Starting phenix.real_space_refine on Tue Feb 20 11:19:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nd8_12279/02_2024/7nd8_12279.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nd8_12279/02_2024/7nd8_12279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nd8_12279/02_2024/7nd8_12279.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nd8_12279/02_2024/7nd8_12279.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nd8_12279/02_2024/7nd8_12279.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nd8_12279/02_2024/7nd8_12279.pdb" } resolution = 3.5 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= 0.002 sd= 0.025 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 117 5.16 5 C 17579 2.51 5 N 4523 2.21 5 O 5440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27659 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "B" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "C" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "H" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1725 Classifications: {'peptide': 228} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215} Chain: "L" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1625 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} 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: "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: "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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 13.88, per 1000 atoms: 0.50 Number of scatterers: 27659 At special positions: 0 Unit cell: (134.48, 162.36, 229.6, 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 117 16.00 O 5440 8.00 N 4523 7.00 C 17579 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 152 " - pdb=" SG CYS H 208 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 234 " " NAG K 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 234 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1098 " " NAG T 1 " - " ASN C1134 " Time building additional restraints: 10.67 Conformation dependent library (CDL) restraints added in 5.2 seconds 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6446 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 58 sheets defined 23.5% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.79 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.564A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.388A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 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: 3.706A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.111A 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 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.870A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.608A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.531A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.402A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 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: 3.716A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.641A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.115A 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 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.937A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.695A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.528A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.366A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 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: 3.721A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.523A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.118A 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 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.897A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.650A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 168 through 170 No H-bonds generated for 'chain 'H' and resid 168 through 170' Processing helix chain 'H' and resid 197 through 201 Processing helix chain 'H' and resid 213 through 216 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.638A pdb=" N VAL L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 removed outlier: 3.603A pdb=" N SER L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.106A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.794A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.584A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.350A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.351A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.068A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.347A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.545A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.041A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 7.016A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.615A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.615A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.536A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.530A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.029A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.879A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.224A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.345A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.007A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.332A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.617A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.215A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.408A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.548A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.548A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.632A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.655A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.960A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.866A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.337A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.547A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.981A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.485A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.235A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.693A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.693A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.550A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'H' and