Starting phenix.real_space_refine on Sun Jun 22 03:03:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sxt_25505/06_2025/7sxt_25505.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sxt_25505/06_2025/7sxt_25505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sxt_25505/06_2025/7sxt_25505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sxt_25505/06_2025/7sxt_25505.map" model { file = "/net/cci-nas-00/data/ceres_data/7sxt_25505/06_2025/7sxt_25505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sxt_25505/06_2025/7sxt_25505.cif" } resolution = 2.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 16074 2.51 5 N 4125 2.21 5 O 4938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25248 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8136 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8136 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8136 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 15.66, per 1000 atoms: 0.62 Number of scatterers: 25248 At special positions: 0 Unit cell: (141, 145, 197, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 4938 8.00 N 4125 7.00 C 16074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 17 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 17 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 6.29 Conformation dependent library (CDL) restraints added in 3.5 seconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5844 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 51 sheets defined 24.8% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.86 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.046A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.682A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.461A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.104A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.680A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.920A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.030A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.562A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.002A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.674A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.910A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.570A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.978A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.633A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.575A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.902A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.521A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.968A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.550A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.810A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.670A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.886A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.530A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.907A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.715A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.964A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.601A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.508A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.266A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.599A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.976A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.789A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.886A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.739A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 11.581A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.259A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.442A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.785A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.739A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.824A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.982A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.993A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.559A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.060A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.829A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.528A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.528A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.206A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.685A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.341A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.985A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.623A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 154 through 163 removed outlier: 