943 (p0) REVERT: B 560 LEU cc_start: 0.7851 (mt) cc_final: 0.7292 (mp) REVERT: B 563 GLN cc_start: 0.8288 (mp10) cc_final: 0.7980 (mm-40) REVERT: B 707 TYR cc_start: 0.8375 (t80) cc_final: 0.8035 (t80) REVERT: B 900 MET cc_start: 0.9093 (mmp) cc_final: 0.8724 (mmp) REVERT: B 936 ASP cc_start: 0.6950 (t0) cc_final: 0.6644 (t0) REVERT: B 1029 MET cc_start: 0.8521 (tmm) cc_final: 0.8069 (tmm) REVERT: C 160 TYR cc_start: 0.6668 (m-10) cc_final: 0.6366 (m-80) REVERT: C 785 VAL cc_start: 0.8943 (m) cc_final: 0.8576 (p) REVERT: C 900 MET cc_start: 0.8350 (mmt) cc_final: 0.8008 (mmt) REVERT: A 238 PHE cc_start: 0.8024 (p90) cc_final: 0.7406 (p90) REVERT: A 366 SER cc_start: 0.7599 (m) cc_final: 0.7379 (p) REVERT: A 811 LYS cc_start: 0.8209 (mmtt) cc_final: 0.7616 (mmmt) REVERT: A 900 MET cc_start: 0.8136 (ppp) cc_final: 0.7077 (ppp) REVERT: A 984 LEU cc_start: 0.8224 (tt) cc_final: 0.7503 (mt) REVERT: D 11 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6590 (mt-10) REVERT: D 12 ILE cc_start: 0.8103 (mt) cc_final: 0.7870 (mt) REVERT: D 14 ARG cc_start: 0.8026 (ptm-80) cc_final: 0.7383 (tpp-160) REVERT: D 26 MET cc_start: 0.7587 (mmm) cc_final: 0.7302 (mmm) REVERT: H 4 TRP cc_start: 0.6049 (m-90) cc_final: 0.5359 (m100) REVERT: H 8 LYS cc_start: 0.8618 (mttt) cc_final: 0.7882 (mmmt) REVERT: H 13 MET cc_start: 0.7702 (mmp) cc_final: 0.7455 (mmm) REVERT: H 23 GLU cc_start: 0.7829 (pm20) cc_final: 0.7200 (pm20) REVERT: H 26 MET cc_start: 0.7963 (ttt) cc_final: 0.7511 (ttm) REVERT: I 26 MET cc_start: 0.3859 (ttt) cc_final: 0.3599 (ttt) REVERT: G 26 MET cc_start: -0.3861 (mtt) cc_final: -0.4872 (tpp) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.3543 time to fit residues: 151.5454 Evaluate side-chains 174 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 15 optimal weight: 8.9990 chunk 174 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 213 optimal weight: 0.0030 chunk 183 optimal weight: 10.0000 chunk 222 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 314 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 243 optimal weight: 0.5980 overall best weight: 3.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN 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 207 HIS 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 = 0.3598 r_free = 0.3598 target = 0.090101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.069673 restraints weight = 109622.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.069188 restraints weight = 133201.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.069582 restraints weight = 111282.240| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27142 Z= 0.173 Angle : 0.774 20.634 36987 Z= 0.369 Chirality : 0.048 0.425 4291 Planarity : 0.005 0.073 4689 Dihedral : 7.890 92.921 4364 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 0.07 % Allowed : 3.49 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.14), residues: 3230 helix: -0.59 (0.18), residues: 778 sheet: -1.78 (0.21), residues: 523 loop : -2.87 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 353 HIS 0.008 0.001 HIS A 207 PHE 0.034 0.002 PHE C 823 TYR 0.022 0.002 TYR A 351 ARG 0.006 0.001 ARG B 509 Details of bonding type rmsd link_TRANS : bond 0.00128 ( 6) link_TRANS : angle 0.61441 ( 18) link_NAG-ASN : bond 0.00975 ( 39) link_NAG-ASN : angle 5.62780 ( 117) hydrogen bonds : bond 0.04244 ( 749) hydrogen bonds : angle 5.69176 ( 2091) SS BOND : bond 0.00430 ( 38) SS BOND : angle 1.82188 ( 76) covalent geometry : bond 0.00398 (27059) covalent geometry : angle 0.70356 (36776) *********************** 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 229 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 227 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 PHE cc_start: 