Starting phenix.real_space_refine on Mon Aug 25 20:07:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yqx_34038/08_2025/7yqx_34038.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yqx_34038/08_2025/7yqx_34038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yqx_34038/08_2025/7yqx_34038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yqx_34038/08_2025/7yqx_34038.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yqx_34038/08_2025/7yqx_34038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yqx_34038/08_2025/7yqx_34038.map" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.051 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 125 5.16 5 C 19156 2.51 5 N 4963 2.21 5 O 5924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30168 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 8544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8544 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 8544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8544 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 8552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8552 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 959 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "F" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 815 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "I" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 959 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 815 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.15, per 1000 atoms: 0.24 Number of scatterers: 30168 At special positions: 0 Unit cell: (187.25, 154.08, 184.04, 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 125 16.00 O 5924 8.00 N 4963 7.00 C 19156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " BETA1-6 " NAG K 1 " - " FUC K 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG O 1 " - " FUC O 4 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 74 " " NAG A1303 " - " ASN A 122 " " NAG A1304 " - " ASN A 149 " " NAG A1305 " - " ASN A 165 " " NAG A1306 " - " ASN A 234 " " NAG A1307 " - " ASN A 282 " " NAG A1309 " - " ASN A 603 " " NAG A1310 " - " ASN A 616 " " NAG A1311 " - " ASN A 657 " " NAG A1312 " - " ASN A 709 " " NAG A1313 " - " ASN A1098 " " NAG A1314 " - " ASN A1134 " " NAG A1315 " - " ASN A 331 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 74 " " NAG B1303 " - " ASN B 122 " " NAG B1304 " - " ASN B 149 " " NAG B1305 " - " ASN B 165 " " NAG B1306 " - " ASN B 234 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 331 " " NAG B1309 " - " ASN B 603 " " NAG B1310 " - " ASN B 616 " " NAG B1311 " - " ASN B 657 " " NAG B1312 " - " ASN B 709 " " NAG B1313 " - " ASN B1098 " " NAG B1314 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 74 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 149 " " NAG C1305 " - " ASN C 165 " " NAG C1306 " - " ASN C 234 " " NAG C1307 " - " ASN C 282 " " NAG C1308 " - " ASN C 331 " " NAG C1309 " - " ASN C 343 " " NAG C1310 " - " ASN C 603 " " NAG C1311 " - " ASN C 616 " " NAG C1312 " - " ASN C 657 " " NAG C1313 " - " ASN C 709 " " NAG C1314 " - " ASN C1098 " " NAG C1315 " - " ASN C1134 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1074 " " NAG K 1 " - " ASN A 343 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1074 " " NAG O 1 " - " ASN B 343 " " NAG P 1 " - " ASN C 717 " " NAG Q 1 " - " ASN C 801 " " NAG R 1 " - " ASN C1074 " Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6978 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 56 sheets defined 18.9% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 196 through 200 removed outlier: 4.069A pdb=" N GLY A 199 " --> pdb=" O ASN A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.883A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.730A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 619 through 624 removed outlier: 3.590A pdb=" N VAL A 622 " --> pdb=" O GLU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.733A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 783 removed outlier: 4.094A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.640A pdb=" N ASP A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 854 removed outlier: 3.569A pdb=" N LYS A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 850 through 854' Processing helix chain 'A' and resid 868 through 880 removed outlier: 3.858A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 898 through 908 removed outlier: 3.810A pdb=" N ALA A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 4.345A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.214A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.741A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.553A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.618A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A1019 " --> pdb=" O ALA A1015 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.516A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.872A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.144A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.579A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.543A pdb=" N GLY B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 869 through 880 