Starting phenix.real_space_refine on Thu Jun 26 08:01:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ws5_32744/06_2025/7ws5_32744.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ws5_32744/06_2025/7ws5_32744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ws5_32744/06_2025/7ws5_32744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ws5_32744/06_2025/7ws5_32744.map" model { file = "/net/cci-nas-00/data/ceres_data/7ws5_32744/06_2025/7ws5_32744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ws5_32744/06_2025/7ws5_32744.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.040 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 132 5.16 5 C 19267 2.51 5 N 4986 2.21 5 O 5843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 2.29s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30228 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 8112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8112 Classifications: {'peptide': 1035} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 57, 'TRANS': 977} Chain breaks: 8 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8135 Classifications: {'peptide': 1036} Link IDs: {'PTRANS': 57, 'TRANS': 978} Chain breaks: 8 Chain: "C" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8130 Classifications: {'peptide': 1036} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 57, 'TRANS': 978} Chain breaks: 8 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 956 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 956 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "H" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 956 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "O" 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: 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: "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: "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: "S" 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: "T" 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: "U" 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: "V" 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: "W" 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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 Time building chain proxies: 18.87, per 1000 atoms: 0.62 Number of scatterers: 30228 At special positions: 0 Unit cell: (143.936, 173.888, 210.496, 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 132 16.00 O 5843 8.00 N 4986 7.00 C 19267 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " 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 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " 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=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 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=2.03 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 D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " 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 J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " 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 P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 709 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 709 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 709 " " NAG J 1 " - " ASN C 801 " " NAG K 1 " - " ASN C1074 " " NAG L 1 " - " ASN C1098 " " NAG M 1 " - " ASN C1134 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1074 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN A 717 " " NAG U 1 " - " ASN A 801 " " NAG V 1 " - " ASN A1098 " " NAG W 1 " - " ASN A1134 " Time building additional restraints: 7.31 Conformation dependent library (CDL) restraints added in 3.5 seconds 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7102 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 65 sheets defined 20.9% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.67 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.719A pdb=" N LEU A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.650A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.025A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.591A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.910A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.065A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.971A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN A 957 " --> pdb=" O ASN