Starting phenix.real_space_refine on Mon Aug 25 19:29:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dm9_27531/08_2025/8dm9_27531.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dm9_27531/08_2025/8dm9_27531.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/cci-nas-00/data/ceres_data/8dm9_27531/08_2025/8dm9_27531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dm9_27531/08_2025/8dm9_27531.map" model { file = "/net/cci-nas-00/data/ceres_data/8dm9_27531/08_2025/8dm9_27531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dm9_27531/08_2025/8dm9_27531.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.024 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 140 5.16 5 C 19142 2.51 5 N 4922 2.21 5 O 5800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30004 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Chain: "B" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Chain: "C" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Chain: "D" Number of atoms: 4833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4833 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} 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: "V" 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 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 Time building chain proxies: 6.95, per 1000 atoms: 0.23 Number of scatterers: 30004 At special positions: 0 Unit cell: (135, 157, 237, 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 140 16.00 O 5800 8.00 N 4922 7.00 C 19142 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, 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=2.04 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=2.04 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=2.02 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=2.04 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=2.02 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 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.05 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " 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 V 1 " - " NAG V 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 234 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 546 " " NAG E 1 " - " ASN A 17 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B 17 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1074 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN C 17 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1074 " " NAG U 1 " - " ASN C1098 " " NAG V 1 " - " ASN C1134 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6944 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 49 sheets defined 32.3% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.645A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.612A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.503A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 407' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.093A 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: 3.590A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.940A 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 1032 removed outlier: 3.969A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.943A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.873A pdb=" N LEU B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.718A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.871A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.861A 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: 3.587A 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 887 through 891 removed outlier: 3.744A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.981A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.552A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.501A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.044A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.954A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.772A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.861A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.555A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.889A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.605A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.992A 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 1032 removed outlier: 4.099A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'D' and resid 21 through 52 removed outlier: 4.259A pdb=" N GLN D 34 " --> pdb=" O ASN D 30 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU D 35 " --> pdb=" O ASN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 3.609A pdb=" N THR D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 through 83' Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.837A pdb=" N GLU D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D 88 " --> pdb=" O LEU D 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 84 through 88' Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.769A pdb=" N SER D 106 " --> pdb=" O SER D 103 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 144 through 155 removed outlier: 5.327A pdb=" N ASP D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLU D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 193 removed outlier: 5.354A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.693A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 218 through 231 removed outlier: 3.652A pdb=" N LEU D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.755A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 319 