Starting phenix.real_space_refine on Thu Mar 5 21:31:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sxs_25504/03_2026/7sxs_25504.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sxs_25504/03_2026/7sxs_25504.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sxs_25504/03_2026/7sxs_25504.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sxs_25504/03_2026/7sxs_25504.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sxs_25504/03_2026/7sxs_25504.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sxs_25504/03_2026/7sxs_25504.map" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.038 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 16059 2.51 5 N 4137 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25245 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 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: 5.28, per 1000 atoms: 0.21 Number of scatterers: 25245 At special positions: 0 Unit cell: (140, 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 4137 7.00 C 16059 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=2.02 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: 2.03 Conformation dependent library (CDL) restraints added in 981.7 milliseconds 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, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 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: 4.087A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.653A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.489A 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: 4.123A 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: 3.673A 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: 3.903A 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: 4.025A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.606A 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: 3.968A 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: 3.695A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.922A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.563A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.986A 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: 3.609A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.500A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.557A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.924A 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: 3.574A 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 1033 removed outlier: 3.948A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.602A 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: 3.747A 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 389 removed outlier: 3.648A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.869A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.576A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.917A 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: 3.694A 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: 3.991A 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: 3.576A 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 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.303A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.567A 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: 8.092A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.960A 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: 3.622A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.251A 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: 3.962A 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: 3.691A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.076A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.214A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.284A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.691A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.726A 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: 6.847A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.945A 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: 5.088A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.449A 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: 3.967A 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: 3.503A 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: 6.021A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.410A 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: 6.848A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.875A 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: 6.565A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.041A 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: 6.565A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.576A 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: 4.155A 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: 3.709A 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: 8.359A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.094A 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: 4.075A 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: 