5.078A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.192A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.677A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.823A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.645A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.041A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.636A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.499A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.499A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.228A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.190A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.190A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.951A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 154 through 163 removed outlier: 9.704A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.790A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 10.133A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.705A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.154A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.723A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.743A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.644A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.254A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.526A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.526A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.155A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 1087 hydrogen bonds defined for protein. 2985 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.61 Time building geometry restraints manager: 7.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7333 1.34 - 1.46: 6169 1.46 - 1.58: 12178 1.58 - 1.70: 0 1.70 - 1.83: 138 Bond restraints: 25818 Sorted by residual: bond pdb=" C LEU C 560 " pdb=" N PRO C 561 " ideal model delta sigma weight residual 1.334 1.387 -0.053 1.51e-02 4.39e+03 1.22e+01 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.65e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.12e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.94e+00 ... (remaining 25813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 34004 1.99 - 3.98: 1011 3.98 - 5.97: 96 5.97 - 7.96: 26 7.96 - 9.95: 8 Bond angle restraints: 35145 Sorted by residual: angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.36 -5.66 1.22e+00 6.72e-01 2.15e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.27 -5.57 1.22e+00 6.72e-01 2.09e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.08 -5.38 1.22e+00 6.72e-01 1.94e+01 angle pdb=" CA GLU C 583 " pdb=" CB GLU C 583 " pdb=" CG GLU C 583 " ideal model delta sigma weight residual 114.10 122.09 -7.99 2.00e+00 2.50e-01 1.60e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 122.60 -4.67 1.20e+00 6.94e-01 1.52e+01 ... (remaining 35140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 14918 17.98 - 35.97: 1015 35.97 - 53.95: 155 53.95 - 71.93: 56 71.93 - 89.92: 29 Dihedral angle restraints: 16173 sinusoidal: 7092 harmonic: 9081 Sorted by residual: dihedral pdb=" CA LEU B 517 " pdb=" C LEU B 517 " pdb=" N LEU B 518 " pdb=" CA LEU B 518 " ideal model delta harmonic sigma weight residual 180.00 153.99 26.01 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual 180.00 154.29 25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA PHE C 515 " pdb=" C PHE C 515 " pdb=" N GLU C 516 " pdb=" CA GLU C 516 " ideal model delta harmonic sigma weight residual 180.00 157.31 22.69 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 16170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3243 0.061 - 0.122: 795 0.122 - 0.183: 103 0.183 - 0.244: 14 0.244 - 0.306: 3 Chirality restraints: 4158 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 4155 not shown) Planarity restraints: 4518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 902 " -0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C MET C 902 " 0.057 2.00e-02 2.50e+03 pdb=" O MET C 902 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA C 903 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 920 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.90e+00 pdb=" C GLN C 920 " 0.052 2.00e-02 2.50e+03 pdb=" O GLN C 920 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS C 921 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A1029 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C MET A1029 " 0.051 2.00e-02 2.50e+03 pdb=" O MET A1029 " -0.019 2.00e-02 2.50e+03 pdb=" N SER A1030 " -0.017 2.00e-02 2.50e+03 ... (remaining 4515 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6828 2.81 - 3.33: 21059 3.33 - 3.85: 43297 3.85 - 4.38: 49762 4.38 - 4.90: 84966 Nonbonded interactions: 205912 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.287 3.040 nonbonded pdb=" OE1 GLN B 115 " pdb=" OG1 THR B 167 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR A 369 " pdb=" O ALA C 475 " model vdw 2.311 3.040 nonbonded pdb=" O ASP B 80 " pdb=" OH TYR B 265 " model vdw 2.329 3.040 nonbonded pdb=" O ASP A 80 " pdb=" OH TYR A 265 " model vdw 2.334 3.040 ... (remaining 205907 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.050 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 61.290 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:17.