Starting phenix.real_space_refine on Sat May 24 13:12:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sxt_25505/05_2025/7sxt_25505.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sxt_25505/05_2025/7sxt_25505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sxt_25505/05_2025/7sxt_25505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sxt_25505/05_2025/7sxt_25505.map" model { file = "/net/cci-nas-00/data/ceres_data/7sxt_25505/05_2025/7sxt_25505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sxt_25505/05_2025/7sxt_25505.cif" } resolution = 2.31 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= 0.035 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 111 5.16 5 C 16074 2.51 5 N 4125 2.21 5 O 4938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25248 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8136 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8136 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8136 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" 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: "G" 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: "H" 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: "I" 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: "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: "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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 15.05, per 1000 atoms: 0.60 Number of scatterers: 25248 At special positions: 0 Unit cell: (141, 145, 197, 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 111 16.00 O 4938 8.00 N 4125 7.00 C 16074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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=2.03 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 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 17 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 17 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 6.47 Conformation dependent library (CDL) restraints added in 3.2 seconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5844 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 51 sheets defined 24.8% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.92 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 364 through 371 removed outlier: 4.046A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.682A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.461A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.104A 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 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.680A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.920A 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 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: 4.030A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.562A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.002A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.674A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.910A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.570A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.978A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 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: 3.633A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.575A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.902A 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 removed outlier: 3.521A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) 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 1032 removed outlier: 3.968A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.550A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.810A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.670A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.886A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.530A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.907A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.715A 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 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.964A 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 965 removed outlier: 3.601A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.508A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.266A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.599A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.976A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.789A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.886A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.739A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 