A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.257A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.539A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.285A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.055A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.628A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.508A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.586A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.524A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.070A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.357A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.393A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.044A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.607A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.802A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.507A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.105A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.657A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.022A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.631A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'I' and resid 62 through 65 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.829A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.355A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.882A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.086A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 142 removed outlier: 8.219A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.397A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.738A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.967A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 327 through 328 removed outlier: 3.650A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.638A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 5.870A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.526A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.975A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.564A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.964A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.552A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.868A pdb=" N LYS A 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.376A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.029A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.176A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.016A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.723A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.082A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.426A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.426A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 787 through 789 removed outlier: 5.440A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.079A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.824A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.540A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 10.208A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.468A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.750A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.340A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.324A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN C 540 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.588A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.893A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.203A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.648A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.648A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF1, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AF2, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AF3, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.534A pdb=" N SER D 53 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR D 98 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 4 through 6 removed outlier: 3.570A pdb=" N THR E 69 " --> pdb=" O GLN E 82 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.848A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY E 50 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP E 59 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.827A pdb=" N LYS E 98 " --> pdb=" O ASP E 111 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AF8, first strand: chain 'F' and resid 10 through 11 Processing sheet with id=AF9, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.590A pdb=" N SER F 53 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN F 90 " --> pdb=" O THR F 98 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR F 98 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.605A pdb=" N THR G 69 " --> pdb=" O GLN G 82 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AG3, first strand: chain 'G' and resid 58 through 60 removed outlier: 3.683A pdb=" N ASP G 59 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY G 50 " --> pdb=" O ASP G 59 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LYS G 98 " --> pdb=" O ASP G 111 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 58 through 60 removed outlier: 3.683A pdb=" N ASP G 59 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY G 50 " --> pdb=" O ASP G 59 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AG6, first strand: chain 'H' and resid 10 through 13 removed outlier: 5.589A pdb=" N LEU H 11 " --> pdb=" O GLU H 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.604A pdb=" N SER H 53 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AG9, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AH1, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.652A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS I 98 " --> pdb=" O ASP I 111 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.652A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) 1228 hydrogen bonds defined for protein. 3324 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: 15.09 Time building geometry restraints manager: 8.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9587 1.34 - 1.46: 7167 1.46 - 1.58: 14005 1.58 - 1.70: 0 1.70 - 1.82: 168 Bond restraints: 30927 Sorted by residual: bond pdb=" N CYS B 738 " pdb=" CA CYS B 738 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.59e+00 bond pdb=" N ASN A 487 " pdb=" CA ASN A 487 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.23e-02 6.61e+03 7.67e+00 bond pdb=" C1 NAG R 1 " pdb=" O5 NAG R 1 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.55e+00 bond pdb=" N LEU A 858 " pdb=" CA LEU A 858 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.22e-02 6.72e+03 6.60e+00 bond pdb=" N THR A 859 " pdb=" CA THR A 859 " ideal model delta sigma weight residual 1.455 1.487 -0.033 1.29e-02 6.01e+03 6.44e+00 ... (remaining 30922 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 40331 1.39 - 2.78: 1411 2.78 - 4.18: 248 4.18 - 5.57: 54 5.57 - 6.96: 7 Bond angle restraints: 42051 Sorted by residual: angle pdb=" N PHE B 855 " pdb=" CA PHE B 855 " pdb=" C PHE B 855 " ideal model delta sigma weight residual 113.18 107.87 5.31 1.21e+00 6.83e-01 1.93e+01 angle pdb=" N LYS A 856 " pdb=" CA LYS A 856 " pdb=" C LYS A 856 " ideal model delta sigma weight residual 113.15 108.01 5.14 1.19e+00 7.06e-01 1.86e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 115.23 -4.53 1.22e+00 6.72e-01 1.38e+01 angle pdb=" N ASP A 571 " pdb=" CA ASP A 571 " pdb=" C ASP A 571 " ideal model delta sigma weight residual 113.23 108.75 4.48 1.22e+00 6.72e-01 1.35e+01 angle pdb=" C ASN A 641 " pdb=" N VAL A 642 " pdb=" CA VAL A 642 " ideal model delta sigma weight residual 123.14 118.35 4.79 1.31e+00 5.83e-01 1.34e+01 ... (remaining 42046 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 17340 17.76 - 35.53: 1233 35.53 - 53.29: 261 53.29 - 71.06: 65 71.06 - 88.82: 34 Dihedral angle restraints: 18933 sinusoidal: 7888 harmonic: 11045 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -17.25 -68.75 1 1.00e+01 1.00e-02 6.12e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 160.52 -67.52 1 1.00e+01 1.00e-02 5.93e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -29.49 -56.51 1 1.00e+01 1.00e-02 4.30e+01 ... (remaining 18930 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.167: 4819 0.167 - 0.333: 10 0.333 - 0.500: 2 0.500 - 0.667: 0 0.667 - 0.833: 2 Chirality restraints: 4833 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-01 2.50e+01 1.74e+01 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.25e+00 ... (remaining 4830 not shown) Planarity restraints: 5406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " 0.034 2.00e-02 2.50e+03 3.13e-02 1.23e+01 pdb=" CG ASN A 61 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " -0.032 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 737 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.90e+00 pdb=" C