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 25920 Z= 0.229 Angle : 0.808 15.083 35409 Z= 0.416 Chirality : 0.053 0.306 4158 Planarity : 0.007 0.065 4476 Dihedral : 12.825 89.918 10203 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.13), residues: 3072 helix: 0.10 (0.18), residues: 650 sheet: 0.11 (0.18), residues: 687 loop : -0.86 (0.13), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 886 HIS 0.004 0.001 HIS C 66 PHE 0.042 0.002 PHE B 135 TYR 0.029 0.002 TYR C1067 ARG 0.017 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00806 ( 42) link_NAG-ASN : angle 3.51227 ( 126) link_BETA1-4 : bond 0.00681 ( 18) link_BETA1-4 : angle 1.38537 ( 54) hydrogen bonds : bond 0.16206 ( 1022) hydrogen bonds : angle 7.94797 ( 2985) SS BOND : bond 0.00258 ( 42) SS BOND : angle 1.30734 ( 84) covalent geometry : bond 0.00488 (25818) covalent geometry : angle 0.77876 (35145) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8344 (m-40) cc_final: 0.7683 (m-40) REVERT: A 153 MET cc_start: 0.4816 (ptt) cc_final: 0.3902 (tpt) REVERT: A 240 THR cc_start: 0.7417 (m) cc_final: 0.6762 (t) REVERT: A 1005 GLN cc_start: 0.8095 (mt0) cc_final: 0.7611 (mt0) REVERT: B 208 THR cc_start: 0.7675 (m) cc_final: 0.7425 (p) REVERT: B 396 TYR cc_start: 0.6611 (m-80) cc_final: 0.6400 (m-80) REVERT: B 403 ARG cc_start: 0.6496 (mtp180) cc_final: 0.6178 (ttt180) REVERT: B 564 GLN cc_start: 0.6636 (tp40) cc_final: 0.6432 (tp40) REVERT: B 985 ASP cc_start: 0.7728 (p0) cc_final: 0.6377 (p0) REVERT: C 54 LEU cc_start: 0.8639 (mm) cc_final: 0.8122 (mm) REVERT: C 453 TYR cc_start: 0.8399 (p90) cc_final: 0.8129 (p90) REVERT: C 565 PHE cc_start: 0.8329 (p90) cc_final: 0.8111 (p90) REVERT: C 740 MET cc_start: 0.7890 (ttt) cc_final: 0.7646 (ttm) REVERT: C 985 ASP cc_start: 0.7480 (p0) cc_final: 0.6906 (p0) outliers start: 0 outliers final: 1 residues processed: 307 average time/residue: 1.3445 time to fit residues: 477.0549 Evaluate side-chains 164 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 540 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 244 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 148 optimal weight: 30.0000 chunk 182 optimal weight: 0.1980 chunk 283 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 755 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 762 GLN B 901 GLN B1002 GLN B1011 GLN C 121 ASN C 207 HIS C 779 GLN C 957 GLN C1002 GLN C1010 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.128291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.077858 restraints weight = 55462.912| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.96 r_work: 0.2937 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 25920 Z= 0.222 Angle : 0.646 20.126 35409 Z= 0.323 Chirality : 0.048 0.564 4158 Planarity : 0.005 0.055 4476 Dihedral : 6.200 59.832 4607 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.21 % Allowed : 6.70 % Favored : 92.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.14), residues: 3072 helix: 1.37 (0.20), residues: 677 sheet: 0.36 (0.19), residues: 682 loop : -0.70 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 886 HIS 0.007 0.001 HIS C 207 PHE 0.022 0.002 PHE B 106 TYR 0.024 0.002 TYR C1067 ARG 0.010 0.001 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00620 ( 42) link_NAG-ASN : angle 3.61088 ( 126) link_BETA1-4 : bond 0.00174 ( 18) link_BETA1-4 : angle 1.28418 ( 54) hydrogen bonds : bond 0.05075 ( 1022) hydrogen bonds : angle 6.20069 ( 2985) SS BOND : bond 0.00367 ( 42) SS BOND : angle 1.09699 ( 84) covalent geometry : bond 0.00502 (25818) covalent geometry : angle 0.60651 (35145) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 2.