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.530A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.537A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.786A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.584A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.585A pdb=" N ASN B 960 " --> pdb=" O ALA B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 968 removed outlier: 3.600A pdb=" N SER B 968 " --> pdb=" O GLN B 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 965 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.004A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR B1027 " --> pdb=" O ASN B1023 " (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 'C' and resid 294 through 303 removed outlier: 3.575A pdb=" N LEU C 303 " --> pdb=" O THR C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.575A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.739A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 619 through 623 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 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 760 through 783 removed outlier: 3.916A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 851 through 855 removed outlier: 3.668A pdb=" N LYS C 854 " --> pdb=" O CYS C 851 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE C 855 " --> pdb=" O ALA C 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 851 through 855' Processing helix chain 'C' and resid 868 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 941 removed outlier: 6.681A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.656A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.684A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.641A pdb=" N ALA C 989 " --> pdb=" O ASP C 985 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C1008 " --> pdb=" O LEU C1004 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE C1013 " --> pdb=" O THR C1009 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.039A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.764A pdb=" N PHE F 84 " --> pdb=" O PRO F 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.998A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 194 Processing sheet with id=AA4, first strand: chain 'A' and resid 168 through 169 removed outlier: 3.773A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 204 through 205 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.557A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 597 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.298A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AA9, first strand: chain 'A' and resid 399 through 402 removed outlier: 3.764A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TYR A 508 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.704A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 610 through 613 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 3.546A pdb=" N GLU A 654 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 722 removed outlier: 6.960A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 725 through 728 removed outlier: 3.742A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.624A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.882A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 129 through 131 removed outlier: 4.067A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.367A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.684A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR B 508 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 539 through 541 removed outlier: 3.802A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 573 through 576 removed outlier: 3.585A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.037A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.588A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B1094 " --> pdb=" O THR B1105 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 722 removed outlier: 7.018A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 725 through 728 removed outlier: 3.594A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD4, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD5, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AD7, first strand: chain 'C' and resid 50 through 55 removed outlier: 4.353A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.549A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 205 through 208 removed outlier: 3.588A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.484A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.293A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.655A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.979A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 727 removed outlier: 6.982A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR C1047 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF1, first strand: chain 'C' and resid 1089 through 1090 Processing sheet with id=AF2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF3, first strand: chain 'H' and resid 49 through 51 removed outlier: 4.121A pdb=" N ASN H 116 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 49 through 51 Processing sheet with id=AF5, first strand: chain 