3.672A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.502A 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: 5.081A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.072A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 10.223A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.237A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.713A 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: 3.671A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.526A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.847A 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: 3.621A 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: 5.930A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.434A 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: 3.606A 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: 6.485A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.085A 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: 6.485A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.494A 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: 4.263A 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: 8.177A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.716A 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: 4.212A 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: 3.932A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.544A 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: 9.823A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.880A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 10.252A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.768A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS C 136 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.923A 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: 5.174A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.861A 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: 3.669A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.669A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) 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: 3.635A 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: 6.210A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.473A 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: 6.474A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.044A 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: 6.652A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.057A 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: 6.474A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.583A 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: 4.136A 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 1098 hydrogen bonds defined for protein. 3015 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.01 Time building geometry restraints manager: 2.53 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: 7529 1.34 - 1.46: 6242 1.46 - 1.58: 11903 1.58 - 1.70: 0 1.70 - 1.83: 138 Bond restraints: 25812 Sorted by residual: bond pdb=" C LEU C 560 " pdb=" N PRO C 561 " ideal model delta sigma weight residual 1.334 1.387 -0.052 1.51e-02 4.39e+03 1.20e+01 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.45e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.41e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.05e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.66e+00 ... (remaining 25807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 34002 1.99 - 3.98: 1006 3.98 - 5.97: 95 5.97 - 7.96: 21 7.96 - 9.95: 9 Bond angle restraints: 35133 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 110.70 116.39 -5.69 1.22e+00 6.72e-01 2.18e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.34 -5.64 1.22e+00 6.72e-01 2.14e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.07 -5.37 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 114.10 122.33 -8.23 2.00e+00 2.50e-01 1.69e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 122.67 -4.74 1.20e+00 6.94e-01 1.56e+01 ... (remaining 35128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 14918 17.98 - 35.96: 1006 35.96 - 53.94: 168 53.94 - 71.93: 58 71.93 - 89.91: 29 Dihedral angle restraints: 16179 sinusoidal: 7101 harmonic: 9078 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 180.00 154.06 25.94 0 5.00e+00 4.00e-02 2.69e+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 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+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 180.00 157.35 22.65 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 16176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3283 0.063 - 0.127: 778 0.127 - 0.190: 84 0.190 - 0.253: 5 0.253 - 0.317: 5 Chirality restraints: 4155 Sorted by residual: 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 -2.08 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.43e+00 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 2.39e+00 ... (remaining 4152 not shown) Planarity restraints: 4521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 902 