Starting phenix.real_space_refine on Mon Feb 19 15:25:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dll_27505/02_2024/8dll_27505.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dll_27505/02_2024/8dll_27505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dll_27505/02_2024/8dll_27505.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dll_27505/02_2024/8dll_27505.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dll_27505/02_2024/8dll_27505.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dll_27505/02_2024/8dll_27505.pdb" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 15987 2.51 5 N 4095 2.21 5 O 4902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25095 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8085 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Chain: "B" Number of atoms: 8085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8085 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Chain: "C" Number of atoms: 8085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8085 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 13.18, per 1000 atoms: 0.53 Number of scatterers: 25095 At special positions: 0 Unit cell: (140, 145, 198, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 4902 8.00 N 4095 7.00 C 15987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 17 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 17 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 11.03 Conformation dependent library (CDL) restraints added in 4.6 seconds 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5802 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 45 sheets defined 25.6% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.46 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.162A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.518A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.612A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.959A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.548A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 887 through 891 removed outlier: 3.895A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.069A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.090A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.514A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) 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: 3.700A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.851A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.737A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.892A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.552A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.933A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.809A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 3.630A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1141 through 1146' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.728A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.739A 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 390 removed outlier: 3.506A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.502A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.811A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.767A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.530A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.058A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.323A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.620A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1141 through 1147' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.593A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.593A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.077A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.967A 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: 3.907A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.711A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.077A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.519A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.110A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.590A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.742A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.271A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.583A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.128A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.706A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.706A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.057A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.662A 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 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.891A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.543A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.554A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.087A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 142 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.907A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.014A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.952A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.200A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.921A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.233A pdb=" N VAL B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.662A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.662A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.110A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.534A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.632A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.391A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.130A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.403A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.159A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 327 through 328 removed outlier: 3.811A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.880A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.284A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.107A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.561A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.561A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.139A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 1034 hydrogen bonds defined for protein. 