resid 11 through 12 removed outlier: 5.789A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.768A pdb=" N ILE H 114 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 132 through 136 removed outlier: 5.973A pdb=" N TYR H 188 " --> pdb=" O ASP H 156 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 132 through 136 removed outlier: 5.973A pdb=" N TYR H 188 " --> pdb=" O ASP H 156 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 163 through 166 removed outlier: 4.085A pdb=" N TYR H 206 " --> pdb=" O VAL H 223 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.980A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.307A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.242A pdb=" N SER L 131 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU L 181 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL L 133 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU L 179 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LEU L 135 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N SER L 177 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ASN L 137 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU L 175 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 153 through 154 1167 hydrogen bonds defined for protein. 3138 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: 13.01 Time building geometry restraints manager: 11.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8787 1.34 - 1.46: 6976 1.46 - 1.58: 12355 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 28262 Sorted by residual: bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.05e+00 bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.03e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.01e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.94e+00 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.68e+00 ... (remaining 28257 not shown) Histogram of bond angle deviations from ideal: 100.12 - 106.90: 886 106.90 - 113.67: 15915 113.67 - 120.45: 10310 120.45 - 127.23: 11101 127.23 - 134.00: 239 Bond angle restraints: 38451 Sorted by residual: angle pdb=" CA CYS A 760 " pdb=" CB CYS A 760 " pdb=" SG CYS A 760 " ideal model delta sigma weight residual 114.40 122.66 -8.26 2.30e+00 1.89e-01 1.29e+01 angle pdb=" CA CYS B 760 " pdb=" CB CYS B 760 " pdb=" SG CYS B 760 " ideal model delta sigma weight residual 114.40 122.44 -8.04 2.30e+00 1.89e-01 1.22e+01 angle pdb=" C GLU C 516 " pdb=" N LEU C 517 " pdb=" CA LEU C 517 " ideal model delta sigma weight residual 122.20 133.96 -11.76 3.42e+00 8.55e-02 1.18e+01 angle pdb=" C GLU A 516 " pdb=" N LEU A 517 " pdb=" CA LEU A 517 " ideal model delta sigma weight residual 122.20 133.76 -11.56 3.42e+00 8.55e-02 1.14e+01 angle pdb=" CA CYS C 760 " pdb=" CB CYS C 760 " pdb=" SG CYS C 760 " ideal model delta sigma weight residual 114.40 121.83 -7.43 2.30e+00 1.89e-01 1.04e+01 ... (remaining 38446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 16693 17.47 - 34.93: 672 34.93 - 52.40: 167 52.40 - 69.87: 66 69.87 - 87.33: 26 Dihedral angle restraints: 17624 sinusoidal: 7607 harmonic: 10017 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -166.15 80.15 1 1.00e+01 1.00e-02 7.96e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -164.04 78.04 1 1.00e+01 1.00e-02 7.61e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -162.82 76.82 1 1.00e+01 1.00e-02 7.41e+01 ... (remaining 17621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 3087 0.041 - 0.082: 980 0.082 - 0.123: 445 0.123 - 0.164: 41 0.164 - 0.205: 4 Chirality restraints: 4557 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CG LEU C 916 " pdb=" CB LEU C 916 " pdb=" CD1 LEU C 916 " pdb=" CD2 LEU C 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.94e-01 chirality pdb=" CG LEU B 916 " pdb=" CB LEU B 916 " pdb=" CD1 LEU B 916 " pdb=" CD2 LEU B 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.85e-01 ... (remaining 4554 not shown) Planarity restraints: 4934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 958 " 0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C ALA C 958 " -0.066 2.00e-02 2.50e+03 pdb=" O ALA C 958 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU C 959 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 954 " 0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C GLN C 954 " -0.065 2.00e-02 2.50e+03 pdb=" O GLN C 954 " 0.024 2.00e-02 2.50e+03 pdb=" N ASN C 955 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 958 " -0.019 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C ALA A 958 " 0.064 2.00e-02 2.50e+03 pdb=" O ALA A 958 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU A 959 " -0.022 2.00e-02 2.50e+03 ... (remaining 4931 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 803 2.70 - 3.25: 26360 3.25 - 3.80: 43843 3.80 - 4.35: 56982 4.35 - 4.90: 96203 Nonbonded interactions: 224191 Sorted by model distance: nonbonded pdb=" OH TYR A 369 " pdb=" OD1 ASN A 388 " model vdw 2.153 2.440 nonbonded pdb=" OG SER A1123 " pdb=" ND2 ASN B 914 " model vdw 2.193 2.520 nonbonded