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8228 (m-40) cc_final: 0.7937 (m-40) REVERT: A 153 MET cc_start: 0.4523 (ptt) cc_final: 0.3507 (tpt) REVERT: A 242 LEU cc_start: 0.7949 (mp) cc_final: 0.7481 (mp) REVERT: A 786 LYS cc_start: 0.8691 (pmtt) cc_final: 0.8032 (mmmt) REVERT: A 868 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8312 (pm20) REVERT: A 1092 GLU cc_start: 0.8545 (pm20) cc_final: 0.8101 (pp20) REVERT: B 153 MET cc_start: 0.6455 (tpp) cc_final: 0.6030 (ppp) REVERT: B 403 ARG cc_start: 0.6558 (mtp180) cc_final: 0.6309 (ttt180) REVERT: B 408 ARG cc_start: 0.7949 (ptt90) cc_final: 0.7343 (ppt170) REVERT: B 960 ASN cc_start: 0.9312 (OUTLIER) cc_final: 0.9083 (t0) REVERT: B 1138 TYR cc_start: 0.8677 (t80) cc_final: 0.8368 (t80) REVERT: C 52 GLN cc_start: 0.7854 (tp-100) cc_final: 0.7523 (tp40) REVERT: C 194 PHE cc_start: 0.7194 (m-10) cc_final: 0.6979 (m-10) REVERT: C 420 ASP cc_start: 0.8913 (m-30) cc_final: 0.8589 (t0) REVERT: C 985 ASP cc_start: 0.7745 (p0) cc_final: 0.7512 (p0) outliers start: 33 outliers final: 10 residues processed: 195 average time/residue: 1.2896 time to fit residues: 294.4593 Evaluate side-chains 160 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 981 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 194 optimal weight: 1.9990 chunk 266 optimal weight: 0.8980 chunk 309 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 281 optimal weight: 0.9990 chunk 172 optimal weight: 0.6980 chunk 245 optimal weight: 6.9990 chunk 175 optimal weight: 0.0370 chunk 163 optimal weight: 0.6980 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 907 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN C 207 HIS ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.129059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.079268 restraints weight = 55351.960| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.00 r_work: 0.2971 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25920 Z= 0.117 Angle : 0.558 15.722 35409 Z= 0.277 Chirality : 0.044 0.285 4158 Planarity : 0.004 0.045 4476 Dihedral : 5.547 59.687 4607 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.35 % Allowed : 7.87 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 3072 helix: 2.00 (0.21), residues: 664 sheet: 0.39 (0.19), residues: 669 loop : -0.57 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 104 HIS 0.006 0.001 HIS A 207 PHE 0.021 0.001 PHE A 168 TYR 0.023 0.001 TYR B 453 ARG 0.006 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00598 ( 42) link_NAG-ASN : angle 3.10023 ( 126) link_BETA1-4 : bond 0.00309 ( 18) link_BETA1-4 : angle 1.03355 ( 54) hydrogen bonds : bond 0.04160 ( 1022) hydrogen bonds : angle 5.75862 ( 2985) SS BOND : bond 0.00217 ( 42) SS BOND : angle 0.70136 ( 84) covalent geometry : bond 0.00252 (25818) covalent geometry : angle 0.52525 (35145) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8139 (m-40) cc_final: 0.7855 (m-40) REVERT: A 153 MET cc_start: 0.5261 (ptt) cc_final: 0.4071 (tmm) REVERT: A 994 ASP cc_start: 0.9035 (OUTLIER) cc_final: 0.8799 (t70) REVERT: A 1092 GLU cc_start: 0.8548 (pm20) cc_final: 0.8081 (pp20) REVERT: B 153 MET cc_start: 0.6465 (tpp) cc_final: 0.5988 (ppp) REVERT: B 309 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8630 (mp0) REVERT: B 400 PHE cc_start: 0.9209 (p90) cc_final: 0.8893 (p90) REVERT: B 403 ARG cc_start: 0.6511 (mtp180) cc_final: 0.6225 (ttt180) REVERT: B 408 ARG cc_start: 0.8000 (ptt90) cc_final: 0.7500 (ptm-80) REVERT: B 1050 MET cc_start: 0.9440 (ptm) cc_final: 0.9210 (ptm) REVERT: B 1091 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8758 (mtm-85) REVERT: B 1138 TYR cc_start: 0.8675 (t80) cc_final: 0.8325 (t80) REVERT: C 189 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7900 (mt) REVERT: C 194 PHE cc_start: 0.7314 (m-10) cc_final: 0.7093 (m-10) REVERT: C 392 PHE cc_start: 0.7754 (m-80) cc_final: 0.7387 (m-10) REVERT: C 420 ASP cc_start: 0.8939 (m-30) cc_final: 0.8613 (t0) REVERT: C 985 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7467 (p0) REVERT: C 988 GLU cc_start: 0.8949 (mp0) cc_final: 0.8634 (pm20) REVERT: C 1141 LEU cc_start: 0.7302 (tt) cc_final: 0.7012 (tm) outliers start: 37 outliers final: 14 residues processed: 183 average time/residue: 1.2413 time to fit residues: 267.1911 Evaluate side-chains 155 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 985 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 163 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 284 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 755 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 907 ASN C 824 ASN C 955 ASN C 957 GLN C1002 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.126410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.076075 restraints weight = 55494.989| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.01 r_work: 0.2892 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 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 : 0.005 0.052 25920 Z= 0.236 Angle : 0.613 14.762 35409 Z= 0.305 Chirality : 0.047 0.257 4158 Planarity : 0.004 0.044 4476 Dihedral : 5.422 59.564 4607 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.50 % Allowed : 8.85 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.15), residues: 3072 helix: 2.06 (0.20), residues: 670 sheet: 0.31 (0.19), residues: 690 loop : -0.56 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 436 HIS 0.007 0.001 HIS A 207 PHE 0.018 0.002 PHE B 898 TYR 0.023 0.002 TYR C1067 ARG 0.006 0.001 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00673 ( 42) link_NAG-ASN : angle 3.13487 ( 126) link_BETA1-4 : bond 0.00290 ( 18) link_BETA1-4 : angle 1.21368 ( 54) hydrogen bonds : bond 0.04746 ( 1022) hydrogen bonds : angle 5.81647 ( 2985) SS BOND : bond 0.00178 ( 42) SS BOND : angle 0.69465 ( 84) covalent geometry : bond 0.00533 (25818) covalent geometry : angle 0.58324 (35145) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 2.