ASP C 737 " 0.049 2.00e-02 2.50e+03 pdb=" O ASP C 737 " -0.019 2.00e-02 2.50e+03 pdb=" N CYS C 738 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 717 " -0.026 2.00e-02 2.50e+03 2.48e-02 7.67e+00 pdb=" CG ASN C 717 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN C 717 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN C 717 " 0.013 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.020 2.00e-02 2.50e+03 ... (remaining 5403 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1123 2.71 - 3.26: 29632 3.26 - 3.81: 48669 3.81 - 4.35: 58966 4.35 - 4.90: 101753 Nonbonded interactions: 240143 Sorted by model distance: nonbonded pdb=" OG1 THR A 323 " pdb=" OE1 GLU A 324 " model vdw 2.168 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.200 3.040 nonbonded pdb=" OD1 ASN F 34 " pdb=" OG SER G 109 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.210 3.040 nonbonded pdb=" OD1 ASN H 34 " pdb=" OG SER I 109 " model vdw 2.211 3.040 ... (remaining 240138 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 497 or (resid 498 and (name N or name CA or nam \ e C or name O or name CB )) or resid 499 through 500 or (resid 501 and (name N o \ r name CA or name C or name O or name CB )) or resid 502 through 518 or (resid 5 \ 19 through 520 and (name N or name CA or name C or name O or name CB )) or resid \ 521 through 827 or resid 853 through 1147 or resid 1301 through 1303)) selection = (chain 'C' and (resid 14 through 497 or (resid 498 and (name N or name CA or nam \ e C or name O or name CB )) or resid 499 through 500 or (resid 501 and (name N o \ r name CA or name C or name O or name CB )) or resid 502 through 827 or resid 85 \ 3 through 1147 or resid 1301 through 1303)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } 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: 10.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.140 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 70.320 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.200 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 : 0.003 0.055 31011 Z= 0.178 Angle : 0.647 21.305 42257 Z= 0.349 Chirality : 0.049 0.833 4833 Planarity : 0.004 0.068 5382 Dihedral : 13.301 88.824 11693 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.49 % Favored : 97.46 % Rotamer: Outliers : 0.09 % Allowed : 0.27 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.14), residues: 3734 helix: 1.62 (0.21), residues: 682 sheet: 0.16 (0.15), residues: 1028 loop : -0.73 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.003 0.001 HIS B1101 PHE 0.023 0.001 PHE C 559 TYR 0.024 0.001 TYR C 904 ARG 0.010 0.000 ARG E 19 Details of bonding type rmsd link_NAG-ASN : bond 0.01107 ( 24) link_NAG-ASN : angle 4.79280 ( 72) link_BETA1-4 : bond 0.00507 ( 14) link_BETA1-4 : angle 1.58442 ( 42) hydrogen bonds : bond 0.14352 ( 1179) hydrogen bonds : angle 7.18717 ( 3324) SS BOND : bond 0.00319 ( 46) SS BOND : angle 1.05872 ( 92) covalent geometry : bond 0.00330 (30927) covalent geometry : angle 0.61330 (42051) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 289 time to evaluate : 3.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8333 (m-80) cc_final: 0.7991 (m-80) REVERT: A 418 ILE cc_start: 0.9270 (pt) cc_final: 0.8591 (pt) REVERT: A 574 ASP cc_start: 0.7467 (p0) cc_final: 0.7100 (t0) REVERT: D 4 MET cc_start: 0.6329 (ptt) cc_final: 0.6014 (tmm) REVERT: D 29 ILE cc_start: 0.7604 (pt) cc_final: 0.7202 (pt) REVERT: D 59 PRO cc_start: 0.8162 (Cg_exo) cc_final: 0.7921 (Cg_endo) REVERT: D 71 PHE cc_start: 0.7089 (m-80) cc_final: 0.6289 (m-10) REVERT: D 72 THR cc_start: 0.7896 (m) cc_final: 0.7559 (m) REVERT: D 89 GLN cc_start: 0.7420 (tt0) cc_final: 0.6632 (mm-40) REVERT: E 94 TYR cc_start: 0.8088 (m-80) cc_final: 0.7879 (m-80) REVERT: E 119 VAL cc_start: 0.2334 (m) cc_final: 0.0968 (t) REVERT: F 33 LEU cc_start: 0.4159 (tt) cc_final: 0.3037 (tp) REVERT: F 34 ASN cc_start: 0.3334 (m110) cc_final: 0.2640 (t0) REVERT: H 45 LYS cc_start: 0.9043 (ttpp) cc_final: 0.8385 (ttpp) REVERT: H 69 THR cc_start: 0.8528 (p) cc_final: 0.8212 (t) REVERT: H 83 PHE cc_start: 0.8247 (t80) cc_final: 0.7769 (t80) REVERT: H 99 PHE cc_start: 0.8683 (m-80) cc_final: 0.8482 (m-80) REVERT: H 105 LEU cc_start: 0.8203 (tp) cc_final: 0.7996 (tp) REVERT: I 59 ASP cc_start: 0.8366 (t0) cc_final: 0.8006 (t0) REVERT: I 95 TYR cc_start: 0.7422 (m-80) cc_final: 0.7014 (m-80) REVERT: I 103 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7981 (tp30) REVERT: I 111 ASP cc_start: 0.8708 (t70) cc_final: 0.7826 (t70) REVERT: I 112 TYR cc_start: 0.8074 (m-80) cc_final: 0.7341 (m-80) outliers start: 3 outliers final: 0 residues processed: 292 average time/residue: 0.4184 time to fit residues: 194.0343 Evaluate side-chains 201 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 3.