pdb=" OH TYR C 369 " pdb=" OD1 ASN C 388 " model vdw 2.203 2.440 nonbonded pdb=" OH TYR B 369 " pdb=" OD1 ASN B 388 " model vdw 2.218 2.440 nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.259 2.440 ... (remaining 224186 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 27 through 1147 or resid 1301 through 1309)) selection = (chain 'C' and (resid 27 through 1147 or resid 1301 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.050 Check model and map are aligned: 0.390 Set scattering table: 0.250 Process input model: 74.590 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 28262 Z= 0.290 Angle : 0.694 11.763 38451 Z= 0.386 Chirality : 0.047 0.205 4557 Planarity : 0.005 0.055 4889 Dihedral : 11.081 87.332 11049 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.51 % Favored : 96.29 % Rotamer: Outliers : 0.30 % Allowed : 1.76 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % 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: 0.12 (0.13), residues: 3395 helix: 0.39 (0.18), residues: 681 sheet: 0.49 (0.17), residues: 873 loop : -0.15 (0.13), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C1102 HIS 0.007 0.001 HIS C1048 PHE 0.020 0.002 PHE C 329 TYR 0.018 0.001 TYR C1067 ARG 0.007 0.001 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 339 time to evaluate : 3.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8323 (t0) cc_final: 0.7570 (m-30) REVERT: A 55 PHE cc_start: 0.7860 (m-80) cc_final: 0.7653 (m-80) REVERT: A 201 PHE cc_start: 0.8477 (t80) cc_final: 0.8226 (t80) REVERT: A 275 PHE cc_start: 0.7507 (m-80) cc_final: 0.7026 (m-80) REVERT: A 427 ASP cc_start: 0.8207 (m-30) cc_final: 0.7920 (t0) REVERT: A 486 PHE cc_start: 0.8257 (t80) cc_final: 0.7861 (t80) REVERT: A 610 VAL cc_start: 0.9167 (t) cc_final: 0.8936 (p) REVERT: A 1029 MET cc_start: 0.8588 (tpp) cc_final: 0.8386 (tpp) REVERT: B 960 ASN cc_start: 0.7512 (m-40) cc_final: 0.7221 (t0) REVERT: C 449 TYR cc_start: 0.8590 (m-80) cc_final: 0.7954 (m-10) REVERT: C 451 TYR cc_start: 0.6344 (m-80) cc_final: 0.5936 (m-80) REVERT: C 1037 SER cc_start: 0.8772 (t) cc_final: 0.8156 (p) REVERT: H 73 ASP cc_start: 0.9309 (t0) cc_final: 0.9088 (t0) REVERT: H 74 ASN cc_start: 0.7977 (m-40) cc_final: 0.7441 (m-40) REVERT: H 158 PHE cc_start: 0.9149 (t80) cc_final: 0.8938 (t80) REVERT: L 36 TYR cc_start: 0.7796 (m-80) cc_final: 0.7126 (m-80) REVERT: L 48 ILE cc_start: 0.8677 (mm) cc_final: 0.8274 (mm) REVERT: L 95 LEU cc_start: 0.9698 (mt) cc_final: 0.9399 (tp) outliers start: 9 outliers final: 3 residues processed: 348 average time/residue: 0.4427 time to fit residues: 235.0464 Evaluate side-chains 169 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 166 time to evaluate : 3.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain C residue 483 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 0.8980 chunk 259 optimal weight: 0.8980 chunk 144 optimal weight: 0.0010 chunk 88 optimal weight: 0.1980 chunk 175 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 268 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 311 optimal weight: 30.0000 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A1002 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 125 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 28262 Z= 0.199 Angle : 0.563 7.089 38451 Z= 0.300 Chirality : 0.044 0.195 4557 Planarity : 0.004 0.054 4889 Dihedral : 6.531 59.784 4944 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.90 % Allowed : 6.12 % Favored : 92.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % 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: 0.83 (0.14), residues: 3395 helix: 1.83 (0.20), residues: 674 sheet: 0.79 (0.16), residues: 906 loop : -0.00 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 36 HIS 0.003 0.001 HIS B1064 PHE 0.031 0.002 PHE H 104 TYR 0.025 0.001 TYR L 173 ARG 0.008 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 187 time to evaluate : 3.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 PHE cc_start: 0.7451 (m-80) cc_final: 0.7002 (m-80) REVERT: A 427 ASP cc_start: 0.8229 (m-30) cc_final: 0.7856 (t0) REVERT: A 486 PHE cc_start: 0.8291 (t80) cc_final: 0.7889 (t80) REVERT: A 508 TYR cc_start: 0.7485 (OUTLIER) cc_final: 0.6947 (t80) REVERT: A 610 VAL cc_start: 0.9188 (t) cc_final: 0.8958 (m) REVERT: A 731 MET cc_start: 0.8028 (ptm) cc_final: 0.7729 (ptm) REVERT: A 1029 MET cc_start: 0.8472 (tpp) cc_final: 0.8218 (tpp) REVERT: B 462 LYS cc_start: 0.8879 (mttm) cc_final: 0.8573 (mttp) REVERT: B 869 MET cc_start: 0.8336 (mtt) cc_final: 0.7808 (mmm) REVERT: B 960 ASN cc_start: 0.7596 (m-40) cc_final: 0.7033 (t0) REVERT: B 1029 MET cc_start: 0.8711 (tpp) cc_final: 0.8489 (tpp) REVERT: C 118 LEU cc_start: 0.6657 (tp) cc_final: 0.6444 (mm) REVERT: C 378 LYS cc_start: 0.7211 (mmtt) cc_final: 0.6971 (mmtt) REVERT: C 449 TYR cc_start: 0.8615 (m-80) cc_final: 0.7984 (m-10) REVERT: C 895 GLN cc_start: 0.7231 (pp30) cc_final: 0.6862 (pp30) REVERT: C 902 MET cc_start: 0.8501 (mmm) cc_final: 0.8172 (mmt) REVERT: C 1037 SER cc_start: 0.8759 (t) cc_final: 0.8162 (p) REVERT: H 34 MET cc_start: 0.9416 (mmt) cc_final: 0.8928 (mmp) REVERT: H 103 ARG cc_start: 0.9030 (mmm160) cc_final: 0.8814 (mmm160) REVERT: H 120 MET cc_start: 0.8082 (tpp) cc_final: 0.7788 (tpp) REVERT: H 158 PHE cc_start: 0.9180 (t80) cc_final: 0.8953 (t80) REVERT: L 36 TYR cc_start: 0.8333 (m-80) cc_final: 0.7528 (m-80) REVERT: L 92 ASN cc_start: 0.8881 (m-40) cc_final: 0.8557 (p0) outliers start: 27 outliers final: 18 residues processed: 203 average time/residue: 0.4212 time to fit residues: 136.0626 Evaluate side-chains 153 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 2.