11.581A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.259A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.442A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.785A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.739A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.824A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.982A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.993A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.559A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.060A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.829A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.528A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.528A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.206A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.685A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.341A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.985A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.623A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 154 through 163 removed outlier: 5.078A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.192A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.677A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.823A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.645A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.041A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.636A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.499A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.499A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.228A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.190A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.190A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.951A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 154 through 163 removed outlier: 9.704A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.790A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 10.133A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.705A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.154A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.723A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.743A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.644A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.254A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.526A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.526A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.155A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 1087 hydrogen bonds defined for protein. 2985 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: 12.35 Time building geometry restraints manager: 7.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7333 1.34 - 1.46: 6169 1.46 - 1.58: 12178 1.58 - 1.70: 0 1.70 - 1.83: 138 Bond restraints: 25818 Sorted by residual: bond pdb=" C LEU C 560 " pdb=" N PRO C 561 " ideal model delta sigma weight residual 1.334 1.387 -0.053 1.51e-02 4.39e+03 1.22e+01 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.65e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.12e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.94e+00 ... (remaining 25813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 34004 1.99 - 3.98: 1011 3.98 - 5.97: 96 5.97 - 7.96: 26 7.96 - 9.95: 8 Bond angle restraints: 35145 Sorted by residual: angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.36 -5.66 1.22e+00 6.72e-01 2.15e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.27 -5.57 1.22e+00 6.72e-01 2.09e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.08 -5.38 1.22e+00 6.72e-01 1.94e+01 angle pdb=" CA GLU C 583 " pdb=" CB GLU C 583 " pdb=" CG GLU C 583 " ideal model delta sigma weight residual 114.10 122.09 -7.99 2.00e+00 2.50e-01 1.60e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 122.60 -4.67 1.20e+00 6.94e-01 1.52e+01 ... (remaining 35140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 14918 17.98 - 35.97: 1015 35.97 - 53.95: 155 53.95 - 71.93: 56 71.93 - 89.92: 29 Dihedral angle restraints: 16173 sinusoidal: 7092 harmonic: 9081 Sorted by residual: dihedral pdb=" CA LEU B 517 " pdb=" C LEU B 517 " pdb=" N LEU B 518 " pdb=" CA LEU B 518 " ideal model delta harmonic sigma weight residual 180.00 153.99 26.01 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual 180.00 154.29 25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA PHE C 515 " pdb=" C PHE C 515 " pdb=" N GLU C 516 " pdb=" CA GLU C 516 " ideal model delta harmonic sigma weight residual 180.00 157.31 22.69 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 16170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3243 0.061 - 0.122: 795 0.122 - 0.183: 103 0.183 - 0.244: 14 0.244 - 0.306: 3 Chirality restraints: 4158 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 4155 not shown) Planarity restraints: 4518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 902 " -0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C MET C 902 " 0.057 2.00e-02 2.50e+03 pdb=" O MET C 902 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA C 903 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 920 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.90e+00 pdb=" C GLN C 920 " 0.052 2.00e-02 2.50e+03 pdb=" O GLN C 920 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS C 921 