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.534A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.724A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 397 through 413 removed outlier: 4.194A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA D 413 " --> pdb=" O SER D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.575A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.473A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.757A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.303A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 4.018A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 598 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.949A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.775A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.970A 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: 3.754A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.108A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.240A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.415A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.560A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.913A 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: 6.739A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.064A 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: 4.868A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.661A 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 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.874A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.802A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.577A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.577A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.319A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.703A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.103A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.055A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.839A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 133 through 142 removed outlier: 6.495A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.562A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.979A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.178A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.995A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.971A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 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 473 through 474 removed outlier: 3.589A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.888A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.461A 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 704 removed outlier: 6.464A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (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: 6.487A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.901A 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: 6.487A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.564A 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: 4.388A 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: 8.235A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.030A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.823A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 133 through 142 removed outlier: 6.536A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.569A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.328A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.011A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.993A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.342A 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: 7.152A 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 473 through 474 removed outlier: 3.811A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.863A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.513A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.513A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.352A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF2, first strand: chain 'D' and resid 131 through 132 removed outlier: 4.100A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.906A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.289A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 1327 hydrogen bonds defined for protein. 3735 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: 7.84 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9473 1.35 - 1.48: 8077 1.48 - 1.60: 12973 1.60 - 1.73: 0 1.73 - 1.86: 188 Bond restraints: 30711 Sorted by residual: bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.08e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.97e+00 bond pdb=" C1 NAG Q 1 " pdb=" O5 NAG Q 1 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.93e+00 ... (remaining 30706 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 41131 2.91 - 5.81: 569 5.81 - 8.72: 57 8.72 - 11.62: 4 11.62 - 14.53: 3 Bond angle restraints: 41764 Sorted by residual: angle pdb=" N ALA C 372 " pdb=" CA ALA C 372 " pdb=" C ALA C 372 " ideal model delta sigma weight residual 109.81 124.34 -14.53 2.21e+00 2.05e-01 4.32e+01 angle pdb=" CB ARG A 995 " pdb=" CG ARG A 995 " pdb=" CD ARG A 995 " ideal model delta sigma weight residual 111.30 125.46 -14.16 2.30e+00 1.89e-01 3.79e+01 angle pdb=" N ALA B 372 " pdb=" CA ALA B 372 " pdb=" C ALA B 372 " ideal model delta sigma weight residual 109.81 121.45 -11.64 2.21e+00 2.05e-01 2.78e+01 angle pdb=" C LEU A 335 " pdb=" N CYS A 336 " pdb=" CA CYS A 336 " ideal model delta sigma weight residual 120.51 128.02 -7.51 1.45e+00 4.76e-01 2.69e+01 angle pdb=" CA PRO C 373 " pdb=" N PRO C 373 " pdb=" CD PRO C 373 " ideal model delta sigma weight residual 112.00 105.16 6.84 1.40e+00 5.10e-01 2.39e+01 ... (remaining 41759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 17548 17.82 - 35.63: 1239 35.63 - 53.45: 230 53.45 - 71.27: 77 71.27 - 89.08: 36 Dihedral angle restraints: 19130 sinusoidal: 8359 harmonic: 10771 Sorted by residual: dihedral pdb=" CA CYS D 133 " pdb=" C CYS D 133 " pdb=" N ASN D 134 " pdb=" CA ASN D 134 " ideal model delta harmonic sigma weight residual -180.00 -138.91 -41.09 0 5.00e+00 4.00e-02 6.75e+01 dihedral pdb=" CA CYS D 141 " pdb=" C CYS D 141 " pdb=" N LEU D 142 " pdb=" CA LEU D 142 " ideal model delta harmonic sigma weight residual -180.00 -147.94 -32.06 0 5.00e+00 4.00e-02 4.11e+01 dihedral pdb=" CA CYS A 391 " pdb=" C CYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta harmonic sigma weight residual 180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 19127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 4049 0.081 - 0.161: 732 0.161 - 0.242: 53 0.242 - 0.322: 6 0.322 - 0.403: 3 Chirality restraints: 4843 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.64e+00 ... (remaining 4840 not shown) Planarity restraints: 5361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 372 " -0.063 5.00e-02 4.00e+02 9.22e-02 1.36e+01 pdb=" N PRO C 373 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO C 373 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 373 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 955 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C ASN B 955 " -0.064 2.00e-02 2.50e+03 pdb=" O ASN B 955 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA B 956 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 952 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.15e+01 pdb=" C VAL B 952 " 0.059 2.00e-02 2.50e+03 pdb=" O VAL B 952 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN B 953 " -0.020 2.00e-02 2.50e+03 ... (remaining 5358 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6885 2.79 - 3.32: 25827 3.32 - 3.85: 51297 3.85 - 4.37: 59124 4.37 - 4.90: 102185 Nonbonded interactions: 245318 Sorted by model distance: nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR B 396 " pdb=" O PRO C 230 " model vdw 2.267 3.040 nonbonded pdb=" O ASP A 80 " pdb=" OH TYR A 265 " model vdw 2.269 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.273 3.040 ... (remaining 245313 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = 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' selection = chain 'V' } 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: 4.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 28.970 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 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 0.080 30818 Z= 0.251 Angle : 0.902 15.559 42038 Z= 0.489 Chirality : 0.059 0.403 4843 Planarity : 0.007 0.092 5317 Dihedral : 13.279 89.082 12054 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.04 % Favored : 97.91 % Rotamer: Outliers : 0.15 % Allowed : 3.46 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.12), residues: 3633 helix: 0.28 (0.14), residues: 1050 sheet: 0.95 (0.19), residues: 668 loop : -0.75 (0.13), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG B 995 TYR 0.036 0.003 TYR B1067 PHE 0.040 0.003 PHE B 981 TRP 0.040 0.002 TRP B 886 HIS 0.033 0.002 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00516 (30711) covalent geometry : angle 0.87929 (41764) SS BOND : bond 0.00401 ( 44) SS BOND : angle 1.38492 ( 88) hydrogen bonds : bond 0.11800 ( 1291) hydrogen bonds : angle 7.27542 ( 3735) Misc. bond : bond 0.00441 ( 1) link_BETA1-4 : bond 0.00659 ( 18) link_BETA1-4 : angle 1.71215 ( 54) link_NAG-ASN : bond 0.00726 ( 44) link_NAG-ASN : angle 3.48675 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 397 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.5780 (m90) cc_final: 0.5005 (m90) REVERT: A 129 LYS cc_start: 0.6348 (mtmt) cc_final: 0.6088 (mmmt) REVERT: A 140 PHE cc_start: 0.6108 (p90) cc_final: 0.5813 (p90) REVERT: A 170 TYR cc_start: 0.7589 (t80) cc_final: 0.7367 (t80) REVERT: A 338 PHE cc_start: 0.6724 (m-10) cc_final: 0.6444 (m-80) REVERT: A 549 THR cc_start: 0.7004 (m) cc_final: 0.6583 (m) REVERT: A 981 PHE cc_start: 0.7072 (m-80) cc_final: 0.6820 (m-10) REVERT: A 988 GLU cc_start: 0.7629 (pm20) cc_final: 0.7230 (pm20) REVERT: B 387 LEU cc_start: 0.7684 (mt) cc_final: 0.7478 (mt) REVERT: B 856 LYS cc_start: 0.5451 (mttt) cc_final: 0.4914 (pmtt) REVERT: B 981 PHE cc_start: 0.7645 (m-80) cc_final: 0.7100 (m-80) REVERT: B 1029 MET cc_start: 0.9269 (tpp) cc_final: 0.8937 (tpp) REVERT: C 88 ASP cc_start: 0.8018 (m-30) cc_final: 0.7480 (p0) REVERT: C 186 PHE cc_start: 0.4899 (m-10) cc_final: 0.4471 (m-80) REVERT: C 189 LEU cc_start: 0.8670 (tp) cc_final: 0.8354 (tm) REVERT: C 242 LEU cc_start: 0.6889 (mt) cc_final: 0.6681 (tp) REVERT: C 271 GLN cc_start: 0.8414 (mp10) cc_final: 0.8030 (mp10) REVERT: C 913 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8356 (pt0) REVERT: C 988 GLU cc_start: 0.8566 (mp0) cc_final: 0.8145 (mp0) REVERT: D 35 GLU cc_start: 0.6909 (mt-10) cc_final: 0.6581 (tp30) REVERT: D 45 LEU cc_start: 0.5304 (tp) cc_final: 0.5024 (pp) REVERT: D 312 GLU cc_start: 0.5692 (tt0) cc_final: 0.4766 (pp20) REVERT: D 455 MET cc_start: 0.4242 (ttt) cc_final: 0.3828 (tpt) REVERT: D 474 MET cc_start: -0.0192 (mmp) cc_final: -0.1167 (mmm) REVERT: D 508 ASN cc_start: 0.4732 (m-40) cc_final: 0.4350 (m-40) REVERT: D 555 LEU cc_start: 0.3308 (mt) cc_final: 0.3101 (tm) REVERT: D 578 ASN cc_start: 0.4926 (t0) cc_final: 0.4348 (t0) REVERT: D 579 MET cc_start: 0.2237 (mtm) cc_final: 0.2032 (mmt) outliers start: 5 outliers final: 3 residues processed: 402 average time/residue: 0.6199 time to fit residues: 294.6002 Evaluate side-chains 179 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 175 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 913 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.0670 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 409 GLN A 954 HIS A 955 ASN B 580 GLN B 606 ASN B 824 ASN C 314 GLN C 370 ASN C 394 ASN C 505 HIS C 954 HIS D 220 ASN ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.160599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.096654 restraints weight = 60834.266| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.36 r_work: 0.3125 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30818 Z= 0.197 Angle : 0.664 23.487 42038 Z= 0.327 Chirality : 0.047 0.338 4843 Planarity : 0.005 0.070 5317 Dihedral : 7.302 59.860 5274 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.19 % Allowed : 8.34 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.13), residues: 3633 helix: 1.24 (0.16), residues: 1049 sheet: 0.62 (0.20), residues: 650 loop : -0.49 (0.13), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 577 TYR 0.025 0.002 TYR C1067 PHE 0.021 0.002 PHE B 981 TRP 0.022 0.002 TRP A 886 HIS 0.012 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00449 (30711) covalent geometry : angle 0.63938 (41764) SS BOND : bond 0.00308 ( 44) SS BOND : angle 1.03615 ( 88) hydrogen bonds : bond 0.04452 ( 1291) hydrogen bonds : angle 5.78162 ( 3735) Misc. bond : bond 0.00108 ( 1) link_BETA1-4 : bond 0.00637 ( 18) link_BETA1-4 : angle 1.21918 ( 54) link_NAG-ASN : bond 0.00582 ( 44) link_NAG-ASN : angle 3.11659 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 192 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASN cc_start: 0.4241 (OUTLIER) cc_final: 0.3845 (m110) REVERT: A 129 LYS cc_start: 0.6529 (mtmt) cc_final: 0.6298 (mmmt) REVERT: A 133 PHE cc_start: 0.6068 (m-80) cc_final: 0.5817 (m-80) REVERT: A 140 PHE cc_start: 0.6311 (p90) cc_final: 0.6038 (p90) REVERT: A 190 ARG cc_start: 0.7106 (mmt90) cc_final: 0.6754 (mmt90) REVERT: A 238 PHE cc_start: 0.7297 (p90) cc_final: 0.6593 (p90) REVERT: A 338 PHE cc_start: 0.6526 (m-10) cc_final: 0.6295 (m-80) REVERT: A 339 ASP cc_start: 0.6887 (m-30) cc_final: 0.6413 (t0) REVERT: A 342 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.7248 (t80) REVERT: A 592 PHE cc_start: 0.3602 (p90) cc_final: 0.3267 (p90) REVERT: A 759 PHE cc_start: 0.8310 (m-80) cc_final: 0.8094 (m-80) REVERT: A 985 ASP cc_start: 0.8433 (m-30) cc_final: 0.7768 (m-30) REVERT: A 988 GLU cc_start: 0.8103 (pm20) cc_final: 0.7428 (pm20) REVERT: A 1010 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8488 (mp10) REVERT: A 1145 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7768 (mm) REVERT: B 66 HIS cc_start: 0.7115 (t-90) cc_final: 0.6877 (t-90) REVERT: B 856 LYS cc_start: 0.5477 (mttt) cc_final: 0.4868 (pmtt) REVERT: C 88 ASP cc_start: 0.8350 (m-30) cc_final: 0.7759 (p0) REVERT: C 189 LEU cc_start: 0.8564 (tp) cc_final: 0.8349 (tm) REVERT: C 190 ARG cc_start: 0.8141 (mtt90) cc_final: 0.7885 (mtt180) REVERT: C 334 ASN cc_start: 0.7109 (t0) cc_final: 0.6701 (p0) REVERT: C 338 PHE cc_start: 0.8588 (m-80) cc_final: 0.8377 (m-80) REVERT: C 362 VAL cc_start: 0.6777 (OUTLIER) cc_final: 0.6287 (m) REVERT: C 508 TYR cc_start: 0.7985 (m-80) cc_final: 0.7260 (m-80) REVERT: C 586 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8090 (m-30) REVERT: D 35 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6699 (tp30) REVERT: D 78 LYS cc_start: 0.6287 (mmtp) cc_final: 0.6014 (mtpm) REVERT: D 455 MET cc_start: 0.3445 (ttt) cc_final: 0.2641 (tpt) REVERT: D 555 LEU cc_start: 0.3431 (mt) cc_final: 0.3172 (tm) outliers start: 71 outliers final: 25 residues processed: 247 average time/residue: 0.5595 time to fit residues: 167.2030 Evaluate side-chains 186 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 210 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 211 optimal weight: 9.9990 chunk 104 optimal weight: 0.0770 chunk 329 optimal weight: 8.9990 chunk 275 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 48 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 824 ASN B 121 ASN B 779 GLN D 24 ASN D 239 HIS D 345 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.160479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.097520 restraints weight = 60553.151| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.31 r_work: 0.3133 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30818 Z= 0.138 Angle : 0.587 20.152 42038 Z= 0.289 Chirality : 0.044 0.257 4843 Planarity : 0.004 0.059 5317 Dihedral : 6.611 59.994 5263 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.88 % Allowed : 9.88 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.13), residues: 3633 helix: 1.67 (0.16), residues: 1051 sheet: 0.58 (0.20), residues: 626 loop : -0.44 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 498 TYR 0.025 0.001 TYR D 215 PHE 0.018 0.001 PHE C 565 TRP 0.016 0.001 TRP D 163 HIS 0.006 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00310 (30711) covalent geometry : angle 0.56571 (41764) SS BOND : bond 0.00219 ( 44) SS BOND : angle 0.88104 ( 88) hydrogen bonds : bond 0.03987 ( 1291) hydrogen bonds : angle 5.51912 ( 3735) Misc. bond : bond 0.00094 ( 1) link_BETA1-4 : bond 0.00334 ( 18) link_BETA1-4 : angle 1.12583 ( 