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain L residue 71 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 173 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 259 optimal weight: 0.8980 chunk 212 optimal weight: 0.0570 chunk 85 optimal weight: 2.9990 chunk 312 optimal weight: 20.0000 chunk 337 optimal weight: 30.0000 chunk 277 optimal weight: 0.7980 chunk 309 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 chunk 250 optimal weight: 1.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 370 ASN A1135 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN L 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 28262 Z= 0.218 Angle : 0.531 10.434 38451 Z= 0.279 Chirality : 0.044 0.183 4557 Planarity : 0.004 0.063 4889 Dihedral : 5.855 57.501 4944 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.30 % Allowed : 6.42 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % 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: 0.82 (0.14), residues: 3395 helix: 1.82 (0.20), residues: 680 sheet: 0.77 (0.16), residues: 911 loop : -0.00 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 436 HIS 0.006 0.001 HIS B1064 PHE 0.022 0.001 PHE B 135 TYR 0.018 0.001 TYR C1067 ARG 0.005 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 157 time to evaluate : 3.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.9160 (t80) cc_final: 0.8533 (t80) REVERT: A 237 ARG cc_start: 0.9271 (mtt90) cc_final: 0.9059 (mmm-85) REVERT: A 383 SER cc_start: 0.8812 (m) cc_final: 0.8261 (t) REVERT: A 427 ASP cc_start: 0.8218 (m-30) cc_final: 0.7873 (t0) REVERT: A 486 PHE cc_start: 0.8333 (t80) cc_final: 0.7924 (t80) REVERT: A 508 TYR cc_start: 0.7179 (OUTLIER) cc_final: 0.6612 (t80) REVERT: A 595 VAL cc_start: 0.9064 (t) cc_final: 0.8543 (p) REVERT: A 610 VAL cc_start: 0.9237 (t) cc_final: 0.9001 (m) REVERT: A 784 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8137 (tt0) REVERT: A 1029 MET cc_start: 0.8378 (tpp) cc_final: 0.8089 (tpp) REVERT: B 462 LYS cc_start: 0.8927 (mttm) cc_final: 0.8594 (mttp) REVERT: B 516 GLU cc_start: 0.6581 (pt0) cc_final: 0.5882 (pm20) REVERT: B 582 LEU cc_start: 0.8997 (mm) cc_final: 0.8699 (mm) REVERT: B 869 MET cc_start: 0.8380 (mtt) cc_final: 0.7861 (mmm) REVERT: B 960 ASN cc_start: 0.7536 (m-40) cc_final: 0.7093 (t0) REVERT: B 1029 MET cc_start: 0.8668 (tpp) cc_final: 0.8405 (tpp) REVERT: B 1076 THR cc_start: 0.8459 (m) cc_final: 0.8061 (p) REVERT: C 86 PHE cc_start: 0.6098 (t80) cc_final: 0.5887 (t80) REVERT: C 104 TRP cc_start: 0.8412 (m-10) cc_final: 0.8144 (m-10) REVERT: C 220 PHE cc_start: 0.5565 (t80) cc_final: 0.5334 (t80) REVERT: C 378 LYS cc_start: 0.7171 (mmtt) cc_final: 0.6840 (mmtt) REVERT: C 410 ILE cc_start: 0.8110 (mm) cc_final: 0.7347 (mp) REVERT: C 449 TYR cc_start: 0.8627 (m-80) cc_final: 0.8005 (m-10) REVERT: C 513 LEU cc_start: 0.9120 (tp) cc_final: 0.8724 (tt) REVERT: C 697 MET cc_start: 0.8066 (ptm) cc_final: 0.7791 (ptm) REVERT: C 759 PHE cc_start: 0.7664 (m-80) cc_final: 0.7432 (t80) REVERT: C 902 MET cc_start: 0.8495 (mmm) cc_final: 0.8239 (mmt) REVERT: H 103 ARG cc_start: 0.8980 (mmm160) cc_final: 0.8512 (mmm160) REVERT: H 115 TRP cc_start: 0.6215 (OUTLIER) cc_final: 0.5670 (m-90) REVERT: H 158 PHE cc_start: 0.9265 (t80) cc_final: 0.9006 (t80) REVERT: L 36 TYR cc_start: 0.8636 (m-80) cc_final: 0.8229 (m-80) REVERT: L 92 ASN cc_start: 0.8894 (t0) cc_final: 0.8274 (m-40) outliers start: 39 outliers final: 25 residues processed: 184 average time/residue: 0.4190 time to fit residues: 123.8440 Evaluate side-chains 162 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 134 time to evaluate : 3.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 115 TRP Chi-restraints excluded: chain L residue 71 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 308 optimal weight: 20.0000 chunk 234 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 chunk 313 optimal weight: 0.5980 chunk 331 optimal weight: 6.9990 chunk 163 optimal weight: 0.7980 chunk 296 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28262 Z= 0.196 Angle : 0.499 7.614 38451 Z= 0.263 Chirality : 0.043 0.159 4557 Planarity : 0.003 0.045 4889 Dihedral : 5.161 52.699 4944 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.20 % Allowed : 7.15 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % 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: 0.87 (0.14), residues: 3395 helix: 1.89 (0.21), residues: 677 sheet: 0.76 (0.16), residues: 926 loop : 0.04 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 36 HIS 0.005 0.001 HIS B1064 PHE 0.037 0.001 PHE A 275 TYR 0.019 0.001 TYR B 265 ARG 0.008 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 144 time to evaluate : 3.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.9210 (t80) cc_final: 0.8568 (t80) REVERT: A 237 ARG cc_start: 0.9274 (mtt90) cc_final: 0.9049 (mmm-85) REVERT: A 383 SER cc_start: 0.8862 (m) cc_final: 0.8332 (t) REVERT: A 427 ASP cc_start: 0.8215 (m-30) cc_final: 0.7877 (t0) REVERT: A 486 PHE cc_start: 0.8370 (t80) cc_final: 0.7947 (t80) REVERT: A 508 TYR cc_start: 0.7238 (OUTLIER) cc_final: 0.6724 (t80) REVERT: A 595 VAL cc_start: 0.9105 (t) cc_final: 0.8599 (p) REVERT: A 610 VAL cc_start: 0.9263 (t) cc_final: 0.9026 (m) REVERT: A 784 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8170 (tt0) REVERT: A 1029 MET cc_start: 0.8350 (tpp) cc_final: 0.8062 (tpp) REVERT: B 462 LYS cc_start: 0.8943 (mttm) cc_final: 0.8580 (mttp) REVERT: B 516 GLU cc_start: 0.6552 (pt0) cc_final: 0.6008 (pm20) REVERT: B 869 MET cc_start: 0.8386 (mtt) cc_final: 0.7903 (mmm) REVERT: B 960 ASN cc_start: 0.7521 (m-40) cc_final: 0.7071 (t0) REVERT: B 1029 MET cc_start: 0.8618 (tpp) cc_final: 0.8313 (tpp) REVERT: B 1076 THR cc_start: 0.8629 (m) cc_final: 