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5284 (ptt) cc_final: 0.3909 (tmm) REVERT: B 153 MET cc_start: 0.6545 (tpp) cc_final: 0.6014 (ppp) REVERT: B 400 PHE cc_start: 0.9258 (p90) cc_final: 0.8946 (p90) REVERT: B 408 ARG cc_start: 0.8082 (ptt90) cc_final: 0.7582 (ptm-80) REVERT: B 512 VAL cc_start: 0.9239 (t) cc_final: 0.9015 (p) REVERT: B 985 ASP cc_start: 0.8419 (p0) cc_final: 0.8175 (p0) REVERT: C 97 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.7137 (mmmm) REVERT: C 229 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7062 (tm) REVERT: C 392 PHE cc_start: 0.7904 (m-80) cc_final: 0.7429 (m-10) REVERT: C 420 ASP cc_start: 0.8858 (m-30) cc_final: 0.8565 (t0) REVERT: C 985 ASP cc_start: 0.8020 (p0) cc_final: 0.7655 (p0) REVERT: C 988 GLU cc_start: 0.9054 (mp0) cc_final: 0.8749 (pm20) REVERT: C 990 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8536 (tm-30) REVERT: C 1141 LEU cc_start: 0.7311 (tt) cc_final: 0.7078 (tm) outliers start: 41 outliers final: 16 residues processed: 182 average time/residue: 1.2640 time to fit residues: 271.5574 Evaluate side-chains 153 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 2.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 540 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 246 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 152 optimal weight: 7.9990 chunk 254 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.126679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.076023 restraints weight = 55213.404| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.99 r_work: 0.2908 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 25920 Z= 0.189 Angle : 0.580 13.858 35409 Z= 0.288 Chirality : 0.045 0.236 4158 Planarity : 0.004 0.048 4476 Dihedral : 5.281 58.816 4607 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.39 % Allowed : 9.37 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.15), residues: 3072 helix: 2.18 (0.20), residues: 670 sheet: 0.22 (0.20), residues: 679 loop : -0.52 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 104 HIS 0.005 0.001 HIS A 207 PHE 0.019 0.001 PHE A 898 TYR 0.024 0.001 TYR B 508 ARG 0.005 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00616 ( 42) link_NAG-ASN : angle 2.99091 ( 126) link_BETA1-4 : bond 0.00205 ( 18) link_BETA1-4 : angle 1.04019 ( 54) hydrogen bonds : bond 0.04421 ( 1022) hydrogen bonds : angle 5.70006 ( 2985) SS BOND : bond 0.00133 ( 42) SS BOND : angle 0.64450 ( 84) covalent geometry : bond 0.00424 (25818) covalent geometry : angle 0.55154 (35145) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 2.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5234 (ptt) cc_final: 0.3870 (tmm) REVERT: A 200 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.7690 (t80) REVERT: A 697 MET cc_start: 0.9354 (ptm) cc_final: 0.9145 (ptp) REVERT: B 153 MET cc_start: 0.6626 (tpp) cc_final: 0.6104 (ppp) REVERT: B 309 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8682 (mp0) REVERT: B 400 PHE cc_start: 0.9279 (p90) cc_final: 0.8902 (p90) REVERT: B 408 ARG cc_start: 0.8121 (ptt90) cc_final: 0.7602 (ptm-80) REVERT: C 97 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7306 (mmmm) REVERT: C 189 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7996 (mt) REVERT: C 229 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7345 (tm) REVERT: C 392 PHE cc_start: 0.8026 (m-80) cc_final: 0.7805 (m-80) REVERT: C 420 ASP cc_start: 0.8834 (m-30) cc_final: 0.8597 (t0) REVERT: C 512 VAL cc_start: 0.8688 (t) cc_final: 0.8309 (m) REVERT: C 990 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8546 (tm-30) outliers start: 38 outliers final: 19 residues processed: 164 average time/residue: 1.1917 time to fit residues: 231.6474 Evaluate side-chains 148 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 540 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 42 optimal weight: 0.8980 chunk 135 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 306 optimal weight: 0.0970 chunk 255 optimal weight: 9.9990 chunk 196 optimal weight: 0.5980 chunk 227 optimal weight: 0.4980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 907 