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.56e+00 pdb=" C MET C 902 " 0.053 2.00e-02 2.50e+03 pdb=" O MET C 902 " -0.020 2.00e-02 2.50e+03 pdb=" N ALA C 903 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 920 " -0.014 2.00e-02 2.50e+03 2.89e-02 8.33e+00 pdb=" C GLN C 920 " 0.050 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=" CB PHE B 135 " 0.014 2.00e-02 2.50e+03 2.17e-02 8.27e+00 pdb=" CG PHE B 135 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE B 135 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE B 135 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 135 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE B 135 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE B 135 " 0.001 2.00e-02 2.50e+03 ... (remaining 4518 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6164 2.80 - 3.32: 21113 3.32 - 3.85: 43056 3.85 - 4.37: 49720 4.37 - 4.90: 85023 Nonbonded interactions: 205076 Sorted by model distance: nonbonded pdb=" OH TYR A 369 " pdb=" O ALA C 475 " model vdw 2.272 3.040 nonbonded pdb=" OE1 GLN B 115 " pdb=" OG1 THR B 167 " model vdw 2.281 3.040 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.287 3.040 nonbonded pdb=" OD1 ASN B 394 " pdb=" OH TYR B 396 " model vdw 2.289 3.040 nonbonded pdb=" O ASP A 80 " pdb=" OH TYR A 265 " model vdw 2.316 3.040 ... (remaining 205071 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: 0.03 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: 3.780 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.650 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 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:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 0.070 25914 Z= 0.226 Angle : 0.805 14.982 35397 Z= 0.415 Chirality : 0.053 0.317 4155 Planarity : 0.007 0.066 4479 Dihedral : 12.905 89.907 10209 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.13), residues: 3072 helix: 0.21 (0.18), residues: 639 sheet: 0.21 (0.19), residues: 684 loop : -0.90 (0.13), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 357 TYR 0.025 0.002 TYR C1067 PHE 0.043 0.002 PHE B 135 TRP 0.023 0.002 TRP A 886 HIS 0.006 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00475 (25812) covalent geometry : angle 0.77616 (35133) SS BOND : bond 0.00240 ( 42) SS BOND : angle 1.29507 ( 84) hydrogen bonds : bond 0.16762 ( 1028) hydrogen bonds : angle 8.04409 ( 3015) link_BETA1-4 : bond 0.00667 ( 18) link_BETA1-4 : angle 1.41482 ( 54) link_NAG-ASN : bond 0.00801 ( 42) link_NAG-ASN : angle 3.49438 ( 126) *********************** 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 219 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PRO cc_start: 0.8970 (Cg_exo) cc_final: 0.8722 (Cg_endo) REVERT: A 153 MET cc_start: 0.3575 (ptt) cc_final: 0.3367 (tpt) REVERT: A 175 PHE cc_start: 0.5143 (m-10) cc_final: 0.4891 (m-10) REVERT: B 140 PHE cc_start: 0.7854 (p90) cc_final: 0.7472 (OUTLIER) REVERT: B 244 LEU cc_start: 0.6402 (mt) cc_final: 0.6059 (tm) REVERT: C 85 PRO cc_start: 0.8669 (Cg_exo) cc_final: 0.8144 (Cg_endo) REVERT: C 218 GLN cc_start: 0.7911 (tt0) cc_final: 0.7661 (tp-100) REVERT: C 226 LEU cc_start: 0.5896 (tp) cc_final: 0.5196 (mm) REVERT: C 403 ARG cc_start: 0.8140 (mtp180) cc_final: 0.7709 (mtp85) REVERT: C 421 TYR cc_start: 0.9113 (m-10) cc_final: 0.8751 (m-10) outliers start: 0 outliers final: 2 residues processed: 219 average time/residue: 0.6807 time to fit residues: 171.0994 Evaluate side-chains 102 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A1005 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN C 580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.104126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.062564 restraints weight = 71631.074| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.38 r_work: 0.2945 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25914 Z= 0.218 Angle : 0.651 13.044 35397 Z= 0.324 Chirality : 0.048 0.706 4155 Planarity : 0.005 0.062 4479 Dihedral : 6.574 59.309 4607 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.77 % Allowed : 5.67 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.14), residues: 3072 helix: 1.53 (0.20), residues: 670 sheet: 0.19 (0.19), residues: 677 loop : -0.60 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 190 TYR 0.021 0.002 TYR C1067 PHE 0.021 0.002 PHE B 135 TRP 0.022 0.002 TRP A 353 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00489 (25812) covalent geometry : angle 0.62206 (35133) SS BOND : bond 0.00210 ( 42) SS BOND : angle 0.79915 ( 84) hydrogen bonds : bond 0.04675 ( 1028) hydrogen bonds : angle 6.14086 ( 3015) link_BETA1-4 : bond 0.00202 ( 18) link_BETA1-4 : angle 1.29161 ( 54) link_NAG-ASN : bond 0.00601 ( 42) link_NAG-ASN : angle 3.16388 ( 126) *********************** 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 130 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3910 (ptt) cc_final: 0.3564 (tpt) REVERT: A 304 LYS cc_start: 0.9413 (mmmm) cc_final: 0.9184 (mmmm) REVERT: B 140 PHE cc_start: 0.8246 (p90) cc_final: 0.8026 (OUTLIER) REVERT: B 858 LEU cc_start: 0.9060 (mt) cc_final: 