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 5.9990 chunk 284 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 191 optimal weight: 0.9980 chunk 151 optimal weight: 20.0000 chunk 293 optimal weight: 0.2980 chunk 113 optimal weight: 2.9990 chunk 178 optimal weight: 0.0060 chunk 218 optimal weight: 8.9990 chunk 340 optimal weight: 3.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN B 81 ASN B 762 GLN B 901 GLN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 853 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.100323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.064329 restraints weight = 102203.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.067107 restraints weight = 51027.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.067534 restraints weight = 30793.157| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31011 Z= 0.126 Angle : 0.586 20.215 42257 Z= 0.296 Chirality : 0.046 0.576 4833 Planarity : 0.004 0.058 5382 Dihedral : 6.172 59.459 4881 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.70 % Allowed : 4.93 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.13), residues: 3734 helix: 1.94 (0.20), residues: 687 sheet: 0.18 (0.15), residues: 1004 loop : -0.76 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 436 HIS 0.007 0.001 HIS I 35 PHE 0.016 0.001 PHE A 186 TYR 0.028 0.001 TYR H 49 ARG 0.005 0.000 ARG H 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00815 ( 24) link_NAG-ASN : angle 4.23369 ( 72) link_BETA1-4 : bond 0.00374 ( 14) link_BETA1-4 : angle 1.12160 ( 42) hydrogen bonds : bond 0.04629 ( 1179) hydrogen bonds : angle 5.66873 ( 3324) SS BOND : bond 0.00350 ( 46) SS BOND : angle 1.32185 ( 92) covalent geometry : bond 0.00277 (30927) covalent geometry : angle 0.55665 (42051) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 224 time to evaluate : 3.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8373 (m-80) cc_final: 0.7903 (m-80) REVERT: A 421 TYR cc_start: 0.9335 (m-80) cc_final: 0.8964 (m-80) REVERT: A 574 ASP cc_start: 0.7515 (p0) cc_final: 0.6987 (t0) REVERT: A 855 PHE cc_start: 0.7704 (p90) cc_final: 0.7136 (p90) REVERT: B 1029 MET cc_start: 0.9137 (tpp) cc_final: 0.8559 (ttm) REVERT: D 4 MET cc_start: 0.7012 (ptt) cc_final: 0.5938 (tmm) REVERT: D 11 LEU cc_start: 0.4850 (mm) cc_final: 0.4093 (tt) REVERT: D 23 CYS cc_start: 0.6077 (p) cc_final: 0.4831 (p) REVERT: D 24 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7520 (mmm160) REVERT: D 42 LYS cc_start: 0.8920 (ptpp) cc_final: 0.8252 (mmmt) REVERT: D 71 PHE cc_start: 0.6991 (m-80) cc_final: 0.6541 (m-10) REVERT: D 89 GLN cc_start: 0.7392 (tt0) cc_final: 0.6481 (mm-40) REVERT: E 38 ARG cc_start: 0.8290 (ttp-170) cc_final: 0.8014 (ttt90) REVERT: E 94 TYR cc_start: 0.8322 (m-80) cc_final: 0.8035 (m-80) REVERT: F 33 LEU cc_start: 0.4026 (tt) cc_final: 0.2918 (tp) REVERT: F 34 ASN cc_start: 0.2493 (m110) cc_final: 0.2194 (t0) REVERT: H 18 ARG cc_start: 0.8778 (tmm-80) cc_final: 0.7834 (tmm-80) REVERT: H 45 LYS cc_start: 0.9095 (ttpp) cc_final: 0.8560 (ptmm) REVERT: I 59 ASP cc_start: 0.8532 (t0) cc_final: 0.8071 (t0) REVERT: I 95 TYR cc_start: 0.7376 (m-80) cc_final: 0.7095 (m-80) REVERT: I 103 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7707 (tp30) REVERT: I 111 ASP cc_start: 0.8738 (t70) cc_final: 0.7715 (t70) REVERT: I 112 TYR cc_start: 0.8119 (m-80) cc_final: 0.7466 (m-10) outliers start: 23 outliers final: 17 residues processed: 234 average time/residue: 0.3981 time to fit residues: 153.3163 Evaluate side-chains 210 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 3.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain I residue 5 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 336 optimal weight: 20.0000 chunk 290 optimal weight: 4.9990 chunk 202 optimal weight: 0.5980 chunk 304 optimal weight: 3.9990 chunk 258 optimal weight: 0.8980 chunk 240 optimal weight: 7.9990 chunk 230 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 chunk 345 optimal weight: 30.0000 chunk 260 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN B 81 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN C 853 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.101944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.065048 restraints weight = 101867.