Starting phenix.real_space_refine on Tue Mar 19 13:37:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lws_23555/03_2024/7lws_23555.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lws_23555/03_2024/7lws_23555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lws_23555/03_2024/7lws_23555.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lws_23555/03_2024/7lws_23555.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lws_23555/03_2024/7lws_23555.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lws_23555/03_2024/7lws_23555.pdb" } resolution = 3.22 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= -0.000 sd= 0.086 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 104 5.16 5 C 15489 2.51 5 N 3957 2.21 5 O 4770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24320 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 7812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7812 Classifications: {'peptide': 1000} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 47, 'TRANS': 952} Chain breaks: 8 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 7813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7813 Classifications: {'peptide': 1000} Link IDs: {'PTRANS': 47, 'TRANS': 952} Chain breaks: 8 Chain: "C" Number of atoms: 7813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7813 Classifications: {'peptide': 1000} Link IDs: {'PTRANS': 47, 'TRANS': 952} Chain breaks: 8 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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: 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 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 12.52, per 1000 atoms: 0.51 Number of scatterers: 24320 At special positions: 0 Unit cell: (130.418, 138.97, 176.385, 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 104 16.00 O 4770 8.00 N 3957 7.00 C 15489 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 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=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 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=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 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=2.01 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.05 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.05 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 331 " " NAG B1310 " - " ASN B 122 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG D 1 " - " ASN A 709 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 709 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 709 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 9.31 Conformation dependent library (CDL) restraints added in 4.5 seconds 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5616 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 47 sheets defined 26.6% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.09 Creating SS restraints... Processing helix chain 'A' and resid 197 through 200 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.742A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.645A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 5.232A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.859A 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 438 through 443 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.196A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 759 removed outlier: 7.002A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 759 " --> pdb=" O TYR A 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 755 through 759' Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.570A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.524A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 4.103A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.814A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.536A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.628A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.541A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.563A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1034 removed outlier: 4.359A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (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 removed outlier: 3.671A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.858A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.749A 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 589 through 593 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.806A pdb=" N GLU B 619 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.552A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.802A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.891A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.715A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.754A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 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 965 removed outlier: 