0.8579 (pt) REVERT: C 378 LYS cc_start: 0.8572 (ttpt) cc_final: 0.7992 (ttpt) REVERT: C 403 ARG cc_start: 0.8019 (mtp180) cc_final: 0.7557 (mmm-85) REVERT: C 417 LYS cc_start: 0.9049 (tptt) cc_final: 0.8641 (tptp) REVERT: C 421 TYR cc_start: 0.9087 (m-10) cc_final: 0.8773 (m-10) outliers start: 21 outliers final: 8 residues processed: 124 average time/residue: 0.6413 time to fit residues: 92.8368 Evaluate side-chains 93 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 369 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 305 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 234 optimal weight: 0.9980 chunk 273 optimal weight: 3.9990 chunk 187 optimal weight: 0.5980 chunk 111 optimal weight: 9.9990 chunk 216 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 205 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 907 ASN B 125 ASN B 762 GLN B 901 GLN C 121 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.103778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.062497 restraints weight = 71607.507| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.25 r_work: 0.2944 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25914 Z= 0.172 Angle : 0.581 10.996 35397 Z= 0.289 Chirality : 0.045 0.445 4155 Planarity : 0.004 0.042 4479 Dihedral : 5.954 54.807 4607 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.06 % Allowed : 6.66 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.15), residues: 3072 helix: 1.91 (0.20), residues: 688 sheet: 0.17 (0.19), residues: 674 loop : -0.50 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 995 TYR 0.020 0.001 TYR C1067 PHE 0.024 0.001 PHE B 565 TRP 0.017 0.001 TRP A 353 HIS 0.003 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00381 (25812) covalent geometry : angle 0.55320 (35133) SS BOND : bond 0.00180 ( 42) SS BOND : angle 0.68291 ( 84) hydrogen bonds : bond 0.04355 ( 1028) hydrogen bonds : angle 5.82708 ( 3015) link_BETA1-4 : bond 0.00236 ( 18) link_BETA1-4 : angle 1.10572 ( 54) link_NAG-ASN : bond 0.00954 ( 42) link_NAG-ASN : angle 2.96169 ( 126) *********************** 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 123 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3696 (ptt) cc_final: 0.3335 (tpt) REVERT: A 1010 GLN cc_start: 0.9262 (OUTLIER) cc_final: 0.8615 (mp10) REVERT: A 1029 MET cc_start: 0.9670 (OUTLIER) cc_final: 0.9372 (tpp) REVERT: B 140 PHE cc_start: 0.8433 (p90) cc_final: 0.8212 (OUTLIER) REVERT: B 434 ILE cc_start: 0.5757 (OUTLIER) cc_final: 0.5345 (pp) REVERT: C 144 TYR cc_start: 0.5303 (m-10) cc_final: 0.5035 (m-80) REVERT: C 218 GLN cc_start: 0.8121 (tt0) cc_final: 0.7622 (tp-100) REVERT: C 403 ARG cc_start: 0.7961 (mtp180) cc_final: 0.7504 (mtp85) REVERT: C 417 LYS cc_start: 0.9106 (tptt) cc_final: 0.8777 (tptp) REVERT: C 421 TYR cc_start: 0.9147 (m-10) cc_final: 0.8778 (m-10) REVERT: C 584 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8116 (mm) outliers start: 29 outliers final: 11 residues processed: 117 average time/residue: 0.5522 time to fit residues: 77.6449 Evaluate side-chains 104 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 745 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 214 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 153 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 243 optimal weight: 0.9980 chunk 144 optimal weight: 9.9990 chunk 270 optimal weight: 0.6980 chunk 192 optimal weight: 0.7980 chunk 147 optimal weight: 40.0000 chunk 107 optimal weight: 0.9980 overall best weight: 2.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN B 245 HIS B 354 ASN B 762 GLN B 824 ASN B 907 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.102015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.060261 restraints weight = 71436.766| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.31 r_work: 0.2890 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 25914 Z= 0.267 Angle : 0.629 14.692 35397 Z= 0.311 Chirality : 0.047 0.536 4155 Planarity : 0.004 0.053 4479 Dihedral : 5.778 56.255 4607 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.46 % Allowed : 7.46 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.15), residues: 3072 helix: 2.05 (0.20), residues: 700 sheet: -0.01 (0.19), residues: 684 loop : -0.50 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 995 TYR 0.020 0.002 TYR C1067 PHE 0.026 0.002 PHE B 565 TRP 0.015 0.002 TRP A 886 HIS 0.004 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00602 (25812) covalent geometry : angle 0.60524 (35133) SS BOND : bond 0.00207 ( 42) SS BOND : angle 0.67765 ( 84) hydrogen bonds : bond 0.04645 ( 1028) hydrogen bonds : angle 5.82485 ( 3015) link_BETA1-4 : bond 0.00193 ( 18) link_BETA1-4 : angle 1.20389 ( 54) link_NAG-ASN : bond 0.00832 ( 42) link_NAG-ASN : angle 2.85552 ( 126) *********************** 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 131 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 91 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3975 (ptt) cc_final: 0.3511 (tpt) REVERT: A 323 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8718 (p) REVERT: A 365 TYR cc_start: 0.8192 (m-80) cc_final: 0.7930 (m-80) REVERT: A 1010 GLN cc_start: 0.9292 (OUTLIER) cc_final: 0.8904 (mp10) REVERT: B 140 PHE cc_start: 0.8482 (p90) cc_final: 0.8269 (OUTLIER) REVERT: B 354 ASN cc_start: 0.8159 (t0) cc_final: 0.7771 (m-40) REVERT: B 392 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.7424 (m-80) REVERT: B 434 ILE cc_start: 0.5893 (OUTLIER) cc_final: 0.5426 (pp) REVERT: B 858 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8734 (pt) REVERT: C 101 ILE cc_start: 0.6389 (mm) cc_final: 0.5889 (OUTLIER) REVERT: C 218 GLN cc_start: 0.8228 (tt0) cc_final: 0.7733 (tp-100) REVERT: C 403 ARG cc_start: 0.7957 (mtp180) cc_final: 0.7568 (mtp-110) REVERT: C 417 LYS cc_start: 0.9150 (tptt) cc_final: 0.8866 (tptp) REVERT: C 421 TYR cc_start: 0.9082 (m-10) cc_final: 0.8694 (m-10) REVERT: C 495 TYR cc_start: 0.6332 (m-80) cc_final: 0.6066 (m-80) REVERT: C 584 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8232 (mm) REVERT: C 995 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8822 (mtp-110) outliers start: 40 outliers final: 15 residues processed: 122 average time/residue: 0.5254 time to fit residues: 77.1987 Evaluate side-chains 106 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 295 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 279 optimal weight: 0.0670 chunk 100 optimal weight: 0.9980 chunk 246 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 190 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 141 optimal weight: 0.9980 chunk 254 optimal weight: 5.9990 overall best weight: 1.3320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 907 ASN C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.102771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.061671 restraints weight = 71114.725| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.24 r_work: 0.2916 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25914 Z= 0.156 Angle : 0.559 11.028 35397 Z= 0.277 Chirality : 0.045 0.410 4155 Planarity : 0.004 0.050 4479 Dihedral : 5.324 54.871 4605 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.91 % Allowed : 8.56 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.15), residues: 3072 helix: 2.23 (0.20), residues: 700 sheet: -0.03 (0.20), residues: 655 loop : -0.43 (0.14), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 995 TYR 0.020 0.001 TYR C1067 PHE 0.026 0.001 PHE C 497 TRP 0.027 0.001 TRP C 104 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00347 (25812) covalent geometry : angle 0.53386 (35133) SS BOND : bond 0.00135 ( 42) SS BOND : angle 0.58308 ( 84) hydrogen bonds : bond 0.04152 ( 1028) hydrogen bonds : angle 5.62474 ( 3015) link_BETA1-4 : bond 0.00245 ( 18) link_BETA1-4 : angle 1.04358 ( 54) link_NAG-ASN : bond 0.00677 ( 42) link_NAG-ASN : angle 2.78008 ( 126) *********************** 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 114 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3864 (ptt) cc_final: 0.3383 (tpp) REVERT: A 323 THR cc_start: 0.9076 (OUTLIER) cc_final: 0.8745 (p) REVERT: A 365 TYR cc_start: 0.8151 (m-80) cc_final: 0.7905 (m-80) REVERT: A 1010 GLN cc_start: 0.9250 (OUTLIER) cc_final: 0.8904 (mp10) REVERT: B 140 PHE cc_start: 0.8532 (p90) cc_final: 0.8279 (OUTLIER) REVERT: B 392 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.7410 (m-80) REVERT: B 434 ILE cc_start: 0.5873 (OUTLIER) cc_final: 0.5404 (pp) REVERT: B 858 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8690 (pt) REVERT: C 218 GLN cc_start: 0.8251 (tt0) cc_final: 0.7798 (tp-100) REVERT: C 237 ARG cc_start: 0.6904 (ttp80) cc_final: 0.6382 (tmm-80) REVERT: C 403 ARG cc_start: 0.7918 (mtp180) cc_final: 0.7597 (mtp-110) REVERT: C 417 LYS cc_start: 0.9191 (tptt) cc_final: 0.8927 (tptp) REVERT: C 421 TYR cc_start: 0.9061 (m-10) cc_final: 0.8647 (m-10) REVERT: C 584 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8239 (mm) REVERT: C 995 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.8917 (mtp-110) outliers start: 25 outliers final: 10 residues processed: 107 average time/residue: 0.5949 time to fit residues: 75.2970 Evaluate side-chains 102 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 995 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 292 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 269 optimal weight: 4.9990 chunk 201 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 255 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 257 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 762 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.101704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.060511 restraints weight = 71622.495| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.30 r_work: 0.2889 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 25914 Z= 0.210 Angle : 0.578 10.877 35397 Z= 0.288 Chirality : 0.045 0.385 4155 Planarity : 0.004 0.051 4479 Dihedral : 5.183 54.548 4605 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.35 % Allowed : 8.82 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.15), residues: 