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.067302 restraints weight = 46766.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.068701 restraints weight = 29600.282| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 31011 Z= 0.175 Angle : 0.586 20.243 42257 Z= 0.295 Chirality : 0.045 0.537 4833 Planarity : 0.004 0.070 5382 Dihedral : 5.860 59.280 4881 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.82 % Allowed : 7.95 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.13), residues: 3734 helix: 1.93 (0.20), residues: 684 sheet: 0.14 (0.15), residues: 1037 loop : -0.79 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 47 HIS 0.004 0.001 HIS B1058 PHE 0.020 0.001 PHE A 238 TYR 0.027 0.001 TYR H 49 ARG 0.008 0.000 ARG I 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00673 ( 24) link_NAG-ASN : angle 4.16882 ( 72) link_BETA1-4 : bond 0.00234 ( 14) link_BETA1-4 : angle 1.11646 ( 42) hydrogen bonds : bond 0.04535 ( 1179) hydrogen bonds : angle 5.44169 ( 3324) SS BOND : bond 0.00443 ( 46) SS BOND : angle 1.26227 ( 92) covalent geometry : bond 0.00404 (30927) covalent geometry : angle 0.55731 (42051) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 210 time to evaluate : 3.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8379 (m-80) cc_final: 0.8026 (m-80) REVERT: A 421 TYR cc_start: 0.9177 (m-80) cc_final: 0.8760 (m-10) REVERT: A 574 ASP cc_start: 0.7652 (p0) cc_final: 0.7143 (t0) REVERT: A 855 PHE cc_start: 0.7281 (p90) cc_final: 0.7066 (p90) REVERT: B 1029 MET cc_start: 0.9125 (tpp) cc_final: 0.8569 (ttm) REVERT: C 390 LEU cc_start: 0.9448 (mt) cc_final: 0.9241 (mt) REVERT: D 4 MET cc_start: 0.7171 (ptt) cc_final: 0.5781 (ppp) REVERT: D 11 LEU cc_start: 0.5123 (mm) cc_final: 0.4511 (tp) REVERT: D 23 CYS cc_start: 0.5704 (p) cc_final: 0.5363 (p) REVERT: D 42 LYS cc_start: 0.8992 (ptpp) cc_final: 0.8378 (mmmt) REVERT: E 38 ARG cc_start: 0.8325 (ttp-170) cc_final: 0.8058 (ttt90) REVERT: F 33 LEU cc_start: 0.4125 (tt) cc_final: 0.2983 (tp) REVERT: F 34 ASN cc_start: 0.3234 (m110) cc_final: 0.2342 (t0) REVERT: H 45 LYS cc_start: 0.9082 (ttpp) cc_final: 0.8641 (ptmm) REVERT: I 35 HIS cc_start: 0.8619 (m170) cc_final: 0.8331 (m-70) REVERT: I 59 ASP cc_start: 0.8576 (t0) cc_final: 0.8120 (t0) REVERT: I 103 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7742 (tp30) REVERT: I 111 ASP cc_start: 0.8700 (t70) cc_final: 0.8331 (t70) outliers start: 27 outliers final: 21 residues processed: 224 average time/residue: 0.4219 time to fit residues: 154.4078 Evaluate side-chains 210 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 3.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 96 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 262 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 341 optimal weight: 5.9990 chunk 131 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 247 optimal weight: 9.9990 chunk 190 optimal weight: 5.9990 chunk 206 optimal weight: 20.0000 chunk 234 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 853 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.101608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.066487 restraints weight = 90051.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.066791 restraints weight = 50464.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.066556 restraints weight = 38451.182| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 31011 Z= 0.186 Angle : 0.586 20.428 42257 Z= 0.294 Chirality : 0.045 0.521 4833 Planarity : 0.004 0.068 5382 Dihedral : 5.680 59.646 4881 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.27 % Allowed : 9.55 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.13), residues: 3734 helix: 1.79 (0.20), residues: 697 sheet: 0.08 (0.15), residues: 1049 loop : -0.83 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 436 HIS 0.004 0.001 HIS C 954 PHE 0.022 0.001 PHE C 759 TYR 0.029 0.001 TYR H 49 ARG 0.005 0.000 ARG I 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00653 ( 24) link_NAG-ASN : angle 4.08092 ( 72) link_BETA1-4 : bond 0.00190 ( 14) link_BETA1-4 : angle 1.08623 ( 42) hydrogen bonds : bond 0.04532 ( 1179) hydrogen bonds : angle 5.31657 ( 3324) SS BOND : bond 0.00311 ( 46) SS BOND : angle 1.33658 ( 92) covalent geometry : bond 0.00431 (30927) covalent geometry : angle 0.55862 (42051) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 3.