54) link_NAG-ASN : bond 0.00522 ( 44) link_NAG-ASN : angle 2.72572 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 174 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASN cc_start: 0.4186 (OUTLIER) cc_final: 0.3868 (m-40) REVERT: A 133 PHE cc_start: 0.6329 (m-80) cc_final: 0.5978 (m-80) REVERT: A 140 PHE cc_start: 0.6197 (p90) cc_final: 0.5924 (p90) REVERT: A 153 MET cc_start: 0.4391 (pp-130) cc_final: 0.3855 (ppp) REVERT: A 190 ARG cc_start: 0.7090 (mmt90) cc_final: 0.6644 (mmt90) REVERT: A 238 PHE cc_start: 0.7284 (p90) cc_final: 0.6723 (p90) REVERT: A 338 PHE cc_start: 0.6636 (m-10) cc_final: 0.6325 (m-80) REVERT: A 339 ASP cc_start: 0.6946 (m-30) cc_final: 0.6478 (t0) REVERT: A 342 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.7139 (t80) REVERT: A 759 PHE cc_start: 0.8344 (m-80) cc_final: 0.8130 (m-80) REVERT: A 985 ASP cc_start: 0.8364 (m-30) cc_final: 0.7792 (m-30) REVERT: A 988 GLU cc_start: 0.8192 (pm20) cc_final: 0.7526 (pm20) REVERT: A 1010 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8596 (mp10) REVERT: B 66 HIS cc_start: 0.7070 (t-90) cc_final: 0.6836 (t-90) REVERT: B 856 LYS cc_start: 0.5478 (mttt) cc_final: 0.4769 (pmtt) REVERT: B 1092 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8676 (mt-10) REVERT: C 88 ASP cc_start: 0.8323 (m-30) cc_final: 0.7834 (p0) REVERT: C 190 ARG cc_start: 0.8041 (mtt90) cc_final: 0.7449 (mtt180) REVERT: C 242 LEU cc_start: 0.6429 (tp) cc_final: 0.6042 (mt) REVERT: C 334 ASN cc_start: 0.7004 (t0) cc_final: 0.6745 (p0) REVERT: C 338 PHE cc_start: 0.8614 (m-80) cc_final: 0.8361 (m-80) REVERT: C 498 ARG cc_start: 0.6511 (mpt90) cc_final: 0.6311 (mpt90) REVERT: C 508 TYR cc_start: 0.8013 (m-80) cc_final: 0.7294 (m-80) REVERT: D 35 GLU cc_start: 0.6907 (mt-10) cc_final: 0.6649 (tp30) REVERT: D 455 MET cc_start: 0.3444 (ttt) cc_final: 0.2637 (tpt) REVERT: D 555 LEU cc_start: 0.3405 (mt) cc_final: 0.3179 (tm) REVERT: D 557 MET cc_start: -0.0544 (tmm) cc_final: -0.1859 (ttp) outliers start: 61 outliers final: 24 residues processed: 219 average time/residue: 0.5991 time to fit residues: 159.3303 Evaluate side-chains 181 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 210 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 74 optimal weight: 0.0050 chunk 253 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 104 optimal weight: 0.0870 chunk 113 optimal weight: 7.9990 chunk 318 optimal weight: 30.0000 chunk 181 optimal weight: 0.5980 chunk 182 optimal weight: 0.6980 chunk 202 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 overall best weight: 0.6774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 907 ASN A 955 ASN D 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.160728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.098939 restraints weight = 60413.698| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.57 r_work: 0.3160 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 30818 Z= 0.111 Angle : 0.552 18.888 42038 Z= 0.272 Chirality : 0.043 0.254 4843 Planarity : 0.004 0.055 5317 Dihedral : 5.979 59.657 5263 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.79 % Allowed : 10.93 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.14), residues: 3633 helix: 1.85 (0.16), residues: 1052 sheet: 0.52 (0.20), residues: 639 loop : -0.34 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 518 TYR 0.021 0.001 TYR A1067 PHE 0.020 0.001 PHE C 565 TRP 0.012 0.001 TRP B 436 HIS 0.005 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00244 (30711) covalent geometry : angle 0.53344 (41764) SS BOND : bond 0.00223 ( 44) SS BOND : angle 0.77950 ( 88) hydrogen bonds : bond 0.03665 ( 1291) hydrogen bonds : angle 5.28805 ( 3735) Misc. bond : bond 0.00066 ( 1) link_BETA1-4 : bond 0.00298 ( 18) link_BETA1-4 : angle 1.09151 ( 54) link_NAG-ASN : bond 0.00460 ( 44) link_NAG-ASN : angle 2.50135 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 175 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASN cc_start: 0.3974 (OUTLIER) cc_final: 0.3676 (m-40) REVERT: A 133 PHE cc_start: 0.6298 (m-80) cc_final: 0.6021 (m-80) REVERT: A 140 PHE cc_start: 0.6173 (p90) cc_final: 0.5893 (p90) REVERT: A 153 MET cc_start: 0.4386 (pp-130) cc_final: 0.3833 (ppp) REVERT: A 223 LEU cc_start: 0.3853 (mp) cc_final: 0.3566 (mt) REVERT: A 338 PHE cc_start: 0.6658 (m-10) cc_final: 0.6367 (m-80) REVERT: A 339 ASP cc_start: 0.6815 (m-30) cc_final: 0.6395 (t0) REVERT: A 342 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.7169 (t80) REVERT: A 592 PHE cc_start: 0.3143 (p90) cc_final: 0.2750 (p90) REVERT: A 759 PHE cc_start: 0.8291 (m-80) cc_final: 0.8047 (m-80) REVERT: A 985 ASP cc_start: 0.8290 (m-30) cc_final: 0.7819 (m-30) REVERT: A 988 GLU cc_start: 0.8153 (pm20) cc_final: 0.7467 (pm20) REVERT: B 66 HIS cc_start: 0.7011 (t-90) cc_final: 0.6795 (t-90) REVERT: B 1092 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8658 (mt-10) REVERT: C 88 ASP cc_start: 0.8404 (m-30) cc_final: 0.7892 (p0) REVERT: C 190 ARG cc_start: 0.8016 (mtt90) cc_final: 0.7445 (mtt180) REVERT: C 242 LEU cc_start: 0.6619 (tp) cc_final: 0.6238 (mt) REVERT: C 271 GLN cc_start: 0.8316 (mp10) cc_final: 0.7813 (mp10) REVERT: C 338 PHE cc_start: 0.8658 (m-80) cc_final: 0.8440 (m-80) REVERT: C 403 ARG cc_start: 0.7891 (mtp180) cc_final: 0.7335 (ttm170) REVERT: D 35 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6692 (tp30) REVERT: D 455 MET cc_start: 0.3573 (ttt) cc_final: 0.2654 (tpt) REVERT: D 497 TYR cc_start: 0.1224 (m-80) cc_final: 0.0920 (m-10) REVERT: D 555 LEU cc_start: 0.3786 (mt) cc_final: 0.3497 (tm) REVERT: D 557 MET