3072 helix: 2.21 (0.20), residues: 700 sheet: -0.04 (0.20), residues: 647 loop : -0.41 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 765 TYR 0.020 0.001 TYR C1067 PHE 0.025 0.001 PHE B 565 TRP 0.010 0.001 TRP A 886 HIS 0.003 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00476 (25812) covalent geometry : angle 0.55378 (35133) SS BOND : bond 0.00163 ( 42) SS BOND : angle 0.63803 ( 84) hydrogen bonds : bond 0.04345 ( 1028) hydrogen bonds : angle 5.64484 ( 3015) link_BETA1-4 : bond 0.00163 ( 18) link_BETA1-4 : angle 1.13707 ( 54) link_NAG-ASN : bond 0.00702 ( 42) link_NAG-ASN : angle 2.77060 ( 126) *********************** 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 127 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 90 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3542 (ptt) cc_final: 0.3212 (tpp) REVERT: A 323 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8648 (p) REVERT: A 365 TYR cc_start: 0.8211 (m-80) cc_final: 0.7919 (m-80) REVERT: A 1010 GLN cc_start: 0.9258 (OUTLIER) cc_final: 0.8920 (mp10) REVERT: B 140 PHE cc_start: 0.8515 (p90) cc_final: 0.8300 (OUTLIER) REVERT: B 392 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.7463 (m-80) REVERT: B 858 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8779 (pt) REVERT: C 237 ARG cc_start: 0.7025 (ttp80) cc_final: 0.6481 (tmm-80) REVERT: C 324 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8882 (pm20) REVERT: C 403 ARG cc_start: 0.7956 (mtp180) cc_final: 0.7662 (mtp-110) REVERT: C 417 LYS cc_start: 0.9173 (tptt) cc_final: 0.8933 (tptm) REVERT: C 505 TYR cc_start: 0.7637 (t80) cc_final: 0.7393 (t80) REVERT: C 584 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8236 (mm) REVERT: C 995 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.8817 (mtp-110) outliers start: 37 outliers final: 15 residues processed: 119 average time/residue: 0.5684 time to fit residues: 80.3929 Evaluate side-chains 102 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 249 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 chunk 230 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 271 optimal weight: 0.7980 chunk 247 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 284 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.102095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.061328 restraints weight = 71169.702| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.18 r_work: 0.2908 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25914 Z= 0.158 Angle : 0.546 10.867 35397 Z= 0.272 Chirality : 0.044 0.376 4155 Planarity : 0.004 0.050 4479 Dihedral : 5.025 53.056 4605 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.13 % Allowed : 9.70 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.15), residues: 3072 helix: 2.31 (0.20), residues: 700 sheet: -0.03 (0.20), residues: 665 loop : -0.38 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 995 TYR 0.019 0.001 TYR C1067 PHE 0.035 0.001 PHE C 497 TRP 0.021 0.001 TRP C 104 HIS 0.003 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00352 (25812) covalent geometry : angle 0.52208 (35133) SS BOND : bond 0.00127 ( 42) SS BOND : angle 0.57798 ( 84) hydrogen bonds : bond 0.04046 ( 1028) hydrogen bonds : angle 5.52194 ( 3015) link_BETA1-4 : bond 0.00230 ( 18) link_BETA1-4 : angle 1.01586 ( 54) link_NAG-ASN : bond 0.00646 ( 42) link_NAG-ASN : angle 2.68305 ( 126) *********************** 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 114 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 83 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3403 (ptt) cc_final: 0.3003 (tpp) REVERT: A 323 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8640 (p) REVERT: A 365 TYR cc_start: 0.8180 (m-80) cc_final: 0.7892 (m-80) REVERT: A 1010 GLN cc_start: 0.9236 (OUTLIER) cc_final: 0.8920 (mp10) REVERT: B 140 PHE cc_start: 0.8503 (p90) cc_final: 0.8263 (OUTLIER) REVERT: B 434 ILE cc_start: 0.6255 (OUTLIER) cc_final: 0.5869 (pp) REVERT: B 858 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8737 (pt) REVERT: C 69 HIS cc_start: 0.5117 (t-90) cc_final: 0.4764 (t-90) REVERT: C 218 GLN cc_start: 0.8480 (tt0) cc_final: 0.8048 (tp-100) REVERT: C 237 ARG cc_start: 0.7126 (ttp80) cc_final: 0.6643 (tmm-80) REVERT: C 324 GLU cc_start: 0.9235 (OUTLIER) cc_final: 0.8853 (pm20) REVERT: C 403 ARG cc_start: 0.7942 (mtp180) cc_final: 0.7663 (mtp-110) REVERT: C 495 TYR cc_start: 0.5304 (m-80) cc_final: 0.4589 (m-80) REVERT: C 497 PHE cc_start: 0.3328 (m-10) cc_final: 0.2501 (m-80) REVERT: C 584 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8311 (mm) REVERT: C 995 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.8906 (mtp-110) outliers start: 31 outliers final: 14 residues processed: 108 average time/residue: 0.5663 time to fit residues: 73.1411 Evaluate side-chains 103 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 116 optimal weight: 20.0000 chunk 243 optimal weight: 6.9990 chunk 188 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 259 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 