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8582 (m-80) cc_final: 0.8218 (m-80) REVERT: A 421 TYR cc_start: 0.9366 (m-80) cc_final: 0.9015 (m-80) REVERT: A 515 PHE cc_start: 0.8408 (m-10) cc_final: 0.8166 (m-10) REVERT: A 571 ASP cc_start: 0.8894 (t0) cc_final: 0.8600 (t0) REVERT: A 574 ASP cc_start: 0.7450 (p0) cc_final: 0.6954 (t0) REVERT: A 855 PHE cc_start: 0.7406 (p90) cc_final: 0.7103 (p90) REVERT: B 1029 MET cc_start: 0.9138 (tpp) cc_final: 0.8539 (ttm) REVERT: C 390 LEU cc_start: 0.9499 (mt) cc_final: 0.9087 (mp) REVERT: C 762 GLN cc_start: 0.8052 (mt0) cc_final: 0.7850 (mt0) REVERT: C 900 MET cc_start: 0.8694 (mtm) cc_final: 0.8471 (mtm) REVERT: C 985 ASP cc_start: 0.7925 (t0) cc_final: 0.7572 (m-30) REVERT: D 4 MET cc_start: 0.7130 (ptt) cc_final: 0.6222 (ppp) REVERT: D 11 LEU cc_start: 0.5206 (mm) cc_final: 0.4682 (tp) REVERT: D 42 LYS cc_start: 0.8900 (ptpp) cc_final: 0.8645 (pttm) REVERT: D 44 PRO cc_start: 0.4510 (Cg_endo) cc_final: 0.4118 (Cg_exo) REVERT: D 99 PHE cc_start: 0.7043 (m-80) cc_final: 0.6815 (m-80) REVERT: E 3 GLN cc_start: 0.8161 (tp-100) cc_final: 0.7720 (tp40) REVERT: F 33 LEU cc_start: 0.3672 (tt) cc_final: 0.2603 (tp) REVERT: F 34 ASN cc_start: 0.2755 (m110) cc_final: 0.2454 (t0) REVERT: G 47 TRP cc_start: 0.3862 (p90) cc_final: 0.3311 (p-90) REVERT: H 45 LYS cc_start: 0.9140 (ttpp) cc_final: 0.8683 (ptmm) REVERT: H 69 THR cc_start: 0.8787 (p) cc_final: 0.7895 (t) REVERT: H 70 ASP cc_start: 0.8577 (p0) cc_final: 0.7978 (t0) REVERT: H 83 PHE cc_start: 0.7925 (t80) cc_final: 0.7493 (t80) REVERT: H 104 LYS cc_start: 0.8432 (tptp) cc_final: 0.8154 (tptp) REVERT: I 35 HIS cc_start: 0.8738 (m170) cc_final: 0.8234 (m-70) REVERT: I 39 GLN cc_start: 0.6967 (tp40) cc_final: 0.6386 (tp-100) REVERT: I 59 ASP cc_start: 0.8416 (t0) cc_final: 0.8027 (t0) REVERT: I 95 TYR cc_start: 0.7050 (m-80) cc_final: 0.6687 (m-80) REVERT: I 103 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7660 (tp30) REVERT: I 112 TYR cc_start: 0.8233 (m-80) cc_final: 0.8002 (m-80) outliers start: 42 outliers final: 24 residues processed: 234 average time/residue: 0.4345 time to fit residues: 165.9840 Evaluate side-chains 216 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 3.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain I residue 110 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 190 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 138 optimal weight: 8.9990 chunk 294 optimal weight: 0.8980 chunk 209 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 287 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 254 optimal weight: 0.3980 chunk 344 optimal weight: 7.9990 chunk 328 optimal weight: 20.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN B 901 GLN C 853 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 HIS F 6 GLN ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.103166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.066181 restraints weight = 101072.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.068434 restraints weight = 46616.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.069681 restraints weight = 29348.855| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 31011 Z= 0.156 Angle : 0.565 20.445 42257 Z= 0.282 Chirality : 0.045 0.509 4833 Planarity : 0.004 0.063 5382 Dihedral : 5.476 59.503 4881 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.48 % Allowed : 10.07 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3734 helix: 2.08 (0.21), residues: 673 sheet: 0.09 (0.15), residues: 1052 loop : -0.84 (0.13), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 436 HIS 0.004 0.001 HIS C 954 PHE 0.018 0.001 PHE C 759 TYR 0.028 0.001 TYR H 49 ARG 0.005 0.000 ARG I 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00627 ( 24) link_NAG-ASN : angle 3.94028 ( 72) link_BETA1-4 : bond 0.00218 ( 14) link_BETA1-4 : angle 1.05509 ( 42) hydrogen bonds : bond 0.04318 ( 1179) hydrogen bonds : angle 5.20570 ( 3324) SS BOND : bond 0.00310 ( 46) SS BOND : angle 1.35994 ( 92) covalent geometry : bond 0.00361 (30927) covalent geometry : angle 0.53809 (42051) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 209 time to evaluate : 3.