0.8212 (p) REVERT: C 104 TRP cc_start: 0.8374 (m-10) cc_final: 0.8033 (m-10) REVERT: C 238 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7042 (p90) REVERT: C 378 LYS cc_start: 0.7144 (mmtt) cc_final: 0.6760 (mmtt) REVERT: C 410 ILE cc_start: 0.8269 (mm) cc_final: 0.7623 (mp) REVERT: C 449 TYR cc_start: 0.8629 (m-80) cc_final: 0.8016 (m-10) REVERT: C 508 TYR cc_start: 0.9060 (OUTLIER) cc_final: 0.7325 (m-80) REVERT: C 513 LEU cc_start: 0.9204 (tp) cc_final: 0.8864 (tt) REVERT: C 759 PHE cc_start: 0.7812 (m-80) cc_final: 0.7530 (t80) REVERT: C 902 MET cc_start: 0.8498 (mmm) cc_final: 0.8257 (mmt) REVERT: C 955 ASN cc_start: 0.9124 (OUTLIER) cc_final: 0.8897 (t0) REVERT: H 103 ARG cc_start: 0.9045 (mmm160) cc_final: 0.8545 (mmp-170) REVERT: H 115 TRP cc_start: 0.6628 (m-10) cc_final: 0.6311 (m-90) REVERT: H 158 PHE cc_start: 0.9257 (t80) cc_final: 0.8976 (t80) REVERT: L 35 TRP cc_start: 0.7832 (m100) cc_final: 0.7444 (m100) REVERT: L 36 TYR cc_start: 0.8617 (m-80) cc_final: 0.8235 (m-80) REVERT: L 92 ASN cc_start: 0.8960 (t0) cc_final: 0.8269 (m-40) outliers start: 36 outliers final: 22 residues processed: 171 average time/residue: 0.4064 time to fit residues: 113.4978 Evaluate side-chains 157 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 3.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 98 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 276 optimal weight: 0.9980 chunk 188 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 246 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 282 optimal weight: 1.9990 chunk 229 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 169 optimal weight: 0.8980 chunk 297 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B1010 GLN C 895 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 28262 Z= 0.209 Angle : 0.501 9.039 38451 Z= 0.261 Chirality : 0.043 0.156 4557 Planarity : 0.003 0.045 4889 Dihedral : 4.821 51.994 4944 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.06 % Allowed : 7.58 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % 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: 0.85 (0.14), residues: 3395 helix: 1.88 (0.21), residues: 676 sheet: 0.71 (0.16), residues: 961 loop : 0.03 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 36 HIS 0.004 0.001 HIS B1064 PHE 0.024 0.001 PHE A 275 TYR 0.019 0.001 TYR C 369 ARG 0.007 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 138 time to evaluate : 3.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.9250 (t80) cc_final: 0.8609 (t80) REVERT: A 383 SER cc_start: 0.8891 (m) cc_final: 0.8380 (t) REVERT: A 427 ASP cc_start: 0.8214 (m-30) cc_final: 0.7877 (t0) REVERT: A 486 PHE cc_start: 0.8395 (t80) cc_final: 0.7968 (t80) REVERT: A 508 TYR cc_start: 0.7268 (OUTLIER) cc_final: 0.6749 (t80) REVERT: A 610 VAL cc_start: 0.9268 (t) cc_final: 0.9047 (m) REVERT: A 784 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: A 1029 MET cc_start: 0.8170 (tpp) cc_final: 0.7871 (tpp) REVERT: B 462 LYS cc_start: 0.8957 (mttm) cc_final: 0.8595 (mttp) REVERT: B 516 GLU cc_start: 0.6377 (pt0) cc_final: 0.5824 (pm20) REVERT: B 869 MET cc_start: 0.8383 (mtt) cc_final: 0.7923 (mmm) REVERT: B 960 ASN cc_start: 0.7536 (m-40) cc_final: 0.7080 (t0) REVERT: B 974 SER cc_start: 0.9147 (t) cc_final: 0.8895 (m) REVERT: B 1029 MET cc_start: 0.8604 (tpp) cc_final: 0.8316 (tpp) REVERT: B 1076 THR cc_start: 0.8623 (m) cc_final: 0.8219 (p) REVERT: C 104 TRP cc_start: 0.8462 (m-10) cc_final: 0.8104 (m-10) REVERT: C 238 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7051 (p90) REVERT: C 242 LEU cc_start: 0.8555 (mm) cc_final: 0.8255 (mm) REVERT: C 378 LYS cc_start: 0.7353 (mmtt) cc_final: 0.7004 (mmtt) REVERT: C 410 ILE cc_start: 0.8231 (mm) cc_final: 0.7648 (mp) REVERT: C 449 TYR cc_start: 0.8668 (m-80) cc_final: 0.8073 (m-10) REVERT: C 513 LEU cc_start: 0.9203 (tp) cc_final: 0.8863 (tt) REVERT: C 759 PHE cc_start: 0.7912 (m-80) cc_final: 0.7615 (t80) REVERT: C 902 MET cc_start: 0.8505 (mmm) cc_final: 0.8282 (mmt) REVERT: H 38 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7911 (ttp80) REVERT: H 103 ARG cc_start: 0.9234 (mmm160) cc_final: 0.8873 (mmm160) REVERT: H 115 TRP cc_start: 0.6527 (m-10) cc_final: 0.6179 (m-90) REVERT: H 158 PHE cc_start: 0.9299 (t80) cc_final: 0.9034 (t80) REVERT: L 35 TRP cc_start: 0.7873 (m100) cc_final: 0.7300 (m100) REVERT: L 36 TYR cc_start: 0.8490 (m-80) cc_final: 0.8061 (m-80) REVERT: L 92 ASN cc_start: 0.9080 (t0) cc_final: 0.8792 (m-40) outliers start: 32 outliers final: 26 residues processed: 162 average time/residue: 0.3917 time to fit residues: 104.9114 Evaluate side-chains 159 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 98 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 111 optimal weight: 0.8980 chunk 298 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 331 optimal weight: 20.0000 chunk 275 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A 957 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS C1106 GLN ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 28262 Z= 0.208 Angle : 0.496 12.819 38451 Z= 0.257 Chirality : 0.043 0.152 4557 Planarity : 0.003 0.044 4889 Dihedral : 4.391 52.069 4944 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.43 % Allowed : 8.22 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % 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: 0.81 (0.14), residues: 3395 helix: 1.75 (0.21), residues: 684 sheet: 0.70 (0.16), residues: 958 loop : 0.04 (0.15), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 36 HIS 0.004 0.001 HIS B1064 PHE 0.022 0.001 PHE A 194 TYR 0.020 0.001 TYR C1067 ARG 0.006 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 149 time to evaluate : 3.