2853 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: 11.76 Time building geometry restraints manager: 11.80 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: 7016 1.33 - 1.46: 6308 1.46 - 1.58: 12203 1.58 - 1.71: 0 1.71 - 1.83: 138 Bond restraints: 25665 Sorted by residual: bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 7.99e+00 bond pdb=" CG LEU A 916 " pdb=" CD1 LEU A 916 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.29e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.65e+00 bond pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 1.335 1.368 -0.032 1.36e-02 5.41e+03 5.61e+00 bond pdb=" CG LEU B 916 " pdb=" CD1 LEU B 916 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.18e+00 ... (remaining 25660 not shown) Histogram of bond angle deviations from ideal: 98.36 - 105.52: 549 105.52 - 112.67: 13283 112.67 - 119.82: 8544 119.82 - 126.97: 12315 126.97 - 134.12: 247 Bond angle restraints: 34938 Sorted by residual: angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.57 -5.87 1.22e+00 6.72e-01 2.32e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.41 -5.71 1.22e+00 6.72e-01 2.19e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.03 -5.33 1.22e+00 6.72e-01 1.91e+01 angle pdb=" CA PRO A 986 " pdb=" C PRO A 986 " pdb=" N PRO A 987 " ideal model delta sigma weight residual 117.93 122.65 -4.72 1.20e+00 6.94e-01 1.55e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 122.43 -4.50 1.20e+00 6.94e-01 1.41e+01 ... (remaining 34933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 14804 17.75 - 35.50: 1005 35.50 - 53.25: 167 53.25 - 70.99: 64 70.99 - 88.74: 25 Dihedral angle restraints: 16065 sinusoidal: 7044 harmonic: 9021 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -20.88 -65.12 1 1.00e+01 1.00e-02 5.56e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -40.47 -45.53 1 1.00e+01 1.00e-02 2.87e+01 dihedral pdb=" CA PHE C 392 " pdb=" C PHE C 392 " pdb=" N THR C 393 " pdb=" CA THR C 393 " ideal model delta harmonic sigma weight residual 180.00 157.97 22.03 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 16062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 3605 0.090 - 0.179: 511 0.179 - 0.269: 12 0.269 - 0.358: 2 0.358 - 0.448: 1 Chirality restraints: 4131 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 4128 not shown) Planarity restraints: 4491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 18 " -0.021 2.00e-02 2.50e+03 2.11e-02 7.81e+00 pdb=" CG PHE B 18 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE B 18 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 18 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 18 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 18 " -0.015 2.00e-02 2.50e+03 pdb=" CZ PHE B 18 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 294 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.11e+00 pdb=" N PRO C 295 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 295 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 295 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET B1029 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C MET B1029 " -0.044 2.00e-02 2.50e+03 pdb=" O MET B1029 " 0.017 2.00e-02 2.50e+03 pdb=" N SER B1030 " 0.015 2.00e-02 2.50e+03 ... (remaining 4488 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6253 2.80 - 3.33: 21452 3.33 - 3.85: 42368 3.85 - 4.38: 47999 4.38 - 4.90: 83438 Nonbonded interactions: 201510 Sorted by model distance: nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.279 2.440 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.296 2.440 nonbonded pdb=" OE1 GLN C 115 " pdb=" OG1 THR C 167 " model vdw 2.300 2.440 nonbonded pdb=" OG1 THR A 618 " pdb=" OE1 GLU A 619 " model vdw 2.305 2.440 nonbonded pdb=" OD2 ASP B 420 " pdb=" OH TYR C 369 " model vdw 2.314 2.440 ... (remaining 201505 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 19.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 70.890 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.330 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:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 25665 Z= 0.327 Angle : 0.783 10.213 34938 Z= 0.414 Chirality : 0.056 0.448 4131 Planarity : 0.006 0.067 4449 Dihedral : 12.786 88.742 10137 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: -0.16 (0.15), residues: 3054 helix: 1.52 (0.20), residues: 650 sheet: -0.04 (0.20), residues: 608 loop : -0.73 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 886 HIS 0.014 0.001 HIS A1048 PHE 0.047 0.002 PHE B 18 TYR 0.016 0.002 TYR A1138 ARG 0.011 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 2.