3.671A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.682A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.004A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' 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 removed outlier: 3.713A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.548A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.933A 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 438 through 443 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.627A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.550A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.551A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.590A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.631A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 948 through 965 Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 986 through 1033 removed outlier: 4.159A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.294A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.132A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.406A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.798A 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: 5.670A 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: 3.715A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.858A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.875A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.857A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.804A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) 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: 6.491A 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 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.078A pdb=" N GLN A1071 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.541A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.207A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.807A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.891A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 5.825A 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: 3.744A 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 Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.677A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 313 through 318 removed outlier: 5.634A pdb=" N GLN B 314 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR B 599 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 316 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.745A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.868A 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 removed outlier: 3.653A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.863A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) 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 654 through 655 removed outlier: 6.548A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.713A pdb=" N GLN B1071 " --> pdb=" O ILE B 716 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.713A pdb=" N GLN B1071 " --> pdb=" O ILE B 716 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.586A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1123 Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.068A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.450A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.775A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.274A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.883A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.638A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.466A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.929A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.965A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.407A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.727A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1022 hydrogen bonds defined for protein. 2763 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: 11.10 Time building geometry restraints manager: 10.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6145 1.33 - 1.46: 4823 1.46 - 1.58: 13746 1.58 - 1.70: 0 1.70 - 1.82: 128 Bond restraints: 24842 Sorted by residual: bond pdb=" C4 NAG M 1 " pdb=" O4 NAG M 1 " ideal model delta sigma weight residual 1.409 1.496 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" C4 NAG U 1 " pdb=" O4 NAG U 1 " ideal model delta sigma weight residual 1.409 1.487 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C5 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C5 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C5 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 24837 not shown) Histogram of bond angle deviations from ideal: 97.67 - 105.13: 427 105.13 - 112.59: 11461 112.59 - 120.05: 11181 120.05 - 127.51: 10564 127.51 - 134.98: 152 Bond angle restraints: 33785 Sorted by residual: angle pdb=" CA ASP A1041 " pdb=" CB ASP A1041 " pdb=" CG ASP A1041 " ideal model delta sigma weight residual 112.60 118.52 -5.92 1.00e+00 1.00e+00 3.51e+01 angle pdb=" CA ASN A 777 " pdb=" CB ASN A 777 " pdb=" CG ASN A 777 " ideal model delta sigma