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8532 (m-80) cc_final: 0.8317 (m-80) REVERT: A 421 TYR cc_start: 0.9200 (m-80) cc_final: 0.8770 (m-10) REVERT: A 574 ASP cc_start: 0.7733 (p0) cc_final: 0.7115 (t0) REVERT: A 855 PHE cc_start: 0.7489 (p90) cc_final: 0.7161 (p90) REVERT: B 1029 MET cc_start: 0.9110 (tpp) cc_final: 0.8547 (ttm) REVERT: C 387 LEU cc_start: 0.9725 (OUTLIER) cc_final: 0.9454 (mm) REVERT: C 390 LEU cc_start: 0.9517 (mt) cc_final: 0.9100 (mp) REVERT: C 762 GLN cc_start: 0.8057 (mt0) cc_final: 0.7835 (mt0) REVERT: C 900 MET cc_start: 0.8734 (mtm) cc_final: 0.8441 (mtm) REVERT: D 4 MET cc_start: 0.7166 (ptt) cc_final: 0.6064 (ppp) REVERT: D 11 LEU cc_start: 0.5415 (mm) cc_final: 0.4785 (tp) REVERT: D 42 LYS cc_start: 0.8953 (ptpp) cc_final: 0.8317 (mmmt) REVERT: E 3 GLN cc_start: 0.8028 (tp-100) cc_final: 0.7557 (tp40) REVERT: E 18 LEU cc_start: 0.5733 (OUTLIER) cc_final: 0.4935 (mp) REVERT: F 32 TYR cc_start: 0.4553 (m-80) cc_final: 0.4345 (m-80) REVERT: F 33 LEU cc_start: 0.3802 (tt) cc_final: 0.2634 (tp) REVERT: F 34 ASN cc_start: 0.3730 (m110) cc_final: 0.2765 (t0) REVERT: H 45 LYS cc_start: 0.9047 (ttpp) cc_final: 0.8654 (ptmm) REVERT: H 69 THR cc_start: 0.8739 (p) cc_final: 0.8321 (t) REVERT: H 83 PHE cc_start: 0.7788 (t80) cc_final: 0.7321 (t80) REVERT: H 104 LYS cc_start: 0.8458 (tptp) cc_final: 0.8173 (tptp) REVERT: I 35 HIS cc_start: 0.8449 (m170) cc_final: 0.8143 (m-70) REVERT: I 39 GLN cc_start: 0.7287 (tp40) cc_final: 0.6669 (tp-100) REVERT: I 59 ASP cc_start: 0.8535 (t0) cc_final: 0.8035 (t0) REVERT: I 103 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7714 (tp30) outliers start: 49 outliers final: 31 residues processed: 240 average time/residue: 0.4335 time to fit residues: 171.9918 Evaluate side-chains 229 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 3.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 89 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- 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: 64.0496 > 50: distance: 54 - 56: 22.472 distance: 56 - 57: 8.803 distance: 57 - 58: 10.794 distance: 57 - 60: 27.786 distance: 58 - 59: 16.636 distance: 58 - 64: 19.405 distance: 60 - 61: 13.874 distance: 60 - 62: 12.835 distance: 61 - 63: 20.932 distance: 64 - 65: 23.634 distance: 64 - 199: 13.411 distance: 65 - 66: 18.698 distance: 65 - 68: 36.980 distance: 66 - 67: 30.711 distance: 66 - 76: 27.363 distance: 67 - 196: 23.885 distance: 68 - 69: 7.444 distance: 69 - 70: 7.001 distance: 69 - 71: 4.219 distance: 70 - 72: 3.962 distance: 71 - 73: 3.103 distance: 73 - 74: 3.300 distance: 74 - 75: 4.816 distance: 76 - 77: 38.311 distance: 77 - 78: 11.451 distance: 77 - 80: 26.294 distance: 78 - 79: 29.567 distance: 78 - 85: 17.095 distance: 80 - 81: 13.593 distance: 81 - 82: 13.314 distance: 82 - 83: 11.937 distance: 82 - 84: 9.261 distance: 85 - 86: 23.286 distance: 85 - 186: 9.649 distance: 86 - 87: 33.635 distance: 86 - 89: 19.600 distance: 87 - 88: 28.283 distance: 87 - 92: 40.103 distance: 89 - 90: 20.754 distance: 89 - 91: 20.302 distance: 92 - 93: 13.470 distance: 93 - 94: 43.869 distance: 93 - 96: 49.117 distance: 94 - 95: 40.253 distance: 94 - 98: 49.247 distance: 96 - 97: 54.547 distance: 98 - 99: 18.261 distance: 99 - 100: 14.325 distance: 99 - 102: 38.389 distance: 100 - 101: 39.999 distance: 100 - 106: 27.816 distance: 102 - 103: 64.050 distance: 103 - 104: 56.395 distance: 103 - 105: 35.870 distance: 106 - 107: 24.540 distance: 107 - 108: 20.640 distance: 107 - 110: 23.918 distance: 108 - 109: 22.490 distance: 108 - 117: 26.195 distance: 110 - 111: 41.857 distance: 111 - 112: 24.334 distance: 111 - 113: 17.625 distance: 112 - 114: 4.652 distance: 113 - 115: 3.729 distance: 114 - 116: 8.338 distance: 115 - 116: 10.332 distance: 117 - 118: 39.782 distance: 118 - 119: 39.867 distance: 118 - 121: 33.923 distance: 119 - 120: 55.247 distance: 119 - 128: 41.699 distance: 121 - 122: 11.237 distance: 122 - 123: 8.550 distance: 123 - 124: 6.004 distance: 124 - 125: 5.074 distance: 125 - 126: 6.302 distance: 125 - 127: 7.655 distance: 128 - 129: 46.878 distance: 129 - 130: 25.388 distance: 129 - 132: 31.194 distance: 130 - 131: 27.503 distance: 130 - 135: 12.502 distance: 132 - 133: 44.769 distance: 132 - 134: 28.818 distance: 135 - 136: 16.123 distance: 136 - 137: 22.550 distance: 136 - 139: 31.840 distance: 137 - 138: 19.407 distance: 137 - 144: 15.618 distance: 139 - 140: 35.405 distance: 140 - 141: 14.794 distance: 141 - 142: 30.189 distance: 141 - 143: 31.986