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.9163 (t80) cc_final: 0.8394 (t80) REVERT: A 383 SER cc_start: 0.8763 (m) cc_final: 0.8289 (t) REVERT: A 427 ASP cc_start: 0.8198 (m-30) cc_final: 0.7872 (t0) REVERT: A 486 PHE cc_start: 0.8451 (t80) cc_final: 0.7982 (t80) REVERT: A 610 VAL cc_start: 0.9274 (t) cc_final: 0.9051 (m) REVERT: A 759 PHE cc_start: 0.8024 (m-10) cc_final: 0.7489 (m-10) REVERT: A 784 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: A 1029 MET cc_start: 0.8135 (tpp) cc_final: 0.7846 (tpp) REVERT: B 392 PHE cc_start: 0.7043 (m-80) cc_final: 0.6401 (m-80) REVERT: B 462 LYS cc_start: 0.8987 (mttm) cc_final: 0.8624 (mttp) REVERT: B 516 GLU cc_start: 0.6326 (pt0) cc_final: 0.5711 (pm20) REVERT: B 869 MET cc_start: 0.8399 (mtt) cc_final: 0.7948 (mmm) REVERT: B 960 ASN cc_start: 0.7384 (m-40) cc_final: 0.7014 (t0) REVERT: B 974 SER cc_start: 0.9112 (t) cc_final: 0.8893 (m) REVERT: B 1029 MET cc_start: 0.8586 (tpp) cc_final: 0.8327 (tpp) REVERT: B 1076 THR cc_start: 0.8770 (m) cc_final: 0.8265 (p) REVERT: C 88 ASP cc_start: 0.8993 (m-30) cc_final: 0.8743 (m-30) REVERT: C 104 TRP cc_start: 0.8346 (m-10) cc_final: 0.7899 (m-10) REVERT: C 238 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7007 (p90) REVERT: C 242 LEU cc_start: 0.8565 (mm) cc_final: 0.8281 (mm) REVERT: C 410 ILE cc_start: 0.8161 (mm) cc_final: 0.7682 (mp) REVERT: C 449 TYR cc_start: 0.8667 (m-80) cc_final: 0.8090 (m-10) REVERT: C 505 TYR cc_start: 0.8305 (t80) cc_final: 0.8045 (t80) REVERT: C 513 LEU cc_start: 0.9204 (tp) cc_final: 0.8847 (tt) REVERT: C 759 PHE cc_start: 0.8063 (m-80) cc_final: 0.7730 (t80) REVERT: C 902 MET cc_start: 0.8599 (mmm) cc_final: 0.8395 (mmt) REVERT: H 36 TRP cc_start: 0.7866 (m100) cc_final: 0.7334 (m100) REVERT: H 103 ARG cc_start: 0.9086 (mmm160) cc_final: 0.8599 (mmm160) REVERT: H 113 ASP cc_start: 0.6863 (OUTLIER) cc_final: 0.6573 (p0) REVERT: H 115 TRP cc_start: 0.6316 (OUTLIER) cc_final: 0.6017 (m-90) REVERT: H 158 PHE cc_start: 0.9299 (t80) cc_final: 0.9017 (t80) REVERT: L 35 TRP cc_start: 0.8001 (m100) cc_final: 0.7399 (m100) REVERT: L 36 TYR cc_start: 0.8447 (m-80) cc_final: 0.7914 (m-80) REVERT: L 92 ASN cc_start: 0.9137 (t0) cc_final: 0.8844 (m-40) outliers start: 43 outliers final: 32 residues processed: 179 average time/residue: 0.3924 time to fit residues: 115.3041 Evaluate side-chains 170 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 134 time to evaluate : 3.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 115 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 319 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 189 optimal weight: 0.6980 chunk 242 optimal weight: 3.9990 chunk 187 optimal weight: 0.9980 chunk 279 optimal weight: 7.9990 chunk 185 optimal weight: 2.9990 chunk 330 optimal weight: 30.0000 chunk 206 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 152 optimal weight: 0.6980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1088 HIS ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 28262 Z= 0.361 Angle : 0.583 9.979 38451 Z= 0.302 Chirality : 0.045 0.160 4557 Planarity : 0.005 0.168 4889 Dihedral : 4.581 52.222 4943 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.46 % Allowed : 9.08 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % 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: 0.59 (0.14), residues: 3395 helix: 1.41 (0.20), residues: 683 sheet: 0.58 (0.17), residues: 939 loop : -0.04 (0.15), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 436 HIS 0.008 0.001 HIS B1064 PHE 0.036 0.002 PHE A 275 TYR 0.027 0.002 TYR C1067 ARG 0.005 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 146 time to evaluate : 3.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.9170 (t80) cc_final: 0.8721 (t80) REVERT: A 237 ARG cc_start: 0.9350 (mtt90) cc_final: 0.9113 (mmm-85) REVERT: A 427 ASP cc_start: 0.8149 (m-30) cc_final: 0.7823 (t0) REVERT: A 486 PHE cc_start: 0.8478 (t80) cc_final: 0.8005 (t80) REVERT: A 755 GLN cc_start: 0.8120 (mt0) cc_final: 0.7907 (mt0) REVERT: A 784 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8318 (tt0) REVERT: A 822 LEU cc_start: 0.9073 (mt) cc_final: 0.8838 (mt) REVERT: A 957 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7969 (tt0) REVERT: B 392 PHE cc_start: 0.7295 (m-80) cc_final: 0.6628 (m-80) REVERT: B 462 LYS cc_start: 0.8940 (mttm) cc_final: 0.8658 (mttp) REVERT: B 516 GLU cc_start: 0.6328 (pt0) cc_final: 0.5937 (pm20) REVERT: B 869 MET cc_start: 0.8445 (mtt) cc_final: 0.7981 (mmm) REVERT: B 1029 MET cc_start: 0.8617 (tpp) cc_final: 0.8290 (tpp) REVERT: B 1076 THR cc_start: 0.8454 (m) cc_final: 0.8103 (p) REVERT: C 104 TRP cc_start: 0.8365 (m-10) cc_final: 0.7850 (m-10) REVERT: C 238 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7095 (p90) REVERT: C 242 LEU cc_start: 0.8536 (mm) cc_final: 0.8250 (mm) REVERT: C 378 LYS cc_start: 0.7544 (mmmt) cc_final: 0.6888 (mmtt) REVERT: C 449 TYR cc_start: 0.8639 (m-80) cc_final: 0.8093 (m-10) REVERT: C 451 TYR cc_start: 0.6363 (m-80) cc_final: 0.5829 (m-10) REVERT: C 505 TYR cc_start: 0.8379 (t80) cc_final: 0.8166 (t80) REVERT: C 508 TYR cc_start: 0.9044 (OUTLIER) cc_final: 0.7120 (m-80) REVERT: C 513 LEU cc_start: 0.9195 (tp) cc_final: 0.8832 (tt) REVERT: C 759 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7746 (t80) REVERT: C 895 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7428 (pp30) REVERT: C 902 MET cc_start: 0.8584 (mmm) cc_final: 0.8339 (mmt) REVERT: H 103 ARG cc_start: 0.9088 (mmm160) cc_final: 0.8664 (mmm160) REVERT: H 104 PHE cc_start: 0.8443 (t80) cc_final: 0.8155 (t80) REVERT: H 158 PHE cc_start: 0.9308 (t80) cc_final: 0.9018 (t80) REVERT: L 35 TRP cc_start: 0.8094 (m100) cc_final: 0.7394 (m100) REVERT: L 92 ASN cc_start: 0.9202 (t0) cc_final: 0.8931 (m-40) outliers start: 44 outliers final: 30 residues processed: 180 average time/residue: 0.3867 time to fit residues: 113.3539 Evaluate side-chains 168 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 132 time to evaluate : 2.