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.127494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.076066 restraints weight = 55077.620| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.82 r_work: 0.2963 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25920 Z= 0.115 Angle : 0.549 13.367 35409 Z= 0.271 Chirality : 0.044 0.243 4158 Planarity : 0.004 0.047 4476 Dihedral : 5.051 57.028 4607 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.32 % Allowed : 9.44 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.15), residues: 3072 helix: 2.34 (0.20), residues: 671 sheet: 0.22 (0.20), residues: 669 loop : -0.42 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 104 HIS 0.004 0.001 HIS A 207 PHE 0.018 0.001 PHE C 79 TYR 0.021 0.001 TYR C 453 ARG 0.006 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00573 ( 42) link_NAG-ASN : angle 2.84951 ( 126) link_BETA1-4 : bond 0.00371 ( 18) link_BETA1-4 : angle 0.98185 ( 54) hydrogen bonds : bond 0.04004 ( 1022) hydrogen bonds : angle 5.49504 ( 2985) SS BOND : bond 0.00094 ( 42) SS BOND : angle 0.56037 ( 84) covalent geometry : bond 0.00250 (25818) covalent geometry : angle 0.52212 (35145) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 2.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5364 (ptt) cc_final: 0.3586 (tmm) REVERT: B 97 LYS cc_start: 0.6941 (OUTLIER) cc_final: 0.6659 (mtpp) REVERT: B 153 MET cc_start: 0.6595 (tpp) cc_final: 0.6196 (ppp) REVERT: B 400 PHE cc_start: 0.9253 (p90) cc_final: 0.8859 (p90) REVERT: B 408 ARG cc_start: 0.8150 (ptt90) cc_final: 0.7638 (ptm160) REVERT: B 512 VAL cc_start: 0.9252 (t) cc_final: 0.9029 (p) REVERT: C 97 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7378 (mmmm) REVERT: C 135 PHE cc_start: 0.7461 (m-80) cc_final: 0.6967 (m-80) REVERT: C 189 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8006 (mt) REVERT: C 194 PHE cc_start: 0.7335 (m-10) cc_final: 0.7059 (m-10) REVERT: C 229 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7398 (tm) REVERT: C 378 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7495 (tmmm) REVERT: C 392 PHE cc_start: 0.8043 (m-80) cc_final: 0.7816 (m-80) REVERT: C 400 PHE cc_start: 0.8555 (p90) cc_final: 0.8252 (p90) REVERT: C 512 VAL cc_start: 0.8763 (t) cc_final: 0.8451 (m) REVERT: C 584 ILE cc_start: 0.7627 (OUTLIER) cc_final: 0.7280 (mm) REVERT: C 988 GLU cc_start: 0.8979 (mp0) cc_final: 0.8733 (pm20) REVERT: C 990 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8532 (tm-30) outliers start: 36 outliers final: 15 residues processed: 170 average time/residue: 1.1993 time to fit residues: 242.5101 Evaluate side-chains 147 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 453 TYR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 584 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 155 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 286 optimal weight: 0.9980 chunk 160 optimal weight: 5.9990 chunk 105 optimal weight: 0.0570 chunk 267 optimal weight: 0.6980 chunk 71 optimal weight: 0.0470 chunk 123 optimal weight: 0.9980 chunk 35 optimal weight: 40.0000 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.127668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.076930 restraints weight = 55446.567| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.72 r_work: 0.2977 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25920 Z= 0.109 Angle : 0.547 12.566 35409 Z= 0.268 Chirality : 0.044 0.246 4158 Planarity : 0.003 0.045 4476 Dihedral : 4.856 54.251 4607 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.24 % Allowed : 9.99 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.15), residues: 3072 helix: 2.39 (0.20), residues: 672 sheet: 0.31 (0.20), residues: 664 loop : -0.40 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 104 HIS 0.004 0.000 HIS A 207 PHE 0.017 0.001 PHE C 79 TYR 0.026 0.001 TYR B 453 ARG 0.004 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 42) link_NAG-ASN : angle 2.75879 ( 126) link_BETA1-4 : bond 0.00272 ( 18) link_BETA1-4 : angle 0.97793 ( 54) hydrogen bonds : bond 0.03839 ( 1022) hydrogen bonds : angle 5.36320 ( 2985) SS BOND : bond 0.00081 ( 42) SS BOND : angle 0.53346 ( 84) covalent geometry : bond 0.00242 (25818) covalent geometry : angle 0.52114 (35145) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 2.