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A1029 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C MET A1029 " 0.051 2.00e-02 2.50e+03 pdb=" O MET A1029 " -0.019 2.00e-02 2.50e+03 pdb=" N SER A1030 " -0.017 2.00e-02 2.50e+03 ... (remaining 4515 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6828 2.81 - 3.33: 21059 3.33 - 3.85: 43297 3.85 - 4.38: 49762 4.38 - 4.90: 84966 Nonbonded interactions: 205912 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.287 3.040 nonbonded pdb=" OE1 GLN B 115 " pdb=" OG1 THR B 167 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR A 369 " pdb=" O ALA C 475 " model vdw 2.311 3.040 nonbonded pdb=" O ASP B 80 " pdb=" OH TYR B 265 " model vdw 2.329 3.040 nonbonded pdb=" O ASP A 80 " pdb=" OH TYR A 265 " model vdw 2.334 3.040 ... (remaining 205907 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.030 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 59.820 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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 : 0.005 0.083 25920 Z= 0.229 Angle : 0.808 15.083 35409 Z= 0.416 Chirality : 0.053 0.306 4158 Planarity : 0.007 0.065 4476 Dihedral : 12.825 89.918 10203 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.67 (0.13), residues: 3072 helix: 0.10 (0.18), residues: 650 sheet: 0.11 (0.18), residues: 687 loop : -0.86 (0.13), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 886 HIS 0.004 0.001 HIS C 66 PHE 0.042 0.002 PHE B 135 TYR 0.029 0.002 TYR C1067 ARG 0.017 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00806 ( 42) link_NAG-ASN : angle 3.51227 ( 126) link_BETA1-4 : bond 0.00681 ( 18) link_BETA1-4 : angle 1.38537 ( 54) hydrogen bonds : bond 0.16206 ( 1022) hydrogen bonds : angle 7.94797 ( 2985) SS BOND : bond 0.00258 ( 42) SS BOND : angle 1.30734 ( 84) covalent geometry : bond 0.00488 (25818) covalent geometry : angle 0.77876 (35145) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8344 (m-40) cc_final: 0.7683 (m-40) REVERT: A 153 MET cc_start: 0.4816 (ptt) cc_final: 0.3902 (tpt) REVERT: A 240 THR cc_start: 0.7417 (m) cc_final: 0.6762 (t) REVERT: A 1005 GLN cc_start: 0.8095 (mt0) cc_final: 0.7611 (mt0) REVERT: B 208 THR cc_start: 0.7675 (m) cc_final: 0.7425 (p) REVERT: B 396 TYR cc_start: 0.6611 (m-80) cc_final: 0.6400 (m-80) REVERT: B 403 ARG cc_start: 0.6496 (mtp180) cc_final: 0.6178 (ttt180) REVERT: B 564 GLN cc_start: 0.6636 (tp40) cc_final: 0.6432 (tp40) REVERT: B 985 ASP cc_start: 0.7728 (p0) cc_final: 0.6377 (p0) REVERT: C 54 LEU cc_start: 0.8639 (mm) cc_final: 0.8122 (mm) REVERT: C 453 TYR cc_start: 0.8399 (p90) cc_final: 0.8129 (p90) REVERT: C 565 PHE cc_start: 0.8329 (p90) cc_final: 0.8111 (p90) REVERT: C 740 MET cc_start: 0.7890 (ttt) cc_final: 0.7646 (ttm) REVERT: C 985 ASP cc_start: 0.7480 (p0) cc_final: 0.6906 (p0) outliers start: 0 outliers final: 1 residues processed: 307 average time/residue: 1.3459 time to fit residues: 478.1445 Evaluate side-chains 164 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 540 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 244 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 148 optimal weight: 30.0000 chunk 182 optimal weight: 0.1980 chunk 283 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 755 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 762 GLN B 901 GLN B1002 GLN B1011 GLN C 121 ASN C 207 HIS C 779 GLN C 957 GLN C1002 GLN C1010 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.128263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.077850 restraints weight = 55468.588| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.96 r_work: 0.2941 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 25920 Z= 0.222 Angle : 0.646 20.122 35409 Z= 0.323 Chirality : 0.048 0.565 4158 Planarity : 0.005 0.055 4476 Dihedral : 6.200 59.831 4607 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.21 % Allowed : 6.70 % Favored : 92.10 % 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 (0.14), residues: 3072 helix: 1.37 (0.20), residues: 677 sheet: 0.36 (0.19), residues: 682 loop : -0.70 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 886 HIS 0.007 0.001 HIS C 207 PHE 0.022 0.002 PHE B 106 TYR 0.024 0.002 TYR C1067 ARG 0.010 0.001 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00619 ( 42) link_NAG-ASN : angle 3.61045 ( 126) link_BETA1-4 : bond 0.00175 ( 18) link_BETA1-4 : angle 1.28370 ( 54) hydrogen bonds : bond 0.05074 ( 1022) hydrogen bonds : angle 6.20046 ( 2985) SS BOND : bond 0.00365 ( 42) SS BOND : angle 1.09658 ( 84) covalent geometry : bond 0.00502 (25818) covalent geometry : angle 0.60651 (35145) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8230 (m-40) cc_final: 0.7939 (m-40) REVERT: A 153 MET cc_start: 0.4511 (ptt) cc_final: 0.3504 (tpt) REVERT: A 242 LEU cc_start: 0.7946 (mp) cc_final: 0.7478 (mp) REVERT: A 786 LYS cc_start: 0.8688 (pmtt) cc_final: 0.8033 (mmmt) REVERT: A 868 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8312 (pm20) REVERT: A 1092 GLU cc_start: 0.8530 (pm20) cc_final: 0.8095 (pp20) REVERT: B 153 MET cc_start: 0.6455 (tpp) cc_final: 0.6031 (ppp) REVERT: B 403 ARG cc_start: 0.6558 (mtp180) cc_final: 0.6310 (ttt180) REVERT: B 408 ARG cc_start: 0.7947 (ptt90) cc_final: 0.7342 (ppt170) REVERT: B 960 ASN cc_start: 0.9313 (OUTLIER) cc_final: 0.9085 (t0) REVERT: B 1138 TYR cc_start: 0.8679 (t80) cc_final: 0.8369 (t80) REVERT: C 52 GLN cc_start: 0.7857 (tp-100) cc_final: 0.7527 (tp40) REVERT: C 194 PHE cc_start: 0.7196 (m-10) cc_final: 0.6981 (m-10) REVERT: C 420 ASP cc_start: 0.8913 (m-30) cc_final: 0.8588 (t0) REVERT: C 985 ASP cc_start: 0.7743 (p0) cc_final: 0.7509 (p0) outliers start: 33 outliers final: 10 residues processed: 195 average time/residue: 1.3667 time to fit residues: 312.2393 Evaluate side-chains 160 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 981 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 194 optimal weight: 1.9990 chunk 266 optimal weight: 3.9990 chunk 309 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 chunk 166 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 281 optimal weight: 0.9980 chunk 172 optimal weight: 0.7980 chunk 245 optimal weight: 5.9990 chunk 175 optimal weight: 0.7980 chunk 163 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 907 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN C 207 HIS ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.128520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.078977 restraints weight = 55352.801| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.91 r_work: 0.2968 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25920 Z= 0.129 Angle : 0.563 15.578 35409 Z= 0.279 Chirality : 0.045 0.287 4158 Planarity : 0.004 0.045 4476 Dihedral : 5.551 59.834 4607 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.32 % Allowed : 7.98 % Favored : 90.71 % 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: 0.31 (0.15), residues: 3072 helix: 2.00 (0.21), residues: 664 sheet: 0.39 (0.19), residues: 668 loop : -0.58 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.006 0.001 HIS A 207 PHE 0.021 0.001 PHE B 168 TYR 0.024 0.001 TYR B 453 ARG 0.008 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 42) link_NAG-ASN : angle 3.09972 ( 126) link_BETA1-4 : bond 0.00331 ( 18) link_BETA1-4 : angle 1.06011 ( 54) hydrogen bonds : bond 0.04227 ( 1022) hydrogen bonds : angle 5.76998 ( 2985) SS BOND : bond 0.00194 ( 42) SS BOND : angle 0.70771 ( 84) covalent geometry : bond 0.00282 (25818) covalent geometry : angle 0.53048 (35145) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 2.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8148 (m-40) cc_final: 0.7873 (m-40) REVERT: A 153 MET cc_start: 0.5362 (ptt) cc_final: 0.4111 (mmm) REVERT: A 1092 GLU cc_start: 0.8541 (pm20) cc_final: 0.8103 (pp20) REVERT: B 153 MET cc_start: 0.6443 (tpp) cc_final: 0.5973 (ppp) REVERT: B 309 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8628 (mp0) REVERT: B 360 ASN cc_start: 0.8366 (t0) cc_final: 0.8161 (t0) REVERT: B 400 PHE cc_start: 0.9241 (p90) cc_final: 0.8925 (p90) REVERT: B 403 ARG cc_start: 0.6466 (mtp180) cc_final: 0.6195 (ttt180) REVERT: B 408 ARG cc_start: 0.8039 (ptt90) cc_final: 0.7536 (ptm-80) REVERT: B 1138 TYR cc_start: 0.8663 (t80) cc_final: 0.8314 (t80) REVERT: C 189 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7903 (mt) REVERT: C 194 PHE cc_start: 0.7345 (m-10) cc_final: 0.7124 (m-10) REVERT: C 392 PHE cc_start: 0.7755 (m-80) cc_final: 0.7490 (m-80) REVERT: C 420 ASP cc_start: 0.8944 (m-30) cc_final: 0.8616 (t0) REVERT: C 985 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7499 (p0) REVERT: C 988 GLU cc_start: 0.8972 (mp0) cc_final: 0.8660 (pm20) REVERT: C 1141 LEU cc_start: 0.7443 (tt) cc_final: 0.7137 (tm) outliers start: 36 outliers final: 13 residues processed: 186 average time/residue: 1.2704 time to fit residues: 277.3750 Evaluate side-chains 151 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 2.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 985 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 163 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 148 optimal weight: 30.0000 chunk 156 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 284 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 755 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 907 ASN C 824 ASN C 955 ASN C 957 GLN C1002 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.126849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.076143 restraints weight = 55511.050| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.87 r_work: 0.2916 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 25920 Z= 0.207 Angle : 0.592 14.788 35409 Z= 0.295 Chirality : 0.046 0.254 4158 Planarity : 0.004 0.045 4476 Dihedral : 5.353 59.825 4607 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.39 % Allowed : 8.93 % Favored : 89.68 % 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: 0.33 (0.15), residues: 3072 helix: 2.10 (0.20), residues: 670 sheet: 0.27 (0.20), residues: 676 