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 98 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 204 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 99 optimal weight: 0.0010 chunk 64 optimal weight: 0.7980 chunk 210 optimal weight: 0.1980 chunk 225 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 259 optimal weight: 0.6980 chunk 300 optimal weight: 3.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 957 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 28262 Z= 0.156 Angle : 0.492 8.768 38451 Z= 0.255 Chirality : 0.043 0.186 4557 Planarity : 0.004 0.139 4889 Dihedral : 4.258 51.614 4943 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.03 % Allowed : 9.61 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % 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: 0.78 (0.15), residues: 3395 helix: 1.84 (0.21), residues: 677 sheet: 0.59 (0.16), residues: 956 loop : 0.04 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 115 HIS 0.003 0.001 HIS B1064 PHE 0.029 0.001 PHE A 275 TYR 0.016 0.001 TYR C1067 ARG 0.006 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 3.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.9186 (t80) cc_final: 0.8427 (t80) REVERT: A 427 ASP cc_start: 0.8127 (m-30) cc_final: 0.7747 (t0) REVERT: A 486 PHE cc_start: 0.8467 (t80) cc_final: 0.7984 (t80) REVERT: A 759 PHE cc_start: 0.7992 (m-10) cc_final: 0.7494 (m-10) REVERT: A 784 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: A 822 LEU cc_start: 0.9053 (mt) cc_final: 0.8834 (mt) REVERT: A 904 TYR cc_start: 0.6829 (m-10) cc_final: 0.6464 (m-10) REVERT: B 392 PHE cc_start: 0.6974 (m-80) cc_final: 0.6269 (m-80) REVERT: B 462 LYS cc_start: 0.8953 (mttm) cc_final: 0.8673 (mttp) REVERT: B 516 GLU cc_start: 0.6416 (pt0) cc_final: 0.5916 (pm20) REVERT: B 869 MET cc_start: 0.8380 (mtt) cc_final: 0.7925 (mmm) REVERT: B 1029 MET cc_start: 0.8560 (tpp) cc_final: 0.8289 (tpp) REVERT: B 1076 THR cc_start: 0.8607 (m) cc_final: 0.8071 (p) REVERT: C 104 TRP cc_start: 0.8261 (m-10) cc_final: 0.7769 (m-10) REVERT: C 238 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.6995 (p90) REVERT: C 242 LEU cc_start: 0.8521 (mm) cc_final: 0.8238 (mm) REVERT: C 378 LYS cc_start: 0.7820 (mmmt) cc_final: 0.7362 (mmtt) REVERT: C 449 TYR cc_start: 0.8654 (m-80) cc_final: 0.8094 (m-10) REVERT: C 508 TYR cc_start: 0.9011 (OUTLIER) cc_final: 0.7061 (m-80) REVERT: C 513 LEU cc_start: 0.9190 (tp) cc_final: 0.8835 (tt) REVERT: C 759 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7685 (t80) REVERT: C 902 MET cc_start: 0.8560 (mmm) cc_final: 0.8357 (mmt) REVERT: H 103 ARG cc_start: 0.9211 (mmm160) cc_final: 0.8826 (mmm160) REVERT: H 104 PHE cc_start: 0.8553 (t80) cc_final: 0.8298 (t80) REVERT: H 158 PHE cc_start: 0.9305 (t80) cc_final: 0.9010 (t80) REVERT: L 35 TRP cc_start: 0.8085 (m100) cc_final: 0.7299 (m100) REVERT: L 92 ASN cc_start: 0.9186 (t0) cc_final: 0.8915 (m-40) outliers start: 31 outliers final: 25 residues processed: 165 average time/residue: 0.3937 time to fit residues: 105.8500 Evaluate side-chains 162 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 98 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 316 optimal weight: 10.0000 chunk 288 optimal weight: 1.9990 chunk 308 optimal weight: 10.0000 chunk 185 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 241 optimal weight: 0.4980 chunk 94 optimal weight: 0.5980 chunk 278 optimal weight: 0.9990 chunk 291 optimal weight: 2.9990 chunk 306 optimal weight: 20.0000 chunk 202 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 28262 Z= 0.255 Angle : 0.524 8.836 38451 Z= 0.270 Chirality : 0.043 0.177 4557 Planarity : 0.004 0.126 4889 Dihedral : 4.281 52.203 4943 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.13 % Allowed : 9.88 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % 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 (0.15), residues: 3395 helix: 1.77 (0.21), residues: 677 sheet: 0.41 (0.16), residues: 996 loop : 0.02 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 436 HIS 0.005 0.001 HIS B1064 PHE 0.028 0.001 PHE A 275 TYR 0.023 0.001 TYR C1067 ARG 0.006 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 137 time to evaluate : 3.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.9165 (t80) cc_final: 0.8725 (t80) REVERT: A 427 ASP cc_start: 0.8134 (m-30) cc_final: 0.7768 (t0) REVERT: A 486 PHE cc_start: 0.8508 (t80) cc_final: 0.8024 (t80) REVERT: A 759 PHE cc_start: 0.8031 (m-10) cc_final: 0.7730 (m-10) REVERT: A 822 LEU cc_start: 0.9199 (mt) cc_final: 0.8961 (mt) REVERT: A 904 TYR cc_start: 0.6866 (m-10) cc_final: 0.6530 (m-10) REVERT: B 392 PHE cc_start: 0.7033 (m-80) cc_final: 0.6299 (m-80) REVERT: B 462 LYS cc_start: 0.8965 (mttm) cc_final: 0.8687 (mttp) REVERT: B 516 GLU cc_start: 0.6469 (pt0) cc_final: 0.5901 (pm20) REVERT: B 869 MET cc_start: 0.8434 (mtt) cc_final: 0.7994 (mmm) REVERT: B 1029 MET cc_start: 0.8579 (tpp) cc_final: 0.8319 (tpp) REVERT: B 1076 THR cc_start: 0.8521 (m) cc_final: 0.8069 (p) REVERT: C 104 TRP cc_start: 0.8326 (m-10) cc_final: 0.7824 (m-10) REVERT: C 238 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7069 (p90) REVERT: C 242 LEU cc_start: 0.8561 (mm) cc_final: 0.8281 (mm) REVERT: C 378 LYS cc_start: 0.7876 (mmmt) cc_final: 0.7425 (mmtt) REVERT: C 449 TYR cc_start: 0.8663 (m-80) cc_final: 0.8120 (m-10) REVERT: C 505 TYR cc_start: 0.8387 (t80) cc_final: 