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8899 (t) cc_final: 0.8617 (m) REVERT: A 104 TRP cc_start: 0.7818 (m-90) cc_final: 0.7501 (m-90) REVERT: A 135 PHE cc_start: 0.6142 (m-80) cc_final: 0.5698 (m-80) REVERT: A 239 GLN cc_start: 0.8273 (mm110) cc_final: 0.8045 (mm-40) REVERT: B 32 PHE cc_start: 0.8476 (m-10) cc_final: 0.8236 (m-10) REVERT: B 240 THR cc_start: 0.7074 (m) cc_final: 0.6434 (p) REVERT: B 400 PHE cc_start: 0.7966 (p90) cc_final: 0.7597 (p90) REVERT: C 386 LYS cc_start: 0.8743 (mmtt) cc_final: 0.8442 (mmtp) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 1.3120 time to fit residues: 282.4293 Evaluate side-chains 88 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 3.9990 chunk 234 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 242 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 147 optimal weight: 0.4980 chunk 180 optimal weight: 3.9990 chunk 280 optimal weight: 9.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 196 ASN A 901 GLN A1002 GLN B 188 ASN B 370 ASN C 824 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25665 Z= 0.302 Angle : 0.557 11.096 34938 Z= 0.292 Chirality : 0.045 0.333 4131 Planarity : 0.004 0.063 4449 Dihedral : 6.541 59.236 4584 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.70 % Allowed : 5.60 % Favored : 93.70 % 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: 0.03 (0.15), residues: 3054 helix: 1.77 (0.20), residues: 665 sheet: 0.12 (0.20), residues: 635 loop : -0.71 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 64 HIS 0.004 0.001 HIS B1048 PHE 0.019 0.001 PHE A 906 TYR 0.021 0.001 TYR A1067 ARG 0.007 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 3.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8821 (t) cc_final: 0.8427 (m) REVERT: A 104 TRP cc_start: 0.7943 (m-90) cc_final: 0.7647 (m-90) REVERT: A 135 PHE cc_start: 0.6275 (m-80) cc_final: 0.5848 (m-80) REVERT: B 400 PHE cc_start: 0.8119 (p90) cc_final: 0.7834 (p90) REVERT: C 386 LYS cc_start: 0.8760 (mmtt) cc_final: 0.8514 (mmtp) REVERT: C 565 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7496 (p90) outliers start: 19 outliers final: 8 residues processed: 109 average time/residue: 1.3145 time to fit residues: 170.5448 Evaluate side-chains 89 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 233 optimal weight: 8.9990 chunk 191 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 281 optimal weight: 0.7980 chunk 303 optimal weight: 1.9990 chunk 250 optimal weight: 9.9990 chunk 278 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 225 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 544 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25665 Z= 0.177 Angle : 0.490 10.080 34938 Z= 0.256 Chirality : 0.044 0.310 4131 Planarity : 0.004 0.061 4449 Dihedral : 5.734 56.451 4584 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.70 % Allowed : 7.40 % Favored : 91.90 % 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: 0.22 (0.15), residues: 3054 helix: 2.00 (0.21), residues: 666 sheet: 0.08 (0.20), residues: 634 loop : -0.54 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 64 HIS 0.002 0.001 HIS C1064 PHE 0.028 0.001 PHE B 192 TYR 0.021 0.001 TYR C1067 ARG 0.005 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 2.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8781 (t) cc_final: 0.8351 (m) REVERT: A 135 PHE cc_start: 0.6282 (m-80) cc_final: 0.5826 (m-80) REVERT: A 169 GLU cc_start: 0.8468 (tp30) cc_final: 0.7848 (mm-30) REVERT: A 1010 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.7990 (mp10) REVERT: B 432 CYS cc_start: 0.4614 (OUTLIER) cc_final: 0.4177 (p) REVERT: C 565 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.7362 (p90) outliers start: 19 outliers final: 6 residues processed: 102 average time/residue: 1.1723 time to fit residues: 146.2804 Evaluate side-chains 88 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 565 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 3.9990 chunk 211 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 31 optimal weight: 20.0000 chunk 134 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 282 optimal weight: 0.9980 chunk 298 optimal weight: 0.2980 chunk 147 optimal weight: 0.6980 chunk 267 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25665 Z= 0.174 Angle : 0.475 8.881 34938 Z= 0.247 Chirality : 0.044 0.309 4131 Planarity : 0.004 0.061 4449 Dihedral : 5.248 53.630 4584 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.96 % Allowed : 8.58 % Favored : 90.46 % 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: 3054 helix: 1.96 (0.20), residues: 684 sheet: 0.09 (0.20), residues: 611 loop : -0.51 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 104 HIS 0.002 0.001 HIS B1048 PHE 0.015 0.001 PHE B 192 TYR 0.021 0.001 TYR C 351 ARG 0.003 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 84 time to evaluate : 3.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8739 (t) cc_final: 0.8277 (m) REVERT: A 135 PHE cc_start: 0.6366 (m-80) cc_final: 0.5901 (m-80) REVERT: A 169 GLU cc_start: 0.8325 (tp30) cc_final: 0.7640 (mm-30) REVERT: A 1010 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8030 (mp10) REVERT: B 432 CYS cc_start: 0.4859 (OUTLIER) cc_final: 0.4338 (p) REVERT: C 565 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.7333 (p90) outliers start: 26 outliers final: 7 residues processed: 99 average time/residue: 1.1914 time to fit residues: 143.4116 Evaluate side-chains 86 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 2.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 565 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 8.9990 chunk 169 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 222 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 254 optimal weight: 1.9990 chunk 206 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 268 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN C 856 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 25665 Z= 0.403 Angle : 0.592 10.316 34938 Z= 0.304 Chirality : 0.046 0.324 4131 Planarity : 0.004 0.063 4449 Dihedral : 5.593 54.672 4584 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.51 % Allowed : 9.10 % Favored : 89.39 % 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: 0.05 (0.15), residues: 3054 helix: 1.84 (0.20), residues: 666 sheet: -0.11 (0.19), residues: 656 loop : -0.62 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 104 HIS 0.005 0.001 HIS C1083 PHE 0.016 0.002 PHE A 898 TYR 0.022 0.002 TYR A1067 ARG 0.004 0.001 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 87 time to evaluate : 2.