'F' and resid 19 through 22 Processing sheet with id=AF6, first strand: chain 'F' and resid 45 through 49 removed outlier: 6.396A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AF8, first strand: chain 'I' and resid 49 through 51 removed outlier: 4.231A pdb=" N GLY I 33 " --> pdb=" O ASP I 99 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASN I 116 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 49 through 51 removed outlier: 4.231A pdb=" N GLY I 33 " --> pdb=" O ASP I 99 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 19 through 22 removed outlier: 3.704A pdb=" N ASP G 71 " --> pdb=" O SER G 68 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 46 through 49 removed outlier: 6.278A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) 829 hydrogen bonds defined for protein. 2205 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.88 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5290 1.33 - 1.45: 8570 1.45 - 1.58: 16848 1.58 - 1.70: 0 1.70 - 1.83: 158 Bond restraints: 30866 Sorted by residual: bond pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.97e+00 bond pdb=" C1 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.55e+00 bond pdb=" C PRO B 330 " pdb=" O PRO B 330 " ideal model delta sigma weight residual 1.233 1.200 0.033 1.23e-02 6.61e+03 7.01e+00 bond pdb=" N ASN A 334 " pdb=" CA ASN A 334 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.83e+00 bond pdb=" N THR A 333 " pdb=" CA THR A 333 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.42e+00 ... (remaining 30861 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 40637 1.68 - 3.36: 1185 3.36 - 5.04: 152 5.04 - 6.72: 33 6.72 - 8.41: 9 Bond angle restraints: 42016 Sorted by residual: angle pdb=" C ASN B 331 " pdb=" CA ASN B 331 " pdb=" CB ASN B 331 " ideal model delta sigma weight residual 110.67 104.21 6.46 1.52e+00 4.33e-01 1.81e+01 angle pdb=" CA PRO B 330 " pdb=" C PRO B 330 " pdb=" O PRO B 330 " ideal model delta sigma weight residual 122.13 117.46 4.67 1.23e+00 6.61e-01 1.44e+01 angle pdb=" N VAL C 620 " pdb=" CA VAL C 620 " pdb=" C VAL C 620 " ideal model delta sigma weight residual 108.88 116.95 -8.07 2.16e+00 2.14e-01 1.40e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 114.98 -4.28 1.22e+00 6.72e-01 1.23e+01 angle pdb=" N ILE B1115 " pdb=" CA ILE B1115 " pdb=" C ILE B1115 " ideal model delta sigma weight residual 106.21 109.96 -3.75 1.07e+00 8.73e-01 1.23e+01 ... (remaining 42011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.41: 18137 25.41 - 50.82: 934 50.82 - 76.23: 108 76.23 - 101.64: 55 101.64 - 127.05: 9 Dihedral angle restraints: 19243 sinusoidal: 8354 harmonic: 10889 Sorted by residual: dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 1.41 -87.41 1 1.00e+01 1.00e-02 9.17e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -1.67 -84.33 1 1.00e+01 1.00e-02 8.65e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 39.57 53.43 1 1.00e+01 1.00e-02 3.88e+01 ... (remaining 19240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 4892 0.147 - 0.295: 30 0.295 - 0.442: 8 0.442 - 0.590: 1 0.590 - 0.737: 1 Chirality restraints: 4932 Sorted by residual: chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.67e+00 ... (remaining 4929 not shown) Planarity restraints: 5406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1315 " 0.064 2.00e-02 2.50e+03 5.28e-02 3.48e+01 pdb=" C7 NAG A1315 " -0.019 2.00e-02 2.50e+03 pdb=" C8 NAG A1315 " 0.049 2.00e-02 2.50e+03 pdb=" N2 NAG A1315 " -0.083 2.00e-02 2.50e+03 pdb=" O7 NAG A1315 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU F 80 " 0.052 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO F 81 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO F 81 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO F 81 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " 0.039 5.00e-02 4.00e+02 5.83e-02 5.43e+00 pdb=" N PRO C 986 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " 0.032 5.00e-02 4.00e+02 ... (remaining 5403 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1138 2.70 - 3.25: 30473 3.25 - 3.80: 45612 3.80 - 4.35: 56542 4.35 - 4.90: 94425 Nonbonded interactions: 228190 Sorted by model distance: nonbonded pdb=" OG1 THR B 393 " pdb=" OE2 GLU B 516 " model vdw 2.151 3.040 nonbonded pdb=" O ALA I 24 " pdb=" OG1 THR I 77 " model vdw 2.175 3.040 nonbonded pdb=" O VAL F 3 " pdb=" OG SER F 26 " model vdw 2.195 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.195 3.040 nonbonded pdb=" NE2 GLN B 804 " pdb=" OE1 GLN B 935 " model vdw 2.203 3.120 ... (remaining 228185 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 25 through 1314) selection = chain 'B' selection = (chain 'C' and (resid 25 through 377 or (resid 378 and (name N or name CA or nam \ e C or name O or name CB )) or resid 379 through 385 or (resid 386 and (name N o \ r name CA or name C or name O or name CB )) or resid 387 through 1314)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = (chain 'F' and resid 1 through 108) selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'K' selection = chain 'O' } 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: 4.