weight residual 112.60 118.22 -5.62 1.00e+00 1.00e+00 3.16e+01 angle pdb=" C GLY B 381 " pdb=" N VAL B 382 " pdb=" CA VAL B 382 " ideal model delta sigma weight residual 122.23 130.29 -8.06 1.44e+00 4.82e-01 3.13e+01 angle pdb=" CA GLY B 416 " pdb=" C GLY B 416 " pdb=" N LYS B 417 " ideal model delta sigma weight residual 114.23 119.09 -4.86 8.80e-01 1.29e+00 3.05e+01 angle pdb=" OE1 GLN C 926 " pdb=" CD GLN C 926 " pdb=" NE2 GLN C 926 " ideal model delta sigma weight residual 122.60 117.26 5.34 1.00e+00 1.00e+00 2.85e+01 ... (remaining 33780 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 14485 17.97 - 35.94: 869 35.94 - 53.91: 157 53.91 - 71.88: 59 71.88 - 89.85: 26 Dihedral angle restraints: 15596 sinusoidal: 6875 harmonic: 8721 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -161.74 75.74 1 1.00e+01 1.00e-02 7.24e+01 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 -158.97 72.97 1 1.00e+01 1.00e-02 6.79e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -150.35 64.35 1 1.00e+01 1.00e-02 5.44e+01 ... (remaining 15593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.284: 4009 0.284 - 0.569: 22 0.569 - 0.853: 0 0.853 - 1.137: 0 1.137 - 1.422: 4 Chirality restraints: 4035 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.04e+02 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.88e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.85e+01 ... (remaining 4032 not shown) Planarity restraints: 4326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 657 " 0.122 2.00e-02 2.50e+03 1.28e-01 2.04e+02 pdb=" CG ASN B 657 " -0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN B 657 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN B 657 " -0.193 2.00e-02 2.50e+03 pdb=" C1 NAG B1308 " 0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " 0.118 2.00e-02 2.50e+03 1.27e-01 2.00e+02 pdb=" CG ASN C 234 " -0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " -0.197 2.00e-02 2.50e+03 pdb=" C1 NAG C1302 " 0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.108 2.00e-02 2.50e+03 1.13e-01 1.59e+02 pdb=" CG ASN C 331 " -0.070 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.172 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " 0.132 2.00e-02 2.50e+03 ... (remaining 4323 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 11842 2.99 - 3.47: 22781 3.47 - 3.95: 39280 3.95 - 4.42: 43772 4.42 - 4.90: 74777 Nonbonded interactions: 192452 Sorted by model distance: nonbonded pdb=" OE1 GLU B 516 " pdb=" OH TYR C 200 " model vdw 2.517 2.440 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.519 2.440 nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.520 2.440 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.532 2.440 nonbonded pdb=" OH TYR A 200 " pdb=" OE1 GLU C 516 " model vdw 2.535 2.440 ... (remaining 192447 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' and (resid 27 through 1147 or resid 1301 through 1308)) selection = (chain 'B' and (resid 27 through 165 or (resid 166 and (name N or name CA or nam \ e C or name O or name CB )) or resid 167 through 1147 or resid 1301 through 1308 \ )) selection = (chain 'C' and (resid 27 through 165 or (resid 166 and (name N or name CA or nam \ e C or name O or name CB )) or resid 167 through 1147 or resid 1301 through 1308 \ )) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.210 Check model and map are aligned: 0.350 Set scattering table: 0.230 Process input model: 66.720 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 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 : 0.014 0.087 24842 Z= 0.913 Angle : 1.797 13.791 33785 Z= 1.198 Chirality : 0.109 1.422 4035 Planarity : 0.013 0.206 4281 Dihedral : 12.963 89.850 9866 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 0.10 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.65 % Favored : 95.01 % Rotamer: Outliers : 0.95 % Allowed : 2.56 % Favored : 96.49 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.14), residues: 2946 helix: -1.60 (0.16), residues: 656 sheet: 0.53 (0.21), residues: 534 loop : -0.72 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.123 0.026 TRP A 886 HIS 0.012 0.003 HIS A1048 PHE 0.086 0.011 PHE A 718 TYR 0.160 0.019 TYR A 904 ARG 0.012 0.001 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 368 time to evaluate : 2.