loop : -0.55 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 104 HIS 0.006 0.001 HIS A 207 PHE 0.020 0.001 PHE C 140 TYR 0.023 0.001 TYR C1067 ARG 0.006 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00644 ( 42) link_NAG-ASN : angle 3.09258 ( 126) link_BETA1-4 : bond 0.00185 ( 18) link_BETA1-4 : angle 1.14057 ( 54) hydrogen bonds : bond 0.04542 ( 1022) hydrogen bonds : angle 5.74751 ( 2985) SS BOND : bond 0.00151 ( 42) SS BOND : angle 0.65539 ( 84) covalent geometry : bond 0.00471 (25818) covalent geometry : angle 0.56165 (35145) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5506 (ptt) cc_final: 0.3976 (tmm) REVERT: B 153 MET cc_start: 0.6513 (tpp) cc_final: 0.6003 (ppp) REVERT: B 360 ASN cc_start: 0.8468 (t0) cc_final: 0.8260 (t0) REVERT: B 400 PHE cc_start: 0.9279 (p90) cc_final: 0.8901 (p90) REVERT: B 408 ARG cc_start: 0.8116 (ptt90) cc_final: 0.7613 (ptm-80) REVERT: B 512 VAL cc_start: 0.9289 (t) cc_final: 0.9066 (p) REVERT: B 985 ASP cc_start: 0.8373 (p0) cc_final: 0.8121 (p0) REVERT: C 97 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.7123 (mmmm) REVERT: C 229 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7098 (tm) REVERT: C 392 PHE cc_start: 0.7903 (m-80) cc_final: 0.7452 (m-10) REVERT: C 420 ASP cc_start: 0.8859 (m-30) cc_final: 0.8563 (t0) REVERT: C 421 TYR cc_start: 0.9099 (m-80) cc_final: 0.8485 (m-80) REVERT: C 985 ASP cc_start: 0.8027 (p0) cc_final: 0.7468 (p0) REVERT: C 988 GLU cc_start: 0.9035 (mp0) cc_final: 0.8717 (pm20) REVERT: C 990 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8549 (tm-30) REVERT: C 1141 LEU cc_start: 0.7414 (tt) cc_final: 0.7175 (tm) outliers start: 38 outliers final: 14 residues processed: 174 average time/residue: 1.2099 time to fit residues: 249.4691 Evaluate side-chains 150 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 2.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 540 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 246 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 277 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 254 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.126537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.074900 restraints weight = 55452.513| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.83 r_work: 0.2939 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25920 Z= 0.190 Angle : 0.579 13.661 35409 Z= 0.288 Chirality : 0.045 0.238 4158 Planarity : 0.004 0.042 4476 Dihedral : 5.210 57.997 4607 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.46 % Allowed : 9.22 % Favored : 89.32 % 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: 0.37 (0.15), residues: 3072 helix: 2.19 (0.20), residues: 670 sheet: 0.24 (0.20), residues: 673 loop : -0.52 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 104 HIS 0.006 0.001 HIS A 207 PHE 0.017 0.001 PHE C 79 TYR 0.021 0.001 TYR C1067 ARG 0.005 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00608 ( 42) link_NAG-ASN : angle 2.97702 ( 126) link_BETA1-4 : bond 0.00166 ( 18) link_BETA1-4 : angle 1.01750 ( 54) hydrogen bonds : bond 0.04394 ( 1022) hydrogen bonds : angle 5.64814 ( 2985) SS BOND : bond 0.00130 ( 42) SS BOND : angle 0.65096 ( 84) covalent geometry : bond 0.00427 (25818) covalent geometry : angle 0.55028 (35145) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 3.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5233 (ptt) cc_final: 0.3682 (tmm) REVERT: B 153 MET cc_start: 0.6597 (tpp) cc_final: 0.6105 (ppp) REVERT: B 168 PHE cc_start: 0.6446 (t80) cc_final: 0.6140 (t80) REVERT: B 309 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8715 (mp0) REVERT: B 360 ASN cc_start: 0.8511 (t0) cc_final: 0.8307 (t0) REVERT: B 400 PHE cc_start: 0.9232 (p90) cc_final: 0.8847 (p90) REVERT: B 408 ARG cc_start: 0.8160 (ptt90) cc_final: 0.7637 (ptm-80) REVERT: B 512 VAL cc_start: 0.9250 (t) cc_final: 0.9031 (p) REVERT: C 97 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7387 (mmmm) REVERT: C 189 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8027 (mt) REVERT: C 229 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7305 (tm) REVERT: C 378 LYS cc_start: 0.8030 (ttmm) cc_final: 0.7551 (tmmm) REVERT: C 392 PHE cc_start: 0.8054 (m-80) cc_final: 0.7818 (m-80) REVERT: C 420 ASP cc_start: 0.8825 (m-30) cc_final: 0.8594 (t0) REVERT: C 512 VAL cc_start: 0.8653 (t) cc_final: 0.8340 (m) REVERT: C 584 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7251 (mm) REVERT: C 990 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8564 (tm-30) outliers start: 40 outliers final: 14 residues processed: 171 average time/residue: 1.2166 time to fit residues: 247.0270 Evaluate side-chains 147 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 2.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 584 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 42 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 144 optimal weight: 20.0000 chunk 140 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 306 optimal weight: 0.4980 chunk 255 optimal weight: 2.9990 chunk 196 optimal weight: 0.5980 chunk 227 optimal weight: 5.