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8739 (t) cc_final: 0.8251 (m) REVERT: A 135 PHE cc_start: 0.6402 (m-80) cc_final: 0.6004 (m-80) REVERT: A 1010 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8102 (mp10) REVERT: A 1145 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7300 (tm) REVERT: B 224 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7375 (pm20) REVERT: B 432 CYS cc_start: 0.5253 (OUTLIER) cc_final: 0.4906 (p) REVERT: C 565 PHE cc_start: 0.8047 (OUTLIER) cc_final: 0.7114 (p90) outliers start: 41 outliers final: 16 residues processed: 115 average time/residue: 1.1148 time to fit residues: 156.8016 Evaluate side-chains 97 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 76 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 565 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 0.8980 chunk 268 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 175 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 298 optimal weight: 0.9980 chunk 248 optimal weight: 0.5980 chunk 138 optimal weight: 9.9990 chunk 24 optimal weight: 0.0870 chunk 98 optimal weight: 0.8980 chunk 156 optimal weight: 0.3980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 580 GLN B 394 ASN C 856 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25665 Z= 0.139 Angle : 0.486 10.281 34938 Z= 0.253 Chirality : 0.044 0.294 4131 Planarity : 0.004 0.062 4449 Dihedral : 5.094 53.747 4584 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.07 % Allowed : 10.35 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.24 (0.15), residues: 3054 helix: 2.02 (0.21), residues: 679 sheet: -0.14 (0.19), residues: 652 loop : -0.45 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 104 HIS 0.002 0.000 HIS B 66 PHE 0.014 0.001 PHE B 192 TYR 0.021 0.001 TYR C1067 ARG 0.003 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 86 time to evaluate : 2.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8683 (t) cc_final: 0.8177 (m) REVERT: A 135 PHE cc_start: 0.6337 (m-80) cc_final: 0.5888 (m-80) REVERT: A 169 GLU cc_start: 0.8434 (tp30) cc_final: 0.7655 (mm-30) REVERT: A 1010 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8020 (mp10) REVERT: C 565 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.7312 (p90) REVERT: C 990 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7212 (pm20) outliers start: 29 outliers final: 13 residues processed: 106 average time/residue: 1.1869 time to fit residues: 151.7230 Evaluate side-chains 95 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 990 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 6.9990 chunk 33 optimal weight: 30.0000 chunk 170 optimal weight: 5.9990 chunk 218 optimal weight: 0.0270 chunk 169 optimal weight: 0.5980 chunk 251 optimal weight: 20.0000 chunk 166 optimal weight: 0.9980 chunk 297 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 chunk 181 optimal weight: 0.9990 chunk 137 optimal weight: 10.0000 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A1002 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 25665 Z= 0.160 Angle : 0.480 11.219 34938 Z= 0.247 Chirality : 0.043 0.296 4131 Planarity : 0.004 0.062 4449 Dihedral : 4.870 53.329 4584 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.07 % Allowed : 10.83 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.15), residues: 3054 helix: 2.11 (0.20), residues: 685 sheet: -0.10 (0.19), residues: 645 loop : -0.44 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 104 HIS 0.001 0.000 HIS C 66 PHE 0.032 0.001 PHE B 392 TYR 0.020 0.001 TYR C1067 ARG 0.003 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 82 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8661 (t) cc_final: 0.8155 (m) REVERT: A 135 PHE cc_start: 0.6332 (m-80) cc_final: 0.5876 (m-80) REVERT: A 169 GLU cc_start: 0.8392 (tp30) cc_final: 0.7604 (mm-30) REVERT: A 1010 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8033 (mp10) REVERT: C 565 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.7317 (p90) REVERT: C 990 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7195 (pm20) REVERT: C 1050 MET cc_start: 0.8868 (ptm) cc_final: 0.8608 (ptm) outliers start: 29 outliers final: 17 residues processed: 104 average time/residue: 1.0744 time to fit residues: 137.5736 Evaluate side-chains 98 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 78 time to evaluate : 2.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 57 optimal weight: 0.0970 chunk 189 optimal weight: 6.9990 chunk 202 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 321 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN C 564 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 25665 Z= 0.356 Angle : 0.561 10.372 34938 Z= 0.287 Chirality : 0.046 0.314 4131 Planarity : 0.004 0.063 4449 Dihedral : 5.200 54.489 4584 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.58 % Allowed : 10.72 % Favored : 87.70 % 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: 0.12 (0.15), residues: 3054 helix: 1.88 (0.20), residues: 698 sheet: -0.11 (0.20), residues: 607 loop : -0.58 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 104 HIS 0.004 0.001 HIS C1083 PHE 0.016 0.001 PHE A 898 TYR 0.020 0.001 TYR A1067 ARG 0.004 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 79 time to evaluate : 2.