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8144 (m-40) cc_final: 0.7773 (m-40) REVERT: A 153 MET cc_start: 0.5425 (ptt) cc_final: 0.3724 (tpt) REVERT: B 97 LYS cc_start: 0.6902 (OUTLIER) cc_final: 0.6343 (mtpp) REVERT: B 153 MET cc_start: 0.6600 (tpp) cc_final: 0.6215 (ppp) REVERT: B 281 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8748 (pp20) REVERT: B 309 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8721 (mp0) REVERT: B 400 PHE cc_start: 0.9249 (p90) cc_final: 0.8861 (p90) REVERT: B 408 ARG cc_start: 0.8179 (ptt90) cc_final: 0.7663 (ptm160) REVERT: B 423 TYR cc_start: 0.7582 (t80) cc_final: 0.7005 (t80) REVERT: B 512 VAL cc_start: 0.9263 (t) cc_final: 0.9025 (p) REVERT: C 97 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7444 (mmmm) REVERT: C 135 PHE cc_start: 0.7457 (m-80) cc_final: 0.6887 (m-80) REVERT: C 189 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8090 (mt) REVERT: C 194 PHE cc_start: 0.7383 (m-10) cc_final: 0.7110 (m-10) REVERT: C 229 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7499 (tt) REVERT: C 378 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7509 (tmmm) REVERT: C 392 PHE cc_start: 0.8144 (m-80) cc_final: 0.7904 (m-80) REVERT: C 400 PHE cc_start: 0.8560 (p90) cc_final: 0.8267 (p90) REVERT: C 512 VAL cc_start: 0.8756 (t) cc_final: 0.8485 (m) REVERT: C 584 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7310 (mm) REVERT: C 661 GLU cc_start: 0.8612 (pm20) cc_final: 0.8237 (pm20) REVERT: C 740 MET cc_start: 0.8931 (ttt) cc_final: 0.8722 (ttm) outliers start: 34 outliers final: 15 residues processed: 165 average time/residue: 1.1790 time to fit residues: 231.7178 Evaluate side-chains 155 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 584 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 48 optimal weight: 6.9990 chunk 297 optimal weight: 0.8980 chunk 219 optimal weight: 7.9990 chunk 157 optimal weight: 0.0070 chunk 85 optimal weight: 0.1980 chunk 280 optimal weight: 1.9990 chunk 204 optimal weight: 0.8980 chunk 146 optimal weight: 8.9990 chunk 184 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 272 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN A1005 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C 957 GLN C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.127580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.077007 restraints weight = 55088.694| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.69 r_work: 0.2981 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25920 Z= 0.109 Angle : 0.541 12.630 35409 Z= 0.265 Chirality : 0.044 0.246 4158 Planarity : 0.003 0.045 4476 Dihedral : 4.723 53.328 4607 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.06 % Allowed : 10.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.15), residues: 3072 helix: 2.46 (0.20), residues: 672 sheet: 0.36 (0.20), residues: 663 loop : -0.37 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 104 HIS 0.004 0.000 HIS A 207 PHE 0.016 0.001 PHE C 79 TYR 0.023 0.001 TYR B 453 ARG 0.008 0.000 ARG A 21 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 42) link_NAG-ASN : angle 2.70216 ( 126) link_BETA1-4 : bond 0.00335 ( 18) link_BETA1-4 : angle 0.99871 ( 54) hydrogen bonds : bond 0.03794 ( 1022) hydrogen bonds : angle 5.28464 ( 2985) SS BOND : bond 0.00081 ( 42) SS BOND : angle 0.53463 ( 84) covalent geometry : bond 0.00240 (25818) covalent geometry : angle 0.51600 (35145) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5322 (ptt) cc_final: 0.3650 (tpt) REVERT: B 97 LYS cc_start: 0.6856 (OUTLIER) cc_final: 0.6491 (mtpp) REVERT: B 153 MET cc_start: 0.6547 (tpp) cc_final: 0.6181 (ppp) REVERT: B 281 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8746 (pp20) REVERT: B 400 PHE cc_start: 0.9251 (p90) cc_final: 0.8808 (p90) REVERT: B 408 ARG cc_start: 0.8225 (ptt90) cc_final: 0.7701 (ptm160) REVERT: B 423 TYR cc_start: 0.7546 (t80) cc_final: 0.6958 (t80) REVERT: B 512 VAL cc_start: 0.9244 (t) cc_final: 0.9009 (p) REVERT: C 97 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7376 (mmmm) REVERT: C 135 PHE cc_start: 0.7433 (m-80) cc_final: 0.6890 (m-80) REVERT: C 189 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8095 (mt) REVERT: C 229 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7506 (tt) REVERT: C 378 LYS cc_start: 0.7990 (ttmm) cc_final: 0.7512 (tmmm) REVERT: C 392 PHE cc_start: 0.8106 (m-80) cc_final: 0.7835 (m-80) REVERT: C 400 PHE cc_start: 0.8509 (p90) cc_final: 0.8184 (p90) REVERT: C 512 VAL cc_start: 0.8731 (t) cc_final: 0.8466 (m) REVERT: C 740 MET cc_start: 0.8880 (ttt) cc_final: 0.8680 (ttm) REVERT: C 988 GLU cc_start: 0.9068 (pm20) cc_final: 0.8721 (pm20) outliers start: 29 outliers final: 14 residues processed: 164 average time/residue: 1.2015 time to fit residues: 234.7114 Evaluate side-chains 154 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 540 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 160 optimal weight: 4.9990 chunk 305 optimal weight: 0.4980 chunk 113 optimal weight: 10.0000 chunk 302 optimal weight: 0.0010 chunk 93 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN C 580 GLN C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.126970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.077034 