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9227 (mt) cc_final: 0.9014 (mp) REVERT: A 88 ASP cc_start: 0.7891 (m-30) cc_final: 0.7654 (m-30) REVERT: A 115 GLN cc_start: 0.6646 (mp10) cc_final: 0.6353 (mp10) REVERT: A 128 ILE cc_start: 0.7654 (mt) cc_final: 0.7397 (mp) REVERT: A 202 LYS cc_start: 0.7720 (mttm) cc_final: 0.7461 (mttp) REVERT: A 237 ARG cc_start: 0.7140 (mtt90) cc_final: 0.6441 (mtm-85) REVERT: A 389 ASP cc_start: 0.8058 (m-30) cc_final: 0.7812 (t0) REVERT: A 400 PHE cc_start: 0.8475 (p90) cc_final: 0.8245 (p90) REVERT: A 574 ASP cc_start: 0.6916 (t70) cc_final: 0.6479 (t0) REVERT: A 673 SER cc_start: 0.8106 (p) cc_final: 0.7855 (p) REVERT: A 740 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7971 (tpp) REVERT: A 886 TRP cc_start: 0.7959 (OUTLIER) cc_final: 0.7231 (m-90) REVERT: A 1128 VAL cc_start: 0.8660 (t) cc_final: 0.8266 (p) REVERT: B 127 VAL cc_start: 0.7718 (t) cc_final: 0.7405 (p) REVERT: B 133 PHE cc_start: 0.7248 (m-80) cc_final: 0.6822 (m-80) REVERT: B 581 THR cc_start: 0.6524 (OUTLIER) cc_final: 0.5890 (m) REVERT: B 646 ARG cc_start: 0.8233 (mmm-85) cc_final: 0.7676 (tpm170) REVERT: B 740 MET cc_start: 0.8513 (tpt) cc_final: 0.7730 (tpt) REVERT: B 902 MET cc_start: 0.8552 (mmm) cc_final: 0.8196 (mmm) REVERT: C 64 TRP cc_start: 0.7428 (t60) cc_final: 0.7154 (t60) REVERT: C 81 ASN cc_start: 0.7989 (p0) cc_final: 0.7773 (p0) REVERT: C 271 GLN cc_start: 0.7986 (mt0) cc_final: 0.7743 (mm-40) REVERT: C 422 ASN cc_start: 0.7185 (m-40) cc_final: 0.6140 (t0) REVERT: C 453 TYR cc_start: 0.5165 (p90) cc_final: 0.4895 (p90) REVERT: C 581 THR cc_start: 0.6641 (m) cc_final: 0.6364 (p) REVERT: C 780 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7618 (mm-30) outliers start: 25 outliers final: 8 residues processed: 391 average time/residue: 0.3924 time to fit residues: 239.3565 Evaluate side-chains 212 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 201 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 0.7980 chunk 227 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 153 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 235 optimal weight: 6.9990 chunk 90 optimal weight: 0.5980 chunk 142 optimal weight: 5.9990 chunk 175 optimal weight: 0.7980 chunk 272 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN A 925 ASN A 960 ASN A1048 HIS B 188 ASN B 370 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN B 907 ASN B 920 GLN B 953 ASN C 804 GLN C1010 GLN C1088 HIS C1118 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24842 Z= 0.195 Angle : 0.659 9.883 33785 Z= 0.343 Chirality : 0.048 0.372 4035 Planarity : 0.004 0.050 4281 Dihedral : 8.268 59.651 4540 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.78 % Favored : 97.11 % Rotamer: Outliers : 1.76 % Allowed : 5.65 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 2946 helix: 0.71 (0.20), residues: 651 sheet: 0.44 (0.19), residues: 673 loop : -0.53 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 64 HIS 0.009 0.001 HIS C1048 PHE 0.025 0.001 PHE B 168 TYR 0.026 0.002 TYR A 369 ARG 0.007 0.001 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 240 time to evaluate : 2.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.5266 (m-10) cc_final: 0.4855 (m-10) REVERT: A 202 LYS cc_start: 0.7681 (mttm) cc_final: 0.7450 (mttp) REVERT: A 389 ASP cc_start: 0.8099 (m-30) cc_final: 0.7857 (t0) REVERT: B 81 ASN cc_start: 0.8173 (p0) cc_final: 0.7680 (p0) REVERT: B 131 CYS cc_start: 0.5848 (m) cc_final: 0.5620 (m) REVERT: B 133 PHE cc_start: 0.7348 (m-80) cc_final: 0.6771 (m-80) REVERT: B 394 ASN cc_start: 0.5761 (t0) cc_final: 0.5442 (t0) REVERT: B 396 TYR cc_start: 0.5444 (m-80) cc_final: 0.4990 (m-10) REVERT: B 505 TYR cc_start: 0.7083 (OUTLIER) cc_final: 0.6810 (t80) REVERT: B 565 PHE cc_start: 0.6588 (m-10) cc_final: 0.6353 (m-10) REVERT: B 646 ARG cc_start: 0.8400 (mmm-85) cc_final: 0.7668 (tpt170) REVERT: B 902 MET cc_start: 0.8402 (mmm) cc_final: 0.8022 (tpt) REVERT: B 994 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7590 (m-30) REVERT: C 64 TRP cc_start: 0.7200 (t60) cc_final: 0.6829 (t60) REVERT: C 81 ASN cc_start: 0.8045 (p0) cc_final: 0.7579 (p0) REVERT: C 170 TYR cc_start: 0.7947 (t80) cc_final: 0.7712 (t80) REVERT: C 205 SER cc_start: 0.8568 (p) cc_final: 0.8104 (t) REVERT: C 278 LYS cc_start: 0.7693 (tttt) cc_final: 0.7476 (tttp) REVERT: C 780 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7478 (mm-30) outliers start: 46 outliers final: 22 residues processed: 272 average time/residue: 0.3565 time to fit residues: 154.7107 Evaluate side-chains 205 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 181 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 226 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 272 optimal weight: 3.9990 chunk 294 optimal weight: 0.9980 chunk 243 optimal weight: 6.9990 chunk 270 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 218 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 935 GLN A 960 ASN B 125 ASN B 354 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24842 Z= 0.200 Angle : 0.583 10.521 33785 Z= 0.303 Chirality : 0.047 0.368 4035 Planarity : 0.004 0.052 4281 Dihedral : 7.661 58.051 4536 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.95 % Favored : 96.95 % Rotamer: Outliers : 2.22 % Allowed : 7.45 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.20 (0.15), residues: 2946 helix: 1.20 (0.21), residues: 649 sheet: 0.37 (0.19), residues: 674 loop : -0.37 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.003 0.001 HIS C1064 PHE 0.032 0.001 PHE A 392 TYR 0.028 0.001 TYR C 369 ARG 0.009 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 202 time to evaluate : 2.