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8727 (t) cc_final: 0.8204 (m) REVERT: A 135 PHE cc_start: 0.6380 (m-80) cc_final: 0.5990 (m-80) REVERT: A 1010 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8112 (mp10) REVERT: B 224 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7436 (pm20) REVERT: B 432 CYS cc_start: 0.5106 (OUTLIER) cc_final: 0.4663 (p) REVERT: C 565 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7376 (p90) REVERT: C 990 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7289 (pm20) outliers start: 43 outliers final: 23 residues processed: 113 average time/residue: 1.1004 time to fit residues: 151.8453 Evaluate side-chains 105 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 77 time to evaluate : 2.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 0.9990 chunk 285 optimal weight: 0.1980 chunk 260 optimal weight: 7.9990 chunk 277 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 217 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 250 optimal weight: 0.0040 chunk 262 optimal weight: 0.7980 chunk 276 optimal weight: 3.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN B 394 ASN C 564 GLN C 856 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25665 Z= 0.146 Angle : 0.486 9.460 34938 Z= 0.251 Chirality : 0.044 0.288 4131 Planarity : 0.004 0.064 4449 Dihedral : 4.810 53.472 4584 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.18 % Allowed : 11.20 % Favored : 87.62 % 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: 0.27 (0.15), residues: 3054 helix: 2.09 (0.20), residues: 695 sheet: -0.13 (0.20), residues: 643 loop : -0.47 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 104 HIS 0.002 0.000 HIS C1048 PHE 0.021 0.001 PHE B 392 TYR 0.020 0.001 TYR C1067 ARG 0.002 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 81 time to evaluate : 3.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8675 (t) cc_final: 0.8144 (m) REVERT: A 135 PHE cc_start: 0.6332 (m-80) cc_final: 0.5901 (m-80) REVERT: A 169 GLU cc_start: 0.8482 (tp30) cc_final: 0.7607 (mm-30) REVERT: A 1010 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8010 (mp10) REVERT: B 432 CYS cc_start: 0.5270 (OUTLIER) cc_final: 0.4679 (p) REVERT: C 565 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7319 (p90) REVERT: C 957 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7642 (tm-30) REVERT: C 994 ASP cc_start: 0.8325 (t70) cc_final: 0.8068 (t0) REVERT: C 1050 MET cc_start: 0.8856 (ptm) cc_final: 0.8636 (ptm) outliers start: 32 outliers final: 23 residues processed: 108 average time/residue: 1.1383 time to fit residues: 151.1060 Evaluate side-chains 103 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 77 time to evaluate : 2.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 0.4980 chunk 293 optimal weight: 0.7980 chunk 179 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 307 optimal weight: 4.9990 chunk 283 optimal weight: 1.9990 chunk 245 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN B 394 ASN C 856 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 25665 Z= 0.321 Angle : 0.540 12.771 34938 Z= 0.276 Chirality : 0.045 0.308 4131 Planarity : 0.004 0.063 4449 Dihedral : 4.946 54.127 4584 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.10 % Allowed : 11.42 % Favored : 87.48 % 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: 0.21 (0.15), residues: 3054 helix: 2.00 (0.20), residues: 701 sheet: -0.16 (0.20), residues: 632 loop : -0.51 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 104 HIS 0.003 0.001 HIS C1088 PHE 0.028 0.001 PHE B 392 TYR 0.021 0.001 TYR A 200 ARG 0.003 0.000 ARG B 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 81 time to evaluate : 3.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8719 (t) cc_final: 0.8192 (m) REVERT: A 135 PHE cc_start: 0.6387 (m-80) cc_final: 0.5966 (m-80) REVERT: A 169 GLU cc_start: 0.8523 (tp30) cc_final: 0.7602 (mm-30) REVERT: A 1010 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8097 (mp10) REVERT: B 432 CYS cc_start: 0.5408 (OUTLIER) cc_final: 0.4790 (p) REVERT: C 565 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7372 (p90) REVERT: C 856 ASN cc_start: 0.6950 (OUTLIER) cc_final: 0.6690 (p0) REVERT: C 957 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7688 (tm-30) outliers start: 30 outliers final: 23 residues processed: 108 average time/residue: 1.1284 time to fit residues: 148.9298 Evaluate side-chains 106 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 79 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 226 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 68 optimal weight: 0.8980 chunk 245 optimal weight: 0.0270 chunk 102 optimal weight: 0.9990 chunk 252 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.118152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.073407 restraints weight = 72699.696| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.83 r_work: 0.3174 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25665 Z= 0.158 Angle : 0.490 9.303 34938 Z= 0.253 Chirality : 0.044 0.292 4131 Planarity : 0.004 0.063 4449 Dihedral : 4.799 53.417 4584 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.10 % Allowed : 11.42 % Favored : 87.48 % 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: 0.29 (0.15), residues: 3054 helix: 2.09 (0.20), residues: 696 sheet: -0.15 (0.19), residues: 654 loop : -0.45 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 104 HIS 0.002 0.000 HIS C1048 PHE 0.026 0.001 PHE B 392 TYR 0.019 0.001 TYR C1067 ARG 0.002 0.000 ARG B 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6324.90 seconds wall clock time: 115 minutes 46.63 seconds (6946.63 seconds total)