0.8298 (m-10) cc_final: 0.8049 (m-10) REVERT: B 319 ARG cc_start: 0.7105 (mpp-170) cc_final: 0.6583 (ptt90) REVERT: B 360 ASN cc_start: 0.7509 (m110) cc_final: 0.6959 (p0) REVERT: B 563 GLN cc_start: 0.8265 (mp10) cc_final: 0.7734 (mp10) REVERT: B 895 GLN cc_start: 0.9126 (pm20) cc_final: 0.8700 (pm20) REVERT: B 900 MET cc_start: 0.9098 (mmp) cc_final: 0.8860 (mmp) REVERT: B 936 ASP cc_start: 0.6871 (t0) cc_final: 0.6578 (t0) REVERT: C 160 TYR cc_start: 0.6612 (m-10) cc_final: 0.6345 (m-80) REVERT: C 434 ILE cc_start: 0.6933 (mp) cc_final: 0.6120 (mp) REVERT: C 868 GLU cc_start: 0.8158 (pp20) cc_final: 0.7889 (mm-30) REVERT: C 900 MET cc_start: 0.8259 (mmt) cc_final: 0.7866 (mmt) REVERT: A 351 TYR cc_start: 0.7151 (p90) cc_final: 0.6673 (p90) REVERT: A 366 SER cc_start: 0.7541 (m) cc_final: 0.7318 (p) REVERT: A 466 ARG cc_start: 0.4786 (mpp-170) cc_final: 0.4456 (mtm-85) REVERT: A 663 ASP cc_start: 0.8531 (p0) cc_final: 0.8027 (t70) REVERT: A 900 MET cc_start: 0.8020 (ppp) cc_final: 0.7032 (ppp) REVERT: A 984 LEU cc_start: 0.7811 (tt) cc_final: 0.6964 (mt) REVERT: A 985 ASP cc_start: 0.8044 (t70) cc_final: 0.7765 (t70) REVERT: D 12 ILE cc_start: 0.8019 (mt) cc_final: 0.7815 (mt) REVERT: D 14 ARG cc_start: 0.8133 (ptm-80) cc_final: 0.7873 (ttp-110) REVERT: D 26 MET cc_start: 0.7468 (mmm) cc_final: 0.7106 (mmm) REVERT: E 7 GLN cc_start: 0.7091 (OUTLIER) cc_final: 0.6720 (pm20) REVERT: E 12 ILE cc_start: 0.8969 (mt) cc_final: 0.8718 (mt) REVERT: H 4 TRP cc_start: 0.5708 (m-90) cc_final: 0.5107 (m100) REVERT: H 8 LYS cc_start: 0.8762 (mttt) cc_final: 0.7818 (mmmt) REVERT: H 23 GLU cc_start: 0.7744 (pm20) cc_final: 0.7091 (pm20) REVERT: I 26 MET cc_start: 0.4136 (ttt) cc_final: 0.3794 (ttt) outliers start: 2 outliers final: 0 residues processed: 229 average time/residue: 0.3707 time to fit residues: 137.6249 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 : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.9991 > 50: distance: 37 - 52: 24.946 distance: 41 - 57: 6.183 distance: 45 - 65: 16.188 distance: 48 - 52: 22.953 distance: 52 - 53: 19.480 distance: 53 - 54: 6.055 distance: 53 - 56: 36.531 distance: 54 - 55: 20.092 distance: 54 - 57: 11.206 distance: 55 - 78: 7.829 distance: 57 - 58: 15.269 distance: 58 - 59: 11.355 distance: 58 - 61: 17.541 distance: 59 - 60: 21.777 distance: 59 - 65: 16.909 distance: 61 - 62: 26.234 distance: 62 - 63: 19.055 distance: 62 - 64: 21.998 distance: 65 - 66: 3.260 distance: 66 - 67: 13.299 distance: 66 - 69: 15.100 distance: 67 - 68: 19.313 distance: 67 - 73: 6.252 distance: 68 - 89: 21.901 distance: 69 - 70: 9.127 distance: 70 - 71: 6.560 distance: 70 - 72: 7.937 distance: 73 - 74: 9.803 distance: 74 - 75: 7.619 distance: 74 - 77: 10.293 distance: 75 - 76: 6.579 distance: 75 - 78: 10.479 distance: 76 - 97: 25.357 distance: 78 - 79: 5.542 distance: 79 - 80: 19.003 distance: 80 - 81: 7.587 distance: 80 - 82: 28.181 distance: 82 - 83: 17.602 distance: 83 - 84: 13.333 distance: 83 - 86: 9.250 distance: 84 - 85: 12.270 distance: 84 - 89: 14.821 distance: 86 - 87: 15.120 distance: 86 - 88: 15.900 distance: 89 - 90: 14.432 distance: 90 - 91: 16.869 distance: 90 - 93: 9.088 distance: 91 - 92: 33.051 distance: 91 - 97: 26.369 distance: 93 - 94: 10.951 distance: 93 - 95: 12.435 distance: 94 - 96: 4.775 distance: 97 - 98: 14.632 distance: 98 - 99: 11.050 distance: 98 - 101: 16.604 distance: 99 - 100: 13.002 distance: 99 - 104: 8.195 distance: 101 - 102: 14.633 distance: 101 - 103: 23.367 distance: 104 - 105: 15.379 distance: 105 - 106: 19.644 distance: 105 - 108: 21.355 distance: 106 - 107: 19.411 distance: 106 - 110: 20.045 distance: 108 - 109: 23.342 distance: 110 - 111: 18.942 distance: 111 - 112: 10.436 distance: 112 - 113: 33.217 distance: 112 - 114: 20.596