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7048 (mtt90) cc_final: 0.6381 (mtm-85) REVERT: A 313 TYR cc_start: 0.8559 (m-80) cc_final: 0.8354 (m-80) REVERT: A 389 ASP cc_start: 0.8077 (m-30) cc_final: 0.7679 (t0) REVERT: A 564 GLN cc_start: 0.8299 (mm110) cc_final: 0.7939 (mm110) REVERT: A 814 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8309 (mmtm) REVERT: B 81 ASN cc_start: 0.8301 (p0) cc_final: 0.7766 (p0) REVERT: B 316 SER cc_start: 0.8491 (OUTLIER) cc_final: 0.8251 (m) REVERT: B 394 ASN cc_start: 0.5722 (t0) cc_final: 0.5360 (t0) REVERT: B 396 TYR cc_start: 0.5931 (m-80) cc_final: 0.5502 (m-10) REVERT: B 505 TYR cc_start: 0.6878 (OUTLIER) cc_final: 0.5786 (t80) REVERT: B 646 ARG cc_start: 0.8436 (mmm-85) cc_final: 0.7707 (tpt170) REVERT: B 902 MET cc_start: 0.8427 (mmm) cc_final: 0.8144 (tpt) REVERT: B 994 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7664 (m-30) REVERT: C 64 TRP cc_start: 0.7225 (t60) cc_final: 0.6826 (t60) REVERT: C 187 LYS cc_start: 0.7084 (mmtt) cc_final: 0.6776 (tptp) REVERT: C 205 SER cc_start: 0.8365 (p) cc_final: 0.8018 (t) REVERT: C 357 ARG cc_start: 0.7164 (ttm110) cc_final: 0.6939 (mtt-85) REVERT: C 780 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7485 (mm-30) outliers start: 58 outliers final: 36 residues processed: 248 average time/residue: 0.3241 time to fit residues: 130.8957 Evaluate side-chains 215 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 175 time to evaluate : 2.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 0.0770 chunk 205 optimal weight: 10.0000 chunk 141 optimal weight: 0.0000 chunk 30 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 183 optimal weight: 3.9990 chunk 273 optimal weight: 2.9990 chunk 289 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 259 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 overall best weight: 0.9946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN C 49 HIS C 207 HIS C 658 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24842 Z= 0.182 Angle : 0.545 10.610 33785 Z= 0.281 Chirality : 0.045 0.353 4035 Planarity : 0.004 0.044 4281 Dihedral : 7.361 58.630 4534 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.72 % Favored : 97.22 % Rotamer: Outliers : 2.10 % Allowed : 8.90 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.30 (0.15), residues: 2946 helix: 1.40 (0.21), residues: 660 sheet: 0.29 (0.18), residues: 693 loop : -0.30 (0.16), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS C 207 PHE 0.032 0.001 PHE B 133 TYR 0.024 0.001 TYR B 170 ARG 0.012 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 195 time to evaluate : 2.536 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 115 GLN cc_start: 0.7733 (mt0) cc_final: 0.7439 (tp-100) REVERT: A 237 ARG cc_start: 0.7025 (mtt90) cc_final: 0.6356 (mtm-85) REVERT: A 313 TYR cc_start: 0.8533 (m-80) cc_final: 0.8311 (m-80) REVERT: A 389 ASP cc_start: 0.7990 (m-30) cc_final: 0.7726 (t0) REVERT: A 564 GLN cc_start: 0.8258 (mm110) cc_final: 0.7861 (mm110) REVERT: A 814 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8245 (mmtm) REVERT: A 1114 ILE cc_start: 0.9015 (mm) cc_final: 0.8653 (tp) REVERT: B 81 ASN cc_start: 0.8317 (p0) cc_final: 0.7816 (p0) REVERT: B 117 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7430 (mm) REVERT: B 316 SER cc_start: 0.8488 (OUTLIER) cc_final: 0.8261 (m) REVERT: B 902 MET cc_start: 0.8397 (mmm) cc_final: 0.8140 (tpt) REVERT: B 904 TYR cc_start: 0.7821 (m-10) cc_final: 0.7405 (m-10) REVERT: B 994 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7650 (m-30) REVERT: C 92 PHE cc_start: 0.7631 (t80) cc_final: 0.7196 (t80) REVERT: C 187 LYS cc_start: 0.7138 (mmtt) cc_final: 0.6808 (tptp) REVERT: C 271 GLN cc_start: 0.8221 (mm-40) cc_final: 0.7947 (mm-40) REVERT: C 780 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7492 (mm-30) REVERT: C 855 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7643 (t80) outliers start: 55 outliers final: 34 residues processed: 237 average time/residue: 0.3130 time to fit residues: 122.4678 Evaluate side-chains 204 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 165 time to evaluate : 3.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 247 optimal weight: 0.1980 chunk 200 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 260 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B1101 HIS C 134 GLN C 926 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24842 Z= 0.231 Angle : 0.552 10.969 33785 Z= 0.285 Chirality : 0.046 0.347 4035 Planarity : 0.004 0.045 4281 Dihedral : 7.162 57.164 4530 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 2.25 % Allowed : 9.70 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.15), residues: 2946 helix: 1.45 (0.21), residues: 660 sheet: 0.25 (0.19), residues: 689 loop : -0.33 (0.16), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 886 HIS 0.004 0.001 HIS C1064 PHE 0.027 0.001 PHE B 133 TYR 0.022 0.001 TYR A 380 ARG 0.010 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 180 time to evaluate : 2.