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.050 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 29.150 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 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 : 0.004 0.055 30973 Z= 0.211 Angle : 0.720 17.263 42299 Z= 0.353 Chirality : 0.051 0.737 4932 Planarity : 0.004 0.079 5352 Dihedral : 15.305 127.053 12151 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.83 % Favored : 91.09 % Rotamer: Outliers : 0.06 % Allowed : 0.37 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.10 (0.13), residues: 3727 helix: -0.16 (0.21), residues: 607 sheet: -0.62 (0.20), residues: 702 loop : -2.09 (0.12), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 190 TYR 0.020 0.001 TYR C 160 PHE 0.026 0.001 PHE C 906 TRP 0.029 0.002 TRP H 117 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00447 (30866) covalent geometry : angle 0.67046 (42016) SS BOND : bond 0.00238 ( 38) SS BOND : angle 1.32757 ( 76) hydrogen bonds : bond 0.22505 ( 808) hydrogen bonds : angle 8.84573 ( 2205) link_BETA1-4 : bond 0.00643 ( 13) link_BETA1-4 : angle 3.21191 ( 39) link_BETA1-6 : bond 0.00328 ( 2) link_BETA1-6 : angle 1.40071 ( 6) link_NAG-ASN : bond 0.00781 ( 54) link_NAG-ASN : angle 3.92353 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 210 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.5369 (m-80) cc_final: 0.5111 (m-80) REVERT: A 508 TYR cc_start: 0.6544 (m-10) cc_final: 0.6124 (m-10) REVERT: A 740 MET cc_start: 0.8259 (tpp) cc_final: 0.8004 (tpt) REVERT: B 186 PHE cc_start: 0.7639 (m-80) cc_final: 0.7248 (m-80) REVERT: C 201 PHE cc_start: 0.7665 (t80) cc_final: 0.7456 (t80) REVERT: C 396 TYR cc_start: 0.7152 (m-80) cc_final: 0.6195 (m-80) REVERT: C 529 LYS cc_start: 0.8843 (pptt) cc_final: 0.8629 (ptpp) REVERT: C 985 ASP cc_start: 0.8371 (t0) cc_final: 0.7991 (p0) REVERT: H 117 TRP cc_start: 0.7114 (m100) cc_final: 0.6555 (m-10) REVERT: F 37 TYR cc_start: 0.8219 (m-10) cc_final: 0.7979 (m-80) REVERT: F 50 TYR cc_start: 0.6443 (p90) cc_final: 0.5871 (p90) outliers start: 2 outliers final: 1 residues processed: 212 average time/residue: 0.1794 time to fit residues: 64.4862 Evaluate side-chains 160 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.0170 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.5022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 GLN A 895 GLN B 121 ASN B 804 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 450 ASN C 913 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.150997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.119783 restraints weight = 99909.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.120104 restraints weight = 85314.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.119756 restraints weight = 62697.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.118806 restraints weight = 53203.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.118918 restraints weight = 58841.520| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30973 Z= 0.150 Angle : 0.697 15.568 42299 Z= 0.333 Chirality : 0.048 0.497 4932 Planarity : 0.004 0.058 5352 Dihedral : 9.554 86.719 5525 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.23 % Favored : 90.74 % Rotamer: Outliers : 0.59 % Allowed : 7.06 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.97 (0.13), residues: 3727 helix: 0.34 (0.21), residues: 632 sheet: -0.47 (0.20), residues: 693 loop : -2.17 (0.12), residues: 2402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 190 TYR 0.020 0.001 TYR B1067 PHE 0.025 0.001 PHE A 220 TRP 0.025 0.001 TRP H 47 HIS 0.004 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00336 (30866) covalent geometry : angle 0.64434 (42016) SS BOND : bond 0.00264 ( 38) SS BOND : angle 1.32120 ( 76) hydrogen bonds : bond 0.05342 ( 808) hydrogen bonds : angle 6.46974 ( 2205) link_BETA1-4 : bond 0.00865 ( 13) link_BETA1-4 : angle 3.15733 ( 39) link_BETA1-6 : bond 0.00328 ( 2) link_BETA1-6 : angle 1.34337 ( 6) link_NAG-ASN : bond 0.00795 ( 54) link_NAG-ASN : angle 3.97100 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.4691 (m-80) cc_final: 0.4439 (m-80) REVERT: A 508 TYR cc_start: 0.6135 (m-10) cc_final: 0.5903 (m-10) REVERT: A 740 MET cc_start: 0.8417 (tpp) cc_final: 0.8173 (tpt) REVERT: C 201 PHE cc_start: 0.7700 (t80) cc_final: 0.7461 (t80) REVERT: C 396 TYR cc_start: 0.6790 (m-80) cc_final: 0.6308 (m-80) REVERT: C 592 PHE cc_start: 0.8353 (p90) cc_final: 0.8119 (p90) REVERT: H 47 TRP cc_start: 0.7291 (t60) cc_final: 0.6962 (p-90) REVERT: H 114 PHE cc_start: 0.8015 (m-80) cc_final: 0.7699 (m-80) REVERT: F 43 GLN cc_start: 0.8351 (mt0) cc_final: 0.8021 (mt0) REVERT: F 50 TYR cc_start: 0.5704 (p90) cc_final: 0.5345 (p90) outliers start: 19 outliers final: 13 residues processed: 186 average time/residue: 0.1781 time to fit residues: 55.7745 Evaluate side-chains 162 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain F residue 93 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 229 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 238 optimal weight: 7.9990 chunk 221 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 358 optimal weight: 40.0000 chunk 188 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 193 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 207 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 519 HIS ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 GLN C1023 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.133283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.088113 restraints weight = 91785.