0.8162 (t80) REVERT: C 508 TYR cc_start: 0.9023 (OUTLIER) cc_final: 0.7080 (m-80) REVERT: C 513 LEU cc_start: 0.9170 (tp) cc_final: 0.8813 (tt) REVERT: C 759 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7947 (t80) REVERT: C 902 MET cc_start: 0.8603 (mmm) cc_final: 0.8397 (mmt) REVERT: H 34 MET cc_start: 0.8972 (mmt) cc_final: 0.8348 (mmp) REVERT: H 103 ARG cc_start: 0.9267 (mmm160) cc_final: 0.8945 (mmm160) REVERT: H 104 PHE cc_start: 0.8566 (t80) cc_final: 0.8323 (t80) REVERT: H 158 PHE cc_start: 0.9310 (t80) cc_final: 0.9017 (t80) REVERT: L 35 TRP cc_start: 0.8133 (m100) cc_final: 0.7289 (m100) REVERT: L 92 ASN cc_start: 0.9208 (t0) cc_final: 0.8931 (m-40) outliers start: 34 outliers final: 25 residues processed: 160 average time/residue: 0.4038 time to fit residues: 105.9250 Evaluate side-chains 157 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 129 time to evaluate : 3.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 98 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 325 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 226 optimal weight: 9.9990 chunk 341 optimal weight: 30.0000 chunk 314 optimal weight: 50.0000 chunk 272 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 210 optimal weight: 10.0000 chunk 166 optimal weight: 0.8980 chunk 216 optimal weight: 0.0570 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B1002 GLN C 895 GLN C1002 GLN C1005 GLN ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28262 Z= 0.210 Angle : 0.503 9.561 38451 Z= 0.259 Chirality : 0.043 0.169 4557 Planarity : 0.003 0.043 4889 Dihedral : 4.204 51.897 4943 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.16 % Allowed : 9.78 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % 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: 0.72 (0.15), residues: 3395 helix: 1.88 (0.21), residues: 677 sheet: 0.42 (0.16), residues: 993 loop : 0.04 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP H 115 HIS 0.004 0.001 HIS B1064 PHE 0.026 0.001 PHE A 275 TYR 0.019 0.001 TYR C1067 ARG 0.007 0.000 ARG C 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 133 time to evaluate : 2.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.9179 (t80) cc_final: 0.8731 (t80) REVERT: A 427 ASP cc_start: 0.8126 (m-30) cc_final: 0.7754 (t0) REVERT: A 486 PHE cc_start: 0.8446 (t80) cc_final: 0.8118 (t80) REVERT: A 492 LEU cc_start: 0.8602 (mp) cc_final: 0.7998 (tt) REVERT: A 759 PHE cc_start: 0.8013 (m-10) cc_final: 0.7719 (m-10) REVERT: A 822 LEU cc_start: 0.9212 (mt) cc_final: 0.8965 (mt) REVERT: A 904 TYR cc_start: 0.6862 (m-10) cc_final: 0.6487 (m-10) REVERT: B 392 PHE cc_start: 0.6996 (m-80) cc_final: 0.6282 (m-80) REVERT: B 462 LYS cc_start: 0.8975 (mttm) cc_final: 0.8697 (mttp) REVERT: B 516 GLU cc_start: 0.6548 (pt0) cc_final: 0.5972 (pm20) REVERT: B 869 MET cc_start: 0.8419 (mtt) cc_final: 0.7940 (mmm) REVERT: B 1029 MET cc_start: 0.8561 (tpp) cc_final: 0.8297 (tpp) REVERT: B 1076 THR cc_start: 0.8373 (m) cc_final: 0.7905 (p) REVERT: C 104 TRP cc_start: 0.8396 (m-10) cc_final: 0.7836 (m-10) REVERT: C 238 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.6980 (p90) REVERT: C 242 LEU cc_start: 0.8578 (mm) cc_final: 0.8298 (mm) REVERT: C 378 LYS cc_start: 0.7864 (mmmt) cc_final: 0.7416 (mmtt) REVERT: C 408 ARG cc_start: 0.8877 (ttp80) cc_final: 0.8485 (tmm160) REVERT: C 449 TYR cc_start: 0.8608 (m-80) cc_final: 0.8072 (m-10) REVERT: C 508 TYR cc_start: 0.9017 (OUTLIER) cc_final: 0.7062 (m-80) REVERT: C 513 LEU cc_start: 0.9170 (tp) cc_final: 0.8812 (tt) REVERT: C 759 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7877 (t80) REVERT: C 902 MET cc_start: 0.8588 (mmm) cc_final: 0.8385 (mmt) REVERT: H 103 ARG cc_start: 0.9269 (mmm160) cc_final: 0.8946 (mmm160) REVERT: H 104 PHE cc_start: 0.8561 (t80) cc_final: 0.8330 (t80) REVERT: H 158 PHE cc_start: 0.9307 (t80) cc_final: 0.9011 (t80) REVERT: L 35 TRP cc_start: 0.7989 (m100) cc_final: 0.6825 (m100) REVERT: L 92 ASN cc_start: 0.9207 (t0) cc_final: 0.8924 (m-40) outliers start: 35 outliers final: 29 residues processed: 157 average time/residue: 0.3951 time to fit residues: 102.7339 Evaluate side-chains 159 residues out of total 3006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 127 time to evaluate : 3.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 98 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 250 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 75 optimal weight: 0.0980 chunk 272 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 279 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 239 optimal weight: 8.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.134388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.082289 restraints weight = 70669.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.085193 restraints weight = 33709.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.086609 restraints weight = 21762.668| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28262 Z= 0.207 Angle : 0.514 12.238 38451 Z= 0.262 Chirality : 0.043 0.164 4557 Planarity : 0.003 0.043 4889 Dihedral : 4.170 51.940 4943 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.03 % Allowed : 10.05 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % 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: 0.74 (0.15), residues: 3395 helix: 1.95 (0.21), residues: 671 sheet: 0.41 (0.16), residues: 997 loop : 0.05 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP H 36 HIS 0.004 0.001 HIS A 519 PHE 0.025 0.001 PHE A 275 TYR 0.019 0.001 TYR C1067 ARG 0.008 0.000 ARG C 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4690.05 seconds wall clock time: 87 minutes 41.94 seconds (5261.94 seconds total)