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7046 (mtt90) cc_final: 0.6398 (mtm-85) REVERT: A 313 TYR cc_start: 0.8565 (m-80) cc_final: 0.8358 (m-80) REVERT: A 389 ASP cc_start: 0.8068 (m-30) cc_final: 0.7740 (t0) REVERT: A 564 GLN cc_start: 0.8228 (mm110) cc_final: 0.7828 (mm110) REVERT: A 814 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8244 (mmtm) REVERT: A 1114 ILE cc_start: 0.9025 (mm) cc_final: 0.8674 (tp) REVERT: B 81 ASN cc_start: 0.8446 (p0) cc_final: 0.7974 (p0) REVERT: B 396 TYR cc_start: 0.6445 (m-80) cc_final: 0.5988 (m-10) REVERT: B 904 TYR cc_start: 0.7824 (m-10) cc_final: 0.7400 (m-10) REVERT: B 994 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7687 (m-30) REVERT: B 1096 VAL cc_start: 0.8765 (OUTLIER) cc_final: 0.8559 (m) REVERT: C 81 ASN cc_start: 0.8297 (p0) cc_final: 0.7656 (p0) REVERT: C 92 PHE cc_start: 0.7659 (t80) cc_final: 0.7209 (t80) REVERT: C 187 LYS cc_start: 0.7143 (mmtt) cc_final: 0.6821 (tptp) REVERT: C 271 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7979 (mm-40) REVERT: C 357 ARG cc_start: 0.7508 (ttm110) cc_final: 0.6793 (mtt-85) REVERT: C 780 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7612 (mt-10) REVERT: C 855 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7701 (t80) outliers start: 59 outliers final: 45 residues processed: 227 average time/residue: 0.3052 time to fit residues: 116.5456 Evaluate side-chains 214 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 165 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 290 optimal weight: 1.9990 chunk 240 optimal weight: 20.0000 chunk 134 optimal weight: 30.0000 chunk 24 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 935 GLN C 926 GLN C1054 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 24842 Z= 0.319 Angle : 0.588 11.279 33785 Z= 0.302 Chirality : 0.047 0.339 4035 Planarity : 0.004 0.051 4281 Dihedral : 7.208 58.318 4530 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.39 % Favored : 96.54 % Rotamer: Outliers : 2.71 % Allowed : 10.24 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 2946 helix: 1.35 (0.21), residues: 660 sheet: 0.24 (0.19), residues: 680 loop : -0.45 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 64 HIS 0.005 0.001 HIS C1064 PHE 0.033 0.002 PHE B 133 TYR 0.020 0.002 TYR B 170 ARG 0.005 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 179 time to evaluate : 2.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.7538 (mt0) cc_final: 0.7070 (mm-40) REVERT: A 116 SER cc_start: 0.6544 (t) cc_final: 0.5891 (p) REVERT: A 218 GLN cc_start: 0.8033 (pp30) cc_final: 0.7658 (pp30) REVERT: A 237 ARG cc_start: 0.7108 (mtt90) cc_final: 0.6442 (mtm-85) REVERT: A 313 TYR cc_start: 0.8594 (m-80) cc_final: 0.8361 (m-80) REVERT: A 389 ASP cc_start: 0.8126 (m-30) cc_final: 0.7885 (t0) REVERT: A 564 GLN cc_start: 0.8162 (mm110) cc_final: 0.7952 (mm110) REVERT: A 814 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8242 (mmtm) REVERT: A 1114 ILE cc_start: 0.9014 (mm) cc_final: 0.8691 (tp) REVERT: B 81 ASN cc_start: 0.8506 (p0) cc_final: 0.8032 (p0) REVERT: B 396 TYR cc_start: 0.6293 (m-80) cc_final: 0.5727 (m-10) REVERT: B 902 MET cc_start: 0.8386 (tpt) cc_final: 0.7947 (tpt) REVERT: C 64 TRP cc_start: 0.7266 (t60) cc_final: 0.6852 (t60) REVERT: C 81 ASN cc_start: 0.8149 (p0) cc_final: 0.7523 (p0) REVERT: C 187 LYS cc_start: 0.7105 (mmtt) cc_final: 0.6793 (tptp) REVERT: C 271 GLN cc_start: 0.8267 (mm-40) cc_final: 0.8003 (mm-40) REVERT: C 780 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7625 (mt-10) REVERT: C 855 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7740 (t80) outliers start: 71 outliers final: 54 residues processed: 235 average time/residue: 0.2955 time to fit residues: 117.7779 Evaluate side-chains 223 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 167 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 chunk 211 optimal weight: 20.0000 chunk 164 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 162 optimal weight: 0.4980 chunk 289 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 926 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24842 Z= 0.229 Angle : 0.547 10.967 33785 Z= 0.281 Chirality : 0.045 0.339 4035 Planarity : 0.004 0.049 4281 Dihedral : 7.079 57.088 4530 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.33 % Favored : 96.61 % Rotamer: Outliers : 2.41 % Allowed : 11.27 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.15), residues: 2946 helix: 1.50 (0.21), residues: 660 sheet: 0.30 (0.19), residues: 689 loop : -0.41 (0.16), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS A1048 PHE 0.036 0.001 PHE B 133 TYR 0.019 0.001 TYR B 170 ARG 0.015 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 172 time to evaluate : 2.