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 907 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.127202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.076843 restraints weight = 55050.278| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.01 r_work: 0.2930 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25920 Z= 0.127 Angle : 0.553 12.977 35409 Z= 0.273 Chirality : 0.044 0.241 4158 Planarity : 0.004 0.046 4476 Dihedral : 5.038 55.589 4607 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.32 % Allowed : 9.66 % Favored : 89.02 % 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: 0.48 (0.15), residues: 3072 helix: 2.29 (0.20), residues: 673 sheet: 0.26 (0.20), residues: 658 loop : -0.43 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 104 HIS 0.004 0.001 HIS A 207 PHE 0.019 0.001 PHE C 79 TYR 0.030 0.001 TYR C 453 ARG 0.004 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 42) link_NAG-ASN : angle 2.84392 ( 126) link_BETA1-4 : bond 0.00238 ( 18) link_BETA1-4 : angle 0.98461 ( 54) hydrogen bonds : bond 0.04068 ( 1022) hydrogen bonds : angle 5.50756 ( 2985) SS BOND : bond 0.00096 ( 42) SS BOND : angle 0.56712 ( 84) covalent geometry : bond 0.00282 (25818) covalent geometry : angle 0.52624 (35145) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5339 (ptt) cc_final: 0.3806 (tmm) REVERT: B 97 LYS cc_start: 0.6903 (OUTLIER) cc_final: 0.6542 (mtpp) REVERT: B 153 MET cc_start: 0.6574 (tpp) cc_final: 0.6150 (ppp) REVERT: B 281 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8738 (pp20) REVERT: B 309 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8700 (mp0) REVERT: B 360 ASN cc_start: 0.8503 (t0) cc_final: 0.8302 (t0) REVERT: B 400 PHE cc_start: 0.9258 (p90) cc_final: 0.8919 (p90) REVERT: B 408 ARG cc_start: 0.8192 (ptt90) cc_final: 0.7650 (ptm-80) REVERT: B 423 TYR cc_start: 0.7625 (t80) cc_final: 0.7180 (t80) REVERT: B 512 VAL cc_start: 0.9246 (t) cc_final: 0.9027 (p) REVERT: C 97 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7423 (mmmm) REVERT: C 189 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8006 (mt) REVERT: C 194 PHE cc_start: 0.7357 (m-10) cc_final: 0.7080 (m-10) REVERT: C 229 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7367 (tt) REVERT: C 378 LYS cc_start: 0.8069 (ttmm) cc_final: 0.7525 (tmmm) REVERT: C 392 PHE cc_start: 0.8036 (m-80) cc_final: 0.7786 (m-80) REVERT: C 400 PHE cc_start: 0.8585 (p90) cc_final: 0.8234 (p90) REVERT: C 421 TYR cc_start: 0.9068 (m-80) cc_final: 0.8490 (m-80) REVERT: C 512 VAL cc_start: 0.8737 (t) cc_final: 0.8392 (m) REVERT: C 584 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7268 (mm) REVERT: C 988 GLU cc_start: 0.9021 (mp0) cc_final: 0.8789 (pm20) REVERT: C 990 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8530 (tm-30) outliers start: 36 outliers final: 13 residues processed: 166 average time/residue: 1.2295 time to fit residues: 244.1239 Evaluate side-chains 149 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 584 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 155 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 77 optimal weight: 0.3980 chunk 192 optimal weight: 1.9990 chunk 286 optimal weight: 0.9980 chunk 160 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 267 optimal weight: 0.8980 chunk 71 optimal weight: 0.0040 chunk 123 optimal weight: 5.9990 chunk 35 optimal weight: 40.0000 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.127461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.076336 restraints weight = 55179.271| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.79 r_work: 0.2966 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25920 Z= 0.115 Angle : 0.543 12.543 35409 Z= 0.267 Chirality : 0.044 0.246 4158 Planarity : 0.003 0.044 4476 Dihedral : 4.831 53.218 4607 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.17 % Allowed : 10.28 % Favored : 88.55 % 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: 0.55 (0.15), residues: 3072 helix: 2.40 (0.20), residues: 672 sheet: 0.28 (0.20), residues: 654 loop : -0.40 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 104 HIS 0.004 0.000 HIS A 207 PHE 0.016 0.001 PHE A 168 TYR 0.024 0.001 TYR B 453 ARG 0.006 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00556 ( 42) link_NAG-ASN : angle 2.75629 ( 126) link_BETA1-4 : bond 0.00275 ( 18) link_BETA1-4 : angle 0.96540 ( 54) hydrogen bonds : bond 0.03869 ( 1022) hydrogen bonds : angle 5.35434 ( 2985) SS BOND : bond 0.00084 ( 42) SS BOND : angle 0.53802 ( 84) covalent geometry : bond 0.00253 (25818) covalent geometry : angle 0.51727 (35145) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 2.