restraints weight = 55392.661| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.95 r_work: 0.2941 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25920 Z= 0.132 Angle : 0.553 12.745 35409 Z= 0.273 Chirality : 0.045 0.240 4158 Planarity : 0.004 0.045 4476 Dihedral : 4.682 53.108 4607 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.10 % Allowed : 10.79 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.15), residues: 3072 helix: 2.40 (0.20), residues: 679 sheet: 0.33 (0.19), residues: 678 loop : -0.36 (0.14), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP C 104 HIS 0.004 0.001 HIS A 207 PHE 0.030 0.001 PHE C 194 TYR 0.024 0.001 TYR C 453 ARG 0.010 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00547 ( 42) link_NAG-ASN : angle 2.70295 ( 126) link_BETA1-4 : bond 0.00276 ( 18) link_BETA1-4 : angle 1.00693 ( 54) hydrogen bonds : bond 0.03947 ( 1022) hydrogen bonds : angle 5.29761 ( 2985) SS BOND : bond 0.00089 ( 42) SS BOND : angle 0.55830 ( 84) covalent geometry : bond 0.00296 (25818) covalent geometry : angle 0.52847 (35145) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 3.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5324 (ptt) cc_final: 0.3697 (tpp) REVERT: B 97 LYS cc_start: 0.6811 (OUTLIER) cc_final: 0.6546 (mtpp) REVERT: B 153 MET cc_start: 0.6565 (tpp) cc_final: 0.6190 (ppp) REVERT: B 281 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8746 (pp20) REVERT: B 400 PHE cc_start: 0.9323 (p90) cc_final: 0.8889 (p90) REVERT: B 408 ARG cc_start: 0.8285 (ptt90) cc_final: 0.7734 (ptm160) REVERT: B 423 TYR cc_start: 0.7532 (t80) cc_final: 0.6968 (t80) REVERT: B 512 VAL cc_start: 0.9246 (t) cc_final: 0.9007 (p) REVERT: C 97 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7379 (mmmm) REVERT: C 135 PHE cc_start: 0.7489 (m-80) cc_final: 0.7009 (m-80) REVERT: C 189 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8089 (mt) REVERT: C 351 TYR cc_start: 0.8429 (p90) cc_final: 0.8137 (p90) REVERT: C 378 LYS cc_start: 0.8071 (ttmm) cc_final: 0.7579 (tmmm) REVERT: C 392 PHE cc_start: 0.8075 (m-80) cc_final: 0.7820 (m-80) REVERT: C 400 PHE cc_start: 0.8565 (p90) cc_final: 0.8221 (p90) REVERT: C 512 VAL cc_start: 0.8805 (t) cc_final: 0.8545 (m) REVERT: C 661 GLU cc_start: 0.8673 (pm20) cc_final: 0.8303 (pm20) outliers start: 30 outliers final: 14 residues processed: 164 average time/residue: 1.2400 time to fit residues: 242.8831 Evaluate side-chains 152 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 540 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.5919 > 50: distance: 39 - 53: 3.200 distance: 43 - 62: 10.038 distance: 47 - 67: 20.599 distance: 51 - 75: 23.595 distance: 54 - 55: 8.546 distance: 54 - 57: 6.797 distance: 55 - 56: 14.938 distance: 55 - 62: 12.940 distance: 56 - 83: 23.771 distance: 57 - 58: 4.217 distance: 58 - 59: 7.726 distance: 59 - 60: 6.223 distance: 59 - 61: 11.607 distance: 62 - 63: 9.018 distance: 63 - 64: 9.451 distance: 63 - 66: 9.848 distance: 64 - 65: 9.011 distance: 64 - 67: 11.792 distance: 65 - 90: 25.661 distance: 67 - 68: 8.721 distance: 68 - 69: 19.466 distance: 68 - 71: 19.730 distance: 69 - 70: 18.161 distance: 69 - 75: 6.824 distance: 70 - 98: 12.011 distance: 71 - 72: 5.308 distance: 72 - 73: 8.284 distance: 72 - 74: 13.013 distance: 75 - 76: 11.740 distance: 76 - 77: 19.676 distance: 76 - 79: 21.801 distance: 77 - 78: 7.972 distance: 77 - 83: 8.186 distance: 78 - 105: 16.847 distance: 79 - 80: 8.351 distance: 80 - 81: 14.044 distance: 80 - 82: 14.261 distance: 83 - 84: 3.024 distance: 84 - 85: 11.519 distance: 84 - 87: 6.074 distance: 85 - 86: 16.684 distance: 85 - 90: 4.396 distance: 86 - 114: 38.913 distance: 87 - 88: 9.381 distance: 87 - 89: 5.930 distance: 90 - 91: 11.361 distance: 91 - 92: 11.876 distance: 91 - 94: 7.606 distance: 92 - 93: 14.818 distance: 94 - 95: 3.591 distance: 95 - 96: 3.578 distance: 95 - 97: 32.420 distance: 98 - 99: 7.381 distance: 99 - 100: 3.739 distance: 100 - 105: 12.673 distance: 102 - 104: 9.498 distance: 105 - 106: 21.487 distance: 106 - 107: 7.704 distance: 106 - 109: 12.127 distance: 107 - 108: 18.577 distance: 107 - 114: 6.880 distance: 109 - 110: 17.166 distance: 110 - 111: 17.401 distance: 111 - 112: 39.952 distance: 112 - 113: 19.322 distance: 114 - 115: 19.332 distance: 115 - 116: 7.339 distance: 115 - 118: 3.175 distance: 116 - 117: 19.703 distance: 116 - 123: 19.668 distance: 118 - 119: 6.427 distance: 119 - 120: 23.148 distance: 120 - 121: 10.270 distance: 120 - 122: 26.955 distance: 123 - 124: 20.150 distance: 124 - 125: 4.855 distance: 124 - 127: 21.105 distance: 125 - 126: 6.214 distance: 125 - 131: 31.671 distance: 127 - 128: 13.241 distance: 128 - 129: 28.885 distance: 128 - 130: 31.750