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.7489 (mt0) cc_final: 0.7005 (mm-40) REVERT: A 116 SER cc_start: 0.6702 (t) cc_final: 0.6049 (p) REVERT: A 235 ILE cc_start: 0.7502 (mm) cc_final: 0.7290 (tt) REVERT: A 237 ARG cc_start: 0.7063 (mtt90) cc_final: 0.6342 (mtm-85) REVERT: A 313 TYR cc_start: 0.8582 (m-80) cc_final: 0.8297 (m-80) REVERT: A 357 ARG cc_start: 0.7211 (ttm110) cc_final: 0.6796 (ttm110) REVERT: A 389 ASP cc_start: 0.8111 (m-30) cc_final: 0.7887 (t0) REVERT: A 564 GLN cc_start: 0.8138 (mm110) cc_final: 0.7918 (mm110) REVERT: A 814 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8220 (mmtm) REVERT: A 1114 ILE cc_start: 0.9023 (mm) cc_final: 0.8699 (tp) REVERT: B 81 ASN cc_start: 0.8513 (p0) cc_final: 0.8054 (p0) REVERT: B 133 PHE cc_start: 0.7768 (m-80) cc_final: 0.5995 (t80) REVERT: B 396 TYR cc_start: 0.6469 (m-80) cc_final: 0.5840 (m-10) REVERT: B 529 LYS cc_start: 0.8798 (mttt) cc_final: 0.8457 (mtmm) REVERT: C 64 TRP cc_start: 0.7234 (t60) cc_final: 0.6764 (t60) REVERT: C 81 ASN cc_start: 0.8194 (p0) cc_final: 0.7559 (p0) REVERT: C 187 LYS cc_start: 0.7075 (mmtt) cc_final: 0.6778 (tptp) REVERT: C 207 HIS cc_start: 0.7088 (OUTLIER) cc_final: 0.6569 (m90) REVERT: C 271 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7985 (mm-40) REVERT: C 780 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7617 (mt-10) REVERT: C 855 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7742 (t80) outliers start: 63 outliers final: 48 residues processed: 220 average time/residue: 0.3074 time to fit residues: 113.4286 Evaluate side-chains 218 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 167 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 chunk 196 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 227 optimal weight: 7.9990 chunk 263 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 926 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24842 Z= 0.175 Angle : 0.526 10.773 33785 Z= 0.270 Chirality : 0.045 0.342 4035 Planarity : 0.004 0.058 4281 Dihedral : 6.920 56.689 4529 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.33 % Favored : 96.61 % Rotamer: Outliers : 2.14 % Allowed : 11.31 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.16), residues: 2946 helix: 1.67 (0.21), residues: 658 sheet: 0.28 (0.19), residues: 684 loop : -0.33 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.013 0.001 HIS C 207 PHE 0.028 0.001 PHE B 133 TYR 0.018 0.001 TYR B 170 ARG 0.011 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 175 time to evaluate : 2.333 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 115 GLN cc_start: 0.7544 (mt0) cc_final: 0.7071 (mm-40) REVERT: A 116 SER cc_start: 0.6668 (t) cc_final: 0.6013 (p) REVERT: A 237 ARG cc_start: 0.7081 (mtt90) cc_final: 0.6354 (mtm-85) REVERT: A 313 TYR cc_start: 0.8569 (m-80) cc_final: 0.8229 (m-80) REVERT: A 389 ASP cc_start: 0.8105 (m-30) cc_final: 0.7878 (t0) REVERT: A 564 GLN cc_start: 0.8121 (mm110) cc_final: 0.7889 (mm110) REVERT: A 814 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8231 (mmtm) REVERT: A 1114 ILE cc_start: 0.9020 (mm) cc_final: 0.8688 (tp) REVERT: B 81 ASN cc_start: 0.8513 (p0) cc_final: 0.8064 (p0) REVERT: B 133 PHE cc_start: 0.7605 (m-80) cc_final: 0.6074 (t80) REVERT: B 396 TYR cc_start: 0.6522 (m-80) cc_final: 0.5887 (m-10) REVERT: B 529 LYS cc_start: 0.8829 (mttt) cc_final: 0.8503 (mtmm) REVERT: B 902 MET cc_start: 0.8399 (tpt) cc_final: 0.8056 (tpt) REVERT: B 904 TYR cc_start: 0.7793 (m-10) cc_final: 0.7426 (m-10) REVERT: C 64 TRP cc_start: 0.7224 (t60) cc_final: 0.6750 (t60) REVERT: C 81 ASN cc_start: 0.8218 (p0) cc_final: 0.7592 (p0) REVERT: C 271 GLN cc_start: 0.8276 (mm-40) cc_final: 0.8009 (mm-40) REVERT: C 780 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7566 (mt-10) REVERT: C 855 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7708 (t80) outliers start: 56 outliers final: 48 residues processed: 218 average time/residue: 0.3154 time to fit residues: 115.5013 Evaluate side-chains 214 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 164 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 3.9990 chunk 252 optimal weight: 5.9990 chunk 269 optimal weight: 0.7980 chunk 276 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 211 optimal weight: 20.0000 chunk 82 optimal weight: 2.9990 chunk 243 optimal weight: 0.4980 chunk 254 optimal weight: 0.9980 chunk 268 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 498 GLN C 926 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24842 Z= 0.188 Angle : 0.526 12.154 33785 Z= 0.269 Chirality : 0.045 0.339 4035 Planarity : 0.003 0.047 4281 Dihedral : 6.798 56.724 4529 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.39 % Favored : 96.54 % Rotamer: Outliers : 1.95 % Allowed : 11.61 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.16), residues: 2946 helix: 1.75 (0.21), residues: 658 sheet: 0.33 (0.19), residues: 666 loop : -0.30 (0.16), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.003 0.001 HIS C1064 PHE 0.014 0.001 PHE B1121 TYR 0.019 0.001 TYR A 170 ARG 0.006 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 171 time to evaluate : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.7528 (mt0) cc_final: 0.7014 (mm-40) REVERT: A 116 SER cc_start: 0.6535 (t) cc_final: 0.5952 (p) REVERT: A 313 TYR cc_start: 0.8563 (m-80) cc_final: 0.8219 (m-80) REVERT: A 389 ASP cc_start: 0.8132 (m-30) cc_final: 0.7919 (t0) REVERT: A 564 GLN cc_start: 0.8108 (mm110) cc_final: 0.7880 (mm110) REVERT: A 814 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8250 (mmtt) REVERT: A 1114 ILE cc_start: 0.9025 (mm) cc_final: 0.8685 (tp) REVERT: B 81 ASN cc_start: 0.8485 (p0) cc_final: 0.8122 (p0) REVERT: B 396 TYR cc_start: 0.6586 (m-80) cc_final: 0.5768 (m-10) REVERT: B 529 LYS cc_start: 0.8858 (mttt) cc_final: 0.8552 (mtmm) REVERT: B 904 TYR cc_start: 0.7797 (m-10) cc_final: 0.7429 (m-10) REVERT: C 64 TRP cc_start: 0.7246 (t60) cc_final: 0.6774 (t60) REVERT: C 81 ASN cc_start: 0.8251 (p0) cc_final: 0.7616 (p0) REVERT: C 271 GLN cc_start: 0.8282 (mm-40) cc_final: 0.8013 (mm-40) REVERT: C 780 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7595 (mt-10) outliers start: 51 outliers final: 44 residues processed: 212 average time/residue: 0.2959 time to fit residues: 106.5583 Evaluate side-chains 207 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 162 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 3.9990 chunk 284 optimal weight: 0.8980 chunk 173 optimal weight: 0.0770 chunk 135 optimal weight: 3.9990 chunk 198 optimal weight: 0.0970 chunk 298 optimal weight: 4.9990 chunk 275 optimal weight: 0.2980 chunk 237 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 926 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 24842 Z= 0.129 Angle : 0.497 11.206 33785 Z= 0.254 Chirality : 0.044 0.347 4035 Planarity : 0.003 0.045 4281 Dihedral : 6.628 55.019 4529 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.05 % Favored : 96.88 % Rotamer: Outliers : 1.49 % Allowed : 12.11 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.16), residues: 2946 helix: 1.94 (0.21), residues: 658 sheet: 0.35 (0.19), residues: 670 loop : -0.20 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 436 HIS 0.002 0.000 HIS C 66 PHE 0.016 0.001 PHE B 133 TYR 0.017 0.001 TYR B 369 ARG 0.006 0.000 ARG A 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 178 time to evaluate : 2.628 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 115 GLN cc_start: 0.7485 (mt0) cc_final: 0.7022 (mm-40) REVERT: A 170 TYR cc_start: 0.7383 (t80) cc_final: 0.6957 (t80) REVERT: A 226 LEU cc_start: 0.7793 (mt) cc_final: 0.7505 (mt) REVERT: A 237 ARG cc_start: 0.7030 (mtt90) cc_final: 0.6333 (mtm-85) REVERT: A 313 TYR cc_start: 0.8505 (m-80) cc_final: 0.8206 (m-80) REVERT: A 389 ASP cc_start: 0.8130 (m-30) cc_final: 0.7761 (t0) REVERT: A 564 GLN cc_start: 0.8105 (mm110) cc_final: 0.7699 (mm110) REVERT: A 814 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8261 (mmtt) REVERT: A 1114 ILE cc_start: 0.9009 (mm) cc_final: 0.8660 (tp) REVERT: B 81 ASN cc_start: 0.8481 (p0) cc_final: 0.8128 (p0) REVERT: B 396 TYR cc_start: 0.6641 (m-80) cc_final: 0.5731 (m-10) REVERT: B 529 LYS cc_start: 0.8851 (mttt) cc_final: 0.8552 (mtmm) REVERT: B 643 PHE cc_start: 0.7809 (t80) cc_final: 0.7579 (t80) REVERT: B 902 MET cc_start: 0.8361 (tpt) cc_final: 0.7923 (tpt) REVERT: B 904 TYR cc_start: 0.7755 (m-10) cc_final: 0.7460 (m-10) REVERT: C 64 TRP cc_start: 0.7242 (t60) cc_final: 0.6779 (t60) REVERT: C 81 ASN cc_start: 0.8273 (p0) cc_final: 0.7642 (p0) REVERT: C 207 HIS cc_start: 0.7026 (OUTLIER) cc_final: 0.6636 (m90) REVERT: C 271 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7915 (mm-40) REVERT: C 780 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7537 (mt-10) outliers start: 39 outliers final: 31 residues processed: 208 average time/residue: 0.3169 time to fit residues: 109.3028 Evaluate side-chains 199 residues out of total 2619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 166 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 0.0570 chunk 253 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 219 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 238 optimal weight: 30.0000 chunk 99 optimal weight: 3.9990 chunk 244 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 926 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.174472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118146 restraints weight = 32672.795| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 3.32 r_work: 0.3186 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 24842 Z= 0.151 Angle : 0.506 11.241 33785 Z= 0.258 Chirality : 0.045 0.338 4035 Planarity : 0.003 0.045 4281 Dihedral : 6.562 55.673 4529 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.16 % Favored : 96.78 % Rotamer: Outliers : 1.38 % Allowed : 12.38 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.16), residues: 2946 helix: 1.97 (0.21), residues: 658 sheet: 0.35 (0.19), residues: 670 loop : -0.18 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.008 0.001 HIS C 207 PHE 0.032 0.001 PHE B 168 TYR 0.016 0.001 TYR B 369 ARG 0.006 0.000 ARG A 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4790.82 seconds wall clock time: 87 minutes 51.31 seconds (5271.31 seconds total)