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5316 (ptt) cc_final: 0.3694 (tpt) REVERT: B 97 LYS cc_start: 0.6906 (OUTLIER) cc_final: 0.6536 (mtpp) REVERT: B 153 MET cc_start: 0.6620 (tpp) cc_final: 0.6228 (ppp) REVERT: B 281 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8747 (pp20) REVERT: B 309 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8718 (mp0) REVERT: B 360 ASN cc_start: 0.8535 (t0) cc_final: 0.8311 (t0) REVERT: B 400 PHE cc_start: 0.9284 (p90) cc_final: 0.8836 (p90) REVERT: B 408 ARG cc_start: 0.8250 (ptt90) cc_final: 0.7742 (ptm160) REVERT: B 423 TYR cc_start: 0.7633 (t80) cc_final: 0.7048 (t80) REVERT: B 512 VAL cc_start: 0.9299 (t) cc_final: 0.9069 (p) REVERT: C 97 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7426 (mmmm) REVERT: C 135 PHE cc_start: 0.7556 (m-80) cc_final: 0.7098 (m-80) REVERT: C 189 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8095 (mt) REVERT: C 194 PHE cc_start: 0.7446 (m-10) cc_final: 0.7163 (m-10) REVERT: C 229 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7505 (tt) REVERT: C 378 LYS cc_start: 0.8101 (ttmm) cc_final: 0.7568 (tmmm) REVERT: C 392 PHE cc_start: 0.8159 (m-80) cc_final: 0.7878 (m-80) REVERT: C 400 PHE cc_start: 0.8550 (p90) cc_final: 0.8215 (p90) REVERT: C 512 VAL cc_start: 0.8813 (t) cc_final: 0.8543 (m) REVERT: C 584 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7410 (mm) REVERT: C 661 GLU cc_start: 0.8642 (pm20) cc_final: 0.8261 (pm20) REVERT: C 990 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8544 (tm-30) outliers start: 32 outliers final: 13 residues processed: 170 average time/residue: 1.1590 time to fit residues: 235.1217 Evaluate side-chains 155 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 584 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 48 optimal weight: 4.9990 chunk 297 optimal weight: 0.0970 chunk 219 optimal weight: 7.9990 chunk 157 optimal weight: 0.2980 chunk 85 optimal weight: 1.9990 chunk 280 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 272 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN A1005 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN C 580 GLN C 955 ASN C 957 GLN C1002 GLN C1011 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.126513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.075893 restraints weight = 55303.361| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.69 r_work: 0.2950 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25920 Z= 0.147 Angle : 0.560 12.590 35409 Z= 0.276 Chirality : 0.045 0.238 4158 Planarity : 0.004 0.045 4476 Dihedral : 4.800 53.000 4607 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.13 % Allowed : 10.65 % Favored : 88.22 % 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: 0.54 (0.15), residues: 3072 helix: 2.31 (0.20), residues: 680 sheet: 0.27 (0.20), residues: 662 loop : -0.38 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 104 HIS 0.004 0.001 HIS A 207 PHE 0.019 0.001 PHE A 79 TYR 0.037 0.001 TYR C 453 ARG 0.004 0.000 ARG A 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00555 ( 42) link_NAG-ASN : angle 2.74083 ( 126) link_BETA1-4 : bond 0.00229 ( 18) link_BETA1-4 : angle 1.01191 ( 54) hydrogen bonds : bond 0.04077 ( 1022) hydrogen bonds : angle 5.40055 ( 2985) SS BOND : bond 0.00159 ( 42) SS BOND : angle 0.71324 ( 84) covalent geometry : bond 0.00330 (25818) covalent geometry : angle 0.53503 (35145) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 2.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5281 (ptt) cc_final: 0.3617 (tpp) REVERT: B 97 LYS cc_start: 0.6918 (OUTLIER) cc_final: 0.6649 (mtpp) REVERT: B 153 MET cc_start: 0.6612 (tpp) cc_final: 0.6227 (ppp) REVERT: B 281 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8727 (pp20) REVERT: B 360 ASN cc_start: 0.8582 (t0) cc_final: 0.8369 (t0) REVERT: B 400 PHE cc_start: 0.9314 (p90) cc_final: 0.8906 (p90) REVERT: B 408 ARG cc_start: 0.8267 (ptt90) cc_final: 0.7747 (ptm160) REVERT: B 423 TYR cc_start: 0.7647 (t80) cc_final: 0.7053 (t80) REVERT: B 512 VAL cc_start: 0.9267 (t) cc_final: 0.9030 (p) REVERT: C 97 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7420 (mmmm) REVERT: C 135 PHE cc_start: 0.7529 (m-80) cc_final: 0.7072 (m-80) REVERT: C 189 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8092 (mt) REVERT: C 351 TYR cc_start: 0.8476 (p90) cc_final: 0.8165 (p90) REVERT: C 392 PHE cc_start: 0.8119 (m-80) cc_final: 0.7862 (m-80) REVERT: C 400 PHE cc_start: 0.8533 (p90) cc_final: 0.8170 (p90) REVERT: C 512 VAL cc_start: 0.8738 (t) cc_final: 0.8454 (m) REVERT: C 584 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7420 (mm) REVERT: C 990 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8554 (tm-30) outliers start: 31 outliers final: 14 residues processed: 162 average time/residue: 1.2063 time to fit residues: 232.4644 Evaluate side-chains 153 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 584 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 160 optimal weight: 4.9990 chunk 305 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 302 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 191 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 264 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 957 