258 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.100950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.060044 restraints weight = 71334.566| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.23 r_work: 0.2869 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 25914 Z= 0.247 Angle : 0.592 10.546 35397 Z= 0.296 Chirality : 0.046 0.369 4155 Planarity : 0.004 0.050 4479 Dihedral : 5.169 53.742 4605 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.21 % Allowed : 9.88 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.15), residues: 3072 helix: 2.27 (0.20), residues: 699 sheet: -0.13 (0.20), residues: 656 loop : -0.42 (0.14), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 765 TYR 0.019 0.001 TYR C1067 PHE 0.028 0.001 PHE B 565 TRP 0.025 0.002 TRP C 104 HIS 0.003 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00561 (25812) covalent geometry : angle 0.56837 (35133) SS BOND : bond 0.00175 ( 42) SS BOND : angle 0.63385 ( 84) hydrogen bonds : bond 0.04393 ( 1028) hydrogen bonds : angle 5.65746 ( 3015) link_BETA1-4 : bond 0.00175 ( 18) link_BETA1-4 : angle 1.13662 ( 54) link_NAG-ASN : bond 0.00708 ( 42) link_NAG-ASN : angle 2.74134 ( 126) *********************** 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 120 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3555 (ptt) cc_final: 0.3100 (tpp) REVERT: A 323 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8611 (p) REVERT: A 365 TYR cc_start: 0.8194 (m-80) cc_final: 0.7852 (m-80) REVERT: A 1010 GLN cc_start: 0.9276 (OUTLIER) cc_final: 0.8907 (mp10) REVERT: B 140 PHE cc_start: 0.8466 (p90) cc_final: 0.8225 (p90) REVERT: B 392 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7437 (m-80) REVERT: B 434 ILE cc_start: 0.6484 (OUTLIER) cc_final: 0.6061 (pp) REVERT: B 858 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8817 (pt) REVERT: C 69 HIS cc_start: 0.5307 (t-90) cc_final: 0.5030 (t-90) REVERT: C 218 GLN cc_start: 0.8530 (tt0) cc_final: 0.7969 (tp40) REVERT: C 237 ARG cc_start: 0.7075 (ttp80) cc_final: 0.6618 (tmm-80) REVERT: C 324 GLU cc_start: 0.9230 (OUTLIER) cc_final: 0.8878 (pm20) REVERT: C 403 ARG cc_start: 0.7939 (mtp180) cc_final: 0.7660 (mtp-110) REVERT: C 417 LYS cc_start: 0.8760 (tptm) cc_final: 0.8409 (tptp) REVERT: C 584 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8196 (pp) REVERT: C 995 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.8839 (mtp-110) REVERT: C 1017 GLU cc_start: 0.9358 (tt0) cc_final: 0.8917 (tm-30) outliers start: 33 outliers final: 15 residues processed: 113 average time/residue: 0.5751 time to fit residues: 76.9087 Evaluate side-chains 108 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 254 optimal weight: 9.9990 chunk 311 optimal weight: 0.0570 chunk 212 optimal weight: 0.7980 chunk 267 optimal weight: 0.6980 chunk 292 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 270 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 242 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 195 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 957 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.102689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.062220 restraints weight = 70905.826| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.19 r_work: 0.2932 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25914 Z= 0.106 Angle : 0.530 10.967 35397 Z= 0.265 Chirality : 0.044 0.366 4155 Planarity : 0.004 0.049 4479 Dihedral : 4.829 52.860 4605 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.77 % Allowed : 10.57 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.15), residues: 3072 helix: 2.41 (0.20), residues: 699 sheet: -0.09 (0.20), residues: 654 loop : -0.32 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 319 TYR 0.020 0.001 TYR C1067 PHE 0.048 0.001 PHE C 497 TRP 0.026 0.001 TRP C 104 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00230 (25812) covalent geometry : angle 0.50731 (35133) SS BOND : bond 0.00113 ( 42) SS BOND : angle 0.56784 ( 84) hydrogen bonds : bond 0.03725 ( 1028) hydrogen bonds : angle 5.37611 ( 3015) link_BETA1-4 : bond 0.00357 ( 18) link_BETA1-4 : angle 0.94529 ( 54) link_NAG-ASN : bond 0.00619 ( 42) link_NAG-ASN : angle 2.57204 ( 126) *********************** 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 113 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3572 (ptt) cc_final: 0.3070 (tpp) REVERT: A 323 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8794 (p) REVERT: A 365 TYR cc_start: 0.8138 (m-80) cc_final: 0.7858 (m-80) REVERT: B 140 PHE cc_start: 0.8459 (p90) cc_final: 0.8174 (OUTLIER) REVERT: B 392 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7409 (m-80) REVERT: B 434 ILE cc_start: 0.6503 (OUTLIER) cc_final: 0.6092 (pp) REVERT: B 858 LEU cc_start: 0.9106 (mm) cc_final: 0.8720 (pt) REVERT: B 934 ILE cc_start: 0.8898 (mm) cc_final: 0.8649 (mp) REVERT: C 69 HIS cc_start: 0.5364 (t-90) cc_final: 0.4997 (t-90) REVERT: C 194 PHE cc_start: 0.7216 (m-10) cc_final: 0.6966 (m-10) REVERT: C 218 GLN cc_start: 0.8538 (tt0) cc_final: 0.8007 (tp-100) REVERT: C 237 ARG cc_start: 0.7095 (ttp80) cc_final: 0.6675 (tmm-80) REVERT: C 324 GLU cc_start: 0.9213 (OUTLIER) cc_final: 0.8868 (pm20) REVERT: C 403 ARG cc_start: 0.7984 (mtp180) cc_final: 0.7660 (mtp85) REVERT: C 417 LYS cc_start: 0.8970 (tptm) cc_final: 0.8720 (tptp) REVERT: C 495 TYR cc_start: 0.5796 (m-80) cc_final: 0.4975 (m-80) REVERT: C 497 PHE cc_start: 0.3164 (m-10) cc_final: 0.2223 (m-80) REVERT: C 584 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8216 (mm) REVERT: C 995 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8860 (mtp-110) outliers start: 21 outliers final: 9 residues processed: 110 average time/residue: 0.5709 time to fit residues: 74.7766 Evaluate side-chains 101 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 159 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 213 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 239 optimal weight: 10.0000 chunk 222 optimal weight: 0.0870 overall best weight: 2.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.100927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.060089 restraints weight = 71097.386| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.23 r_work: 0.2872 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25914 Z= 0.232 Angle : 0.592 12.191 35397 Z= 0.296 Chirality : 0.046 0.359 4155 Planarity : 0.004 0.053 4479 Dihedral : 4.980 53.344 4605 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.66 % Allowed : 10.76 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.15), residues: 3072 helix: 2.39 (0.20), residues: 691 sheet: -0.16 (0.20), residues: 670 loop : -0.35 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 319 TYR 0.020 0.001 TYR C1067 PHE 0.043 0.001 PHE C 497 TRP 0.030 0.002 TRP C 104 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00525 (25812) covalent geometry : angle 0.56865 (35133) SS BOND : bond 0.00175 ( 42) SS BOND : angle 0.63531 ( 84) hydrogen bonds : bond 0.04379 ( 1028) hydrogen bonds : angle 5.60651 ( 3015) link_BETA1-4 : bond 0.00183 ( 18) link_BETA1-4 : angle 1.17363 ( 54) link_NAG-ASN : bond 0.00694 ( 42) link_NAG-ASN : angle 2.70109 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 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 98 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3608 (ptt) cc_final: 0.2953 (tpp) REVERT: A 323 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8623 (p) REVERT: B 140 PHE cc_start: 0.8431 (p90) cc_final: 0.8169 (p90) REVERT: B 354 ASN cc_start: 0.8169 (t0) cc_final: 0.7845 (m-40) REVERT: B 392 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7453 (m-80) REVERT: B 434 ILE cc_start: 0.6591 (OUTLIER) cc_final: 0.6172 (pp) REVERT: B 858 LEU cc_start: 0.9171 (mm) cc_final: 0.8792 (pt) REVERT: C 194 PHE cc_start: 0.7560 (m-10) cc_final: 0.7259 (m-10) REVERT: C 218 GLN cc_start: 0.8552 (tt0) cc_final: 0.8045 (tp-100) REVERT: C 324 GLU cc_start: 0.9246 (OUTLIER) cc_final: 0.8850 (pm20) REVERT: C 403 ARG cc_start: 0.7907 (mtp180) cc_final: 0.7558 (mtp85) REVERT: C 417 LYS cc_start: 0.8961 (tptm) cc_final: 0.8692 (tptp) REVERT: C 584 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8179 (pp) REVERT: C 995 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8808 (mtp-110) REVERT: C 1092 GLU cc_start: 0.8984 (pt0) cc_final: 0.8659 (pm20) outliers start: 18 outliers final: 9 residues processed: 96 average time/residue: 0.5655 time to fit residues: 64.6066 Evaluate side-chains 91 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 68 optimal weight: 1.9990 chunk 287 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 273 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 305 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 241 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 69 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.102221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.061361 restraints weight = 70989.728| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.33 r_work: 0.2916 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25914 Z= 0.118 Angle : 0.533 10.631 35397 Z= 0.267 Chirality : 0.044 0.361 4155 Planarity : 0.004 0.049 4479 Dihedral : 4.797 52.673 4605 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.66 % Allowed : 10.90 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.15), residues: 3072 helix: 2.47 (0.20), residues: 689 sheet: -0.13 (0.20), residues: 668 loop : -0.29 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 319 TYR 0.020 0.001 TYR C1067 PHE 0.044 0.001 PHE C 497 TRP 0.042 0.001 TRP C 104 HIS 0.002 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00263 (25812) covalent geometry : angle 0.51030 (35133) SS BOND : bond 0.00104 ( 42) SS BOND : angle 0.58087 ( 84) hydrogen bonds : bond 0.03834 ( 1028) hydrogen bonds : angle 5.40957 ( 3015) link_BETA1-4 : bond 0.00316 ( 18) link_BETA1-4 : angle 0.97500 ( 54) link_NAG-ASN : bond 0.00604 ( 42) link_NAG-ASN : angle 2.58110 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12975.70 seconds wall clock time: 220 minutes 20.33 seconds (13220.33 seconds total)