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.087819 restraints weight = 58520.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.088542 restraints weight = 46402.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.089263 restraints weight = 35436.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.089286 restraints weight = 32038.982| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 30973 Z= 0.331 Angle : 0.830 14.558 42299 Z= 0.405 Chirality : 0.053 0.547 4932 Planarity : 0.005 0.070 5352 Dihedral : 8.770 61.966 5523 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.19 % Favored : 88.78 % Rotamer: Outliers : 1.86 % Allowed : 11.36 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.39 (0.13), residues: 3727 helix: -0.22 (0.20), residues: 635 sheet: -0.75 (0.20), residues: 668 loop : -2.37 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 237 TYR 0.025 0.002 TYR B1067 PHE 0.040 0.002 PHE B1121 TRP 0.017 0.002 TRP H 117 HIS 0.008 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00777 (30866) covalent geometry : angle 0.78341 (42016) SS BOND : bond 0.00348 ( 38) SS BOND : angle 1.54260 ( 76) hydrogen bonds : bond 0.06018 ( 808) hydrogen bonds : angle 6.64693 ( 2205) link_BETA1-4 : bond 0.00958 ( 13) link_BETA1-4 : angle 3.25211 ( 39) link_BETA1-6 : bond 0.00078 ( 2) link_BETA1-6 : angle 1.48910 ( 6) link_NAG-ASN : bond 0.00897 ( 54) link_NAG-ASN : angle 4.11923 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7454 Ramachandran restraints generated. 3727 Oldfield, 0 Emsley, 3727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 162 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7414 (mtt180) cc_final: 0.7135 (mpp80) REVERT: A 396 TYR cc_start: 0.5645 (m-80) cc_final: 0.5365 (m-80) REVERT: A 740 MET cc_start: 0.8628 (tpp) cc_final: 0.8419 (tpt) REVERT: A 902 MET cc_start: 0.9390 (tpt) cc_final: 0.9044 (tpt) REVERT: B 127 VAL cc_start: 0.8263 (OUTLIER) cc_final: 0.7958 (p) REVERT: B 186 PHE cc_start: 0.7708 (m-80) cc_final: 0.7308 (m-80) REVERT: B 368 LEU cc_start: 0.9366 (mm) cc_final: 0.9091 (pp) REVERT: B 660 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.6470 (m-10) REVERT: H 10 GLU cc_start: 0.2390 (mp0) cc_final: 0.2077 (mp0) REVERT: H 47 TRP cc_start: 0.8354 (t60) cc_final: 0.7937 (p-90) REVERT: F 37 TYR cc_start: 0.7875 (m-80) cc_final: 0.7537 (m-80) outliers start: 60 outliers final: 37 residues processed: 208 average time/residue: 0.1754 time to fit residues: 61.8244 Evaluate side-chains 190 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 93 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.0577 > 50: distance: 45 - 49: 8.626 distance: 49 - 50: 21.814 distance: 50 - 51: 12.348 distance: 50 - 53: 16.824 distance: 51 - 52: 4.580 distance: 51 - 54: 13.401 distance: 54 - 55: 24.103 distance: 55 - 56: 17.717 distance: 55 - 58: 27.172 distance: 56 - 57: 24.662 distance: 56 - 64: 6.050 distance: 58 - 59: 11.571 distance: 59 - 60: 8.246 distance: 59 - 61: 29.970 distance: 60 - 62: 12.881 distance: 61 - 63: 8.410 distance: 62 - 63: 26.406 distance: 64 - 65: 23.347 distance: 64 - 202: 21.882 distance: 65 - 66: 18.489 distance: 65 - 68: 22.345 distance: 66 - 67: 18.740 distance: 66 - 75: 30.582 distance: 67 - 199: 23.773 distance: 68 - 69: 6.981 distance: 69 - 70: 16.009 distance: 69 - 71: 15.321 distance: 70 - 72: 25.533 distance: 71 - 73: 19.219 distance: 72 - 74: 20.670 distance: 73 - 74: 24.594 distance: 75 - 76: 23.285 distance: 75 - 81: 16.014 distance: 76 - 77: 31.259 distance: 76 - 79: 13.957 distance: 77 - 78: 9.453 distance: 77 - 82: 18.749 distance: 79 - 80: 20.049 distance: 80 - 81: 12.776 distance: 82 - 83: 3.435 distance: 83 - 84: 14.307 distance: 83 - 86: 28.721 distance: 84 - 85: 13.045 distance: 84 - 93: 17.983 distance: 86 - 87: 19.754 distance: 87 - 88: 17.289 distance: 88 - 89: 13.865 distance: 93 - 94: 34.864 distance: 94 - 95: 23.669 distance: 94 - 97: 16.502 distance: 95 - 96: 14.735 distance: 95 - 102: 40.115 distance: 97 - 98: 20.970 distance: 98 - 99: 6.483 distance: 99 - 100: 5.646 distance: 99 - 101: 13.018 distance: 102 - 103: 27.736 distance: 103 - 104: 45.376 distance: 104 - 105: 35.379 distance: 104 - 106: 7.736 distance: 106 - 107: 21.595 distance: 107 - 108: 13.073 distance: 107 - 110: 29.110 distance: 108 - 109: 29.496 distance: 108 - 113: 20.690 distance: 109 - 163: 13.268 distance: 110 - 111: 9.412 distance: 110 - 112: 21.919 distance: 113 - 114: 14.674 distance: 114 - 115: 15.554 distance: 114 - 117: 39.718 distance: 115 - 116: 7.462 distance: 115 - 124: 19.444 distance: 117 - 118: 11.627 distance: 118 - 119: 14.177 distance: 118 - 120: 6.299 distance: 119 - 121: 19.147 distance: 120 - 122: 23.201 distance: 121 - 123: 16.534 distance: 122 - 123: 15.296 distance: 124 - 125: 13.068 distance: 124 - 152: 21.336 distance: 125 - 126: 11.812 distance: 125 - 128: 6.565 distance: 126 - 127: 5.824 distance: 126 - 131: 15.326 distance: 127 - 149: 15.589 distance: 128 - 129: 21.650 distance: 128 - 130: 17.918