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.126570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.075721 restraints weight = 55464.592| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.72 r_work: 0.2952 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25920 Z= 0.136 Angle : 0.552 12.697 35409 Z= 0.272 Chirality : 0.045 0.247 4158 Planarity : 0.003 0.045 4476 Dihedral : 4.728 52.913 4607 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.99 % Allowed : 10.94 % Favored : 88.07 % 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: 0.57 (0.15), residues: 3072 helix: 2.32 (0.20), residues: 681 sheet: 0.28 (0.20), residues: 666 loop : -0.35 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP C 104 HIS 0.004 0.001 HIS A 207 PHE 0.025 0.001 PHE C 194 TYR 0.022 0.001 TYR B 453 ARG 0.004 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 42) link_NAG-ASN : angle 2.72753 ( 126) link_BETA1-4 : bond 0.00263 ( 18) link_BETA1-4 : angle 0.98202 ( 54) hydrogen bonds : bond 0.03967 ( 1022) hydrogen bonds : angle 5.34841 ( 2985) SS BOND : bond 0.00133 ( 42) SS BOND : angle 0.57565 ( 84) covalent geometry : bond 0.00303 (25818) covalent geometry : angle 0.52780 (35145) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 2.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5275 (ptt) cc_final: 0.3618 (tpp) REVERT: A 518 LEU cc_start: 0.2999 (OUTLIER) cc_final: 0.2575 (tt) REVERT: B 97 LYS cc_start: 0.6978 (OUTLIER) cc_final: 0.6715 (mtpp) REVERT: B 153 MET cc_start: 0.6492 (tpp) cc_final: 0.6191 (ppp) REVERT: B 281 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8771 (pp20) REVERT: B 309 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8710 (mp0) REVERT: B 360 ASN cc_start: 0.8581 (t0) cc_final: 0.8373 (t0) REVERT: B 400 PHE cc_start: 0.9331 (p90) cc_final: 0.8907 (p90) REVERT: B 408 ARG cc_start: 0.8283 (ptt90) cc_final: 0.7734 (ptm160) REVERT: B 423 TYR cc_start: 0.7586 (t80) cc_final: 0.6998 (t80) REVERT: B 512 VAL cc_start: 0.9282 (t) cc_final: 0.9039 (p) REVERT: C 97 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7434 (mmmm) REVERT: C 135 PHE cc_start: 0.7518 (m-80) cc_final: 0.7017 (m-80) REVERT: C 189 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8125 (mt) REVERT: C 378 LYS cc_start: 0.8159 (ttmm) cc_final: 0.7733 (tmmm) REVERT: C 392 PHE cc_start: 0.8070 (m-80) cc_final: 0.7793 (m-80) REVERT: C 400 PHE cc_start: 0.8540 (p90) cc_final: 0.8178 (p90) REVERT: C 512 VAL cc_start: 0.8763 (t) cc_final: 0.8496 (m) REVERT: C 740 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8173 (tmm) REVERT: C 988 GLU cc_start: 0.9016 (pm20) cc_final: 0.8733 (pm20) outliers start: 27 outliers final: 13 residues processed: 159 average time/residue: 1.2299 time to fit residues: 231.9538 Evaluate side-chains 151 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 3.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 740 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 60.332 > 50: distance: 39 - 53: 3.046 distance: 43 - 62: 14.204 distance: 47 - 67: 22.378 distance: 51 - 75: 31.572 distance: 53 - 54: 4.079 distance: 54 - 55: 7.092 distance: 54 - 57: 10.428 distance: 55 - 56: 19.315 distance: 55 - 62: 17.617 distance: 56 - 83: 27.457 distance: 57 - 58: 5.193 distance: 58 - 59: 13.323 distance: 59 - 60: 4.767 distance: 59 - 61: 11.419 distance: 62 - 63: 13.883 distance: 63 - 64: 13.254 distance: 63 - 66: 7.356 distance: 64 - 65: 9.267 distance: 64 - 67: 9.272 distance: 65 - 90: 26.232 distance: 67 - 68: 3.616 distance: 68 - 69: 17.498 distance: 68 - 71: 17.182 distance: 69 - 70: 10.111 distance: 69 - 75: 6.430 distance: 70 - 98: 23.989 distance: 71 - 72: 4.861 distance: 72 - 73: 8.405 distance: 72 - 74: 13.815 distance: 75 - 76: 4.220 distance: 76 - 77: 16.041 distance: 76 - 79: 10.952 distance: 77 - 78: 4.374 distance: 77 - 83: 7.409 distance: 78 - 105: 14.629 distance: 79 - 80: 22.537 distance: 80 - 81: 5.744 distance: 80 - 82: 5.981 distance: 83 - 84: 18.830 distance: 84 - 85: 10.013 distance: 84 - 87: 5.776 distance: 85 - 86: 13.852 distance: 86 - 114: 42.133 distance: 87 - 88: 12.526 distance: 87 - 89: 5.060 distance: 90 - 91: 13.305 distance: 91 - 92: 13.283 distance: 91 - 94: 9.722 distance: 92 - 93: 5.685 distance: 92 - 98: 7.357 distance: 95 - 96: 4.229 distance: 95 - 97: 35.506 distance: 98 - 99: 3.612 distance: 99 - 100: 3.484 distance: 99 - 102: 5.417 distance: 100 - 105: 14.578 distance: 102 - 104: 4.447 distance: 105 - 106: 31.493 distance: 106 - 109: 16.014 distance: 107 - 114: 12.741 distance: 109 - 110: 23.495 distance: 110 - 111: 18.679 distance: 111 - 112: 38.583 distance: 112 - 113: 21.173 distance: 114 - 115: 18.709 distance: 115 - 116: 17.362 distance: 115 - 118: 4.473 distance: 116 - 117: 6.861 distance: 116 - 123: 17.749 distance: 119 - 120: 16.936 distance: 120 - 121: 15.205 distance: 120 - 122: 18.836 distance: 123 - 124: 17.784 distance: 124 - 127: 39.347 distance: 125 - 131: 34.602 distance: 127 - 128: 10.190 distance: 128 - 129: 40.357 distance: 128 - 130: 29.134