cc_start: -0.0359 (tmm) cc_final: -0.1593 (ttp) outliers start: 58 outliers final: 24 residues processed: 220 average time/residue: 0.5269 time to fit residues: 141.1687 Evaluate side-chains 178 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 210 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 155 optimal weight: 9.9990 chunk 204 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 342 optimal weight: 4.9990 chunk 259 optimal weight: 0.6980 chunk 177 optimal weight: 3.9990 chunk 341 optimal weight: 7.9990 chunk 290 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN B 580 GLN C 505 HIS C 824 ASN C1011 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.157190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.093182 restraints weight = 59945.436| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 3.28 r_work: 0.3066 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 30818 Z= 0.274 Angle : 0.662 19.452 42038 Z= 0.327 Chirality : 0.048 0.369 4843 Planarity : 0.005 0.059 5317 Dihedral : 6.057 59.201 5263 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.44 % Allowed : 11.58 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.13), residues: 3633 helix: 1.66 (0.16), residues: 1061 sheet: 0.12 (0.20), residues: 631 loop : -0.43 (0.13), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 518 TYR 0.024 0.002 TYR A1067 PHE 0.045 0.002 PHE C 186 TRP 0.015 0.002 TRP D 163 HIS 0.005 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00655 (30711) covalent geometry : angle 0.64181 (41764) SS BOND : bond 0.00328 ( 44) SS BOND : angle 1.25167 ( 88) hydrogen bonds : bond 0.04555 ( 1291) hydrogen bonds : angle 5.58984 ( 3735) Misc. bond : bond 0.00080 ( 1) link_BETA1-4 : bond 0.00310 ( 18) link_BETA1-4 : angle 1.36241 ( 54) link_NAG-ASN : bond 0.00592 ( 44) link_NAG-ASN : angle 2.72900 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 163 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASN cc_start: 0.4379 (OUTLIER) cc_final: 0.4073 (m-40) REVERT: A 133 PHE cc_start: 0.6395 (m-80) cc_final: 0.6129 (m-80) REVERT: A 140 PHE cc_start: 0.6123 (p90) cc_final: 0.5865 (p90) REVERT: A 170 TYR cc_start: 0.7939 (t80) cc_final: 0.7491 (t80) REVERT: A 190 ARG cc_start: 0.7367 (mmt90) cc_final: 0.7074 (mmt90) REVERT: A 338 PHE cc_start: 0.6813 (m-10) cc_final: 0.6435 (m-80) REVERT: A 339 ASP cc_start: 0.6882 (m-30) cc_final: 0.6498 (t0) REVERT: A 342 PHE cc_start: 0.7598 (t80) cc_final: 0.7170 (t80) REVERT: A 759 PHE cc_start: 0.8427 (m-80) cc_final: 0.8212 (m-80) REVERT: A 902 MET cc_start: 0.9390 (tpp) cc_final: 0.9189 (tpp) REVERT: A 985 ASP cc_start: 0.8356 (m-30) cc_final: 0.7852 (m-30) REVERT: A 988 GLU cc_start: 0.8234 (pm20) cc_final: 0.7514 (pm20) REVERT: B 153 MET cc_start: 0.3764 (OUTLIER) cc_final: 0.3272 (pmm) REVERT: B 324 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7819 (pm20) REVERT: B 586 ASP cc_start: 0.6110 (OUTLIER) cc_final: 0.5804 (m-30) REVERT: B 740 MET cc_start: 0.8180 (mtp) cc_final: 0.7964 (ttt) REVERT: B 1092 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8631 (mt-10) REVERT: C 88 ASP cc_start: 0.8433 (m-30) cc_final: 0.7972 (OUTLIER) REVERT: C 158 ARG cc_start: 0.6190 (OUTLIER) cc_final: 0.5916 (ptp-110) REVERT: C 190 ARG cc_start: 0.8053 (mtt90) cc_final: 0.7739 (mtt180) REVERT: C 242 LEU cc_start: 0.6451 (tp) cc_final: 0.6078 (mt) REVERT: C 338 PHE cc_start: 0.8758 (m-80) cc_final: 0.8484 (m-80) REVERT: C 347 PHE cc_start: 0.6877 (OUTLIER) cc_final: 0.5626 (m-10) REVERT: C 403 ARG cc_start: 0.7814 (mtp180) cc_final: 0.7391 (ttm-80) REVERT: C 586 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.8140 (m-30) REVERT: D 35 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6718 (tp30) REVERT: D 387 ARG cc_start: 0.5712 (OUTLIER) cc_final: 0.5224 (ptt90) REVERT: D 455 MET cc_start: 0.3724 (ttt) cc_final: 0.2852 (tpt) REVERT: D 474 MET cc_start: -0.1014 (mmm) cc_final: -0.1599 (mmm) REVERT: D 483 GLU cc_start: 0.3612 (OUTLIER) cc_final: 0.3320 (pt0) REVERT: D 497 TYR cc_start: 0.1049 (m-80) cc_final: 0.0811 (m-10) REVERT: D 555 LEU cc_start: 0.3791 (mt) cc_final: 0.3507 (tm) outliers start: 79 outliers final: 37 residues processed: 226 average time/residue: 0.5111 time to fit residues: 141.3887 Evaluate side-chains 188 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 142 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 483 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 30 optimal weight: 30.0000 chunk 175 optimal weight: 0.9980 chunk 233 optimal weight: 0.9990 chunk 275 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 238 optimal weight: 0.7980 chunk 347 optimal weight: 5.9990 chunk 250 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.158741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.097061 restraints weight = 59637.157| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.27 r_work: 0.3103 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 30818 Z= 0.122 Angle : 0.557 10.524 42038 Z= 0.277 Chirality : 0.044 0.262 4843 Planarity : 0.004 0.069 5317 Dihedral : 5.653 59.100 5263 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.91 % Allowed : 12.29 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.14), residues: 3633 helix: 1.89 (0.16), residues: 1057 sheet: 0.22 (0.20), residues: 610 loop : -0.33 (0.14), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C 493 TYR 0.020 0.001 TYR A1067 PHE 0.020 0.001 PHE C 565 TRP 0.014 0.001 TRP D 163 HIS 0.004 0.000 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00274 (30711) covalent geometry : angle 0.53874 (41764) SS BOND : bond 0.00190 ( 44) SS BOND : angle 0.91738 ( 88) hydrogen bonds : bond 0.03742 ( 1291) hydrogen bonds : angle 5.31616 ( 3735) Misc. bond : bond 0.00056 ( 1) link_BETA1-4 : bond 0.00346 ( 18) link_BETA1-4 : angle 1.08254 ( 54) link_NAG-ASN : bond 0.00455 ( 44) link_NAG-ASN : angle 2.42160 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 163 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASN cc_start: 0.4312 (OUTLIER) cc_final: 0.4074 (m-40) REVERT: A 133 PHE cc_start: 0.6370 (m-80) cc_final: 0.6132 (m-80) REVERT: A 140 PHE cc_start: 0.5966 (p90) cc_final: 0.5757 (p90) REVERT: A 170 TYR cc_start: 0.7801 (t80) cc_final: 0.7380 (t80) REVERT: A 190 ARG cc_start: 0.7329 (mmt90) cc_final: 0.6821 (mmt90) REVERT: A 197 ILE cc_start: 0.4124 (OUTLIER) cc_final: 0.3886 (mm) REVERT: A 338 PHE cc_start: 0.6705 (m-10) cc_final: 0.6491 (m-80) REVERT: A 339 ASP cc_start: 0.6838 (m-30) cc_final: 0.6459 (t0) REVERT: A 342 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.7226 (t80) REVERT: A 759 PHE cc_start: 0.8368 (m-80) cc_final: 0.8133 (m-80) REVERT: A 985 ASP cc_start: 0.8293 (m-30) cc_final: 0.7846 (m-30) REVERT: A 988 GLU cc_start: 0.8243 (pm20) cc_final: 0.7482 (pm20) REVERT: B 324 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7881 (pm20) REVERT: B 759 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.8006 (t80) REVERT: C 88 ASP cc_start: 0.8376 (m-30) cc_final: 0.7959 (OUTLIER) REVERT: C 100 ILE cc_start: 0.7772 (mm) cc_final: 0.7535 (mp) REVERT: C 158 ARG cc_start: 0.6288 (OUTLIER) cc_final: 0.6074 (ptp-110) REVERT: C 190 ARG cc_start: 0.8159 (mtt90) cc_final: 0.7872 (mtt180) REVERT: C 205 SER cc_start: 0.8660 (t) cc_final: 0.8441 (p) REVERT: C 242 LEU cc_start: 0.6511 (tp) cc_final: 0.6167 (mt) REVERT: C 347 PHE cc_start: 0.6871 (OUTLIER) cc_final: 0.5721 (m-10) REVERT: D 35 GLU cc_start: 0.6841 (mt-10) cc_final: 0.6612 (tp30) REVERT: D 141 CYS cc_start: -0.1896 (OUTLIER) cc_final: -0.2262 (m) REVERT: D 387 ARG cc_start: 0.5889 (ptt90) cc_final: 0.5335 (mmm160) REVERT: D 455 MET cc_start: 0.3611 (ttt) cc_final: 0.2813 (tpt) REVERT: D 483 GLU cc_start: 0.3623 (OUTLIER) cc_final: 0.3310 (pt0) REVERT: D 555 LEU cc_start: 0.3773 (mt) cc_final: 0.3497 (tm) REVERT: D 557 MET cc_start: -0.0222 (tmm) cc_final: -0.1520 (ttp) outliers start: 62 outliers final: 30 residues processed: 208 average time/residue: 0.5610 time to fit residues: 142.6501 Evaluate side-chains 184 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 483 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 172 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 354 optimal weight: 10.0000 chunk 187 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 309 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.158340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.095754 restraints weight = 59465.941| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.23 r_work: 0.3105 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 30818 Z= 0.141 Angle : 0.565 10.488 42038 Z= 0.280 Chirality : 0.044 0.252 4843 Planarity : 0.004 0.057 5317 Dihedral : 5.403 58.754 5263 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.04 % Allowed : 12.91 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.14), residues: 3633 helix: 1.98 (0.16), residues: 1055 sheet: 0.17 (0.20), residues: 623 loop : -0.28 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 482 TYR 0.021 0.001 TYR C1067 PHE 0.018 0.001 PHE C 565 TRP 0.018 0.001 TRP A 104 HIS 0.004 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00325 (30711) covalent geometry : angle 0.54775 (41764) SS BOND : bond 0.00271 ( 44) SS BOND : angle 0.92897 ( 88) hydrogen bonds : bond 0.03764 ( 1291) hydrogen bonds : angle 5.23224 ( 3735) Misc. bond : bond 0.00061 ( 1) link_BETA1-4 : bond 0.00314 ( 18) link_BETA1-4 : angle 1.13496 ( 54) link_NAG-ASN : bond 0.00459 ( 44) link_NAG-ASN : angle 2.38850 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 153 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASN cc_start: 0.4311 (OUTLIER) cc_final: 0.4109 (m-40) REVERT: A 133 PHE cc_start: 0.6397 (m-80) cc_final: 0.6150 (m-80) REVERT: A 140 PHE cc_start: 0.5920 (p90) cc_final: 0.5660 (p90) REVERT: A 170 TYR cc_start: 0.7806 (t80) cc_final: 0.7581 (t80) REVERT: A 197 ILE cc_start: 0.4058 (OUTLIER) cc_final: 0.3809 (mm) REVERT: A 338 PHE cc_start: 0.6771 (m-10) cc_final: 0.6453 (m-80) REVERT: A 339 ASP cc_start: 0.6760 (m-30) cc_final: 0.6371 (t0) REVERT: A 342 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.7241 (t80) REVERT: A 759 PHE cc_start: 0.8343 (m-80) cc_final: 0.8060 (m-80) REVERT: A 985 ASP cc_start: 0.8287 (m-30) cc_final: 0.7711 (m-30) REVERT: A 988 GLU cc_start: 0.8253 (pm20) cc_final: 0.7580 (pm20) REVERT: B 153 MET cc_start: 0.3519 (OUTLIER) cc_final: 0.3212 (pmm) REVERT: B 324 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7922 (pm20) REVERT: B 740 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7888 (ttt) REVERT: B 759 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7610 (t80) REVERT: B 1092 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8577 (mt-10) REVERT: C 88 ASP cc_start: 0.8395 (m-30) cc_final: 0.7975 (OUTLIER) REVERT: C 100 ILE cc_start: 0.7718 (mm) cc_final: 0.7472 (mp) REVERT: C 158 ARG cc_start: 0.6416 (OUTLIER) cc_final: 0.6215 (ptp-110) REVERT: C 190 ARG cc_start: 0.8167 (mtt90) cc_final: 0.7888 (mtt180) REVERT: C 205 SER cc_start: 0.8606 (t) cc_final: 0.8404 (p) REVERT: C 242 LEU cc_start: 0.6676 (tp) cc_final: 0.6345 (mt) REVERT: C 964 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8454 (mmmt) REVERT: D 35 GLU cc_start: 0.6836 (mt-10) cc_final: 0.6619 (tp30) REVERT: D 323 MET cc_start: 0.1137 (mpp) cc_final: 0.0642 (mpp) REVERT: D 387 ARG cc_start: 0.5772 (ptt90) cc_final: 0.5297 (mmm160) REVERT: D 455 MET cc_start: 0.3799 (ttt) cc_final: 0.2917 (tpt) REVERT: D 474 MET cc_start: -0.0822 (mmm) cc_final: -0.1044 (mmm) REVERT: D 555 LEU cc_start: 0.3778 (mt) cc_final: 0.3511 (tm) REVERT: D 557 MET cc_start: 0.0030 (tmm) cc_final: -0.1230 (ttp) outliers start: 66 outliers final: 36 residues processed: 205 average time/residue: 0.5165 time to fit residues: 130.3693 Evaluate side-chains 188 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 143 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain D residue 195 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 65 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 211 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 53 optimal weight: 0.2980 chunk 93 optimal weight: 1.9990 chunk 210 optimal weight: 0.9990 chunk 239 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 137 ASN ** 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 = 0.4421 r_free = 0.4421 target = 0.158553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.096148 restraints weight = 59892.627| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.57 r_work: 0.3093 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 30818 Z= 0.130 Angle : 0.567 17.010 42038 Z= 0.279 Chirality : 0.044 0.260 4843 Planarity : 0.004 0.053 5317 Dihedral : 5.308 58.660 5263 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.98 % Allowed : 13.18 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.14), residues: 3633 helix: 1.97 (0.16), residues: 1064 sheet: 0.21 (0.20), residues: 605 loop : -0.27 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 498 TYR 0.020 0.001 TYR A1067 PHE 0.024 0.001 PHE B 140 TRP 0.022 0.001 TRP A 104 HIS 0.005 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00300 (30711) covalent geometry : angle 0.55025 (41764) SS BOND : bond 0.00209 ( 44) SS BOND : angle 1.11023 ( 88) hydrogen bonds : bond 0.03661 ( 1291) hydrogen bonds : angle 5.18236 ( 3735) Misc. bond : bond 0.00053 ( 1) link_BETA1-4 : bond 0.00326 ( 18) link_BETA1-4 : angle 1.06439 ( 54) link_NAG-ASN : bond 0.00440 ( 44) link_NAG-ASN : angle 2.31228 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 150 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6435 (m-80) cc_final: 0.6158 (m-80) REVERT: A 140 PHE cc_start: 0.5819 (p90) cc_final: 0.5549 (p90) REVERT: A 170 TYR cc_start: 0.7857 (t80) cc_final: 0.7647 (t80) REVERT: A 190 ARG cc_start: 0.7256 (mmt90) cc_final: 0.6843 (mmt90) REVERT: A 197 ILE cc_start: 0.4068 (OUTLIER) cc_final: 0.3840 (mm) REVERT: A 338 PHE cc_start: 0.6750 (m-10) cc_final: 0.6494 (m-80) REVERT: A 339 ASP cc_start: 0.6725 (m-30) cc_final: 0.6334 (t0) REVERT: A 342 PHE cc_start: 0.7656 (OUTLIER) cc_final: 0.7247 (t80) REVERT: A 759 PHE cc_start: 0.8348 (m-80) cc_final: 0.8069 (m-80) REVERT: A 985 ASP cc_start: 0.8206 (m-30) cc_final: 0.7691 (m-30) REVERT: A 988 GLU cc_start: 0.8226 (pm20) cc_final: 0.7580 (pm20) REVERT: B 140 PHE cc_start: 0.7612 (p90) cc_final: 0.7400 (p90) REVERT: B 324 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7862 (pm20) REVERT: B 759 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7624 (t80) REVERT: B 1092 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8639 (mt-10) REVERT: C 88 ASP cc_start: 0.8511 (m-30) cc_final: 0.8031 (OUTLIER) REVERT: C 100 ILE cc_start: 0.7720 (mm) cc_final: 0.7491 (mp) REVERT: C 158 ARG cc_start: 0.6384 (OUTLIER) cc_final: 0.6181 (ptp-110) REVERT: C 170 TYR cc_start: 0.8094 (t80) cc_final: 0.7852 (t80) REVERT: C 190 ARG cc_start: 0.8122 (mtt90) cc_final: 0.7311 (mtt-85) REVERT: C 242 LEU cc_start: 0.6765 (tp) cc_final: 0.6454 (mt) REVERT: C 324 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8237 (pm20) REVERT: C 347 PHE cc_start: 0.6805 (OUTLIER) cc_final: 0.5628 (m-80) REVERT: C 964 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8452 (mmmt) REVERT: D 383 MET cc_start: 0.5438 (mmm) cc_final: 0.4881 (ttm) REVERT: D 387 ARG cc_start: 0.5777 (ptt90) cc_final: 0.5379 (mmm160) REVERT: D 455 MET cc_start: 0.3533 (ttt) cc_final: 0.2669 (tpt) REVERT: D 483 GLU cc_start: 0.3540 (OUTLIER) cc_final: 0.3259 (pt0) REVERT: D 555 LEU cc_start: 0.3772 (mt) cc_final: 0.3543 (tm) REVERT: D 557 MET cc_start: 0.0070 (tmm) cc_final: -0.1123 (ttp) outliers start: 64 outliers final: 40 residues processed: 201 average time/residue: 0.5111 time to fit residues: 125.9606 Evaluate side-chains 191 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 142 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 483 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 121 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 342 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 246 optimal weight: 5.9990 chunk 298 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 141 optimal weight: 30.0000 chunk 362 optimal weight: 7.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.157863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.095828 restraints weight = 59847.981| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.55 r_work: 0.3072 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30818 Z= 0.156 Angle : 0.585 14.561 42038 Z= 0.289 Chirality : 0.045 0.257 4843 Planarity : 0.004 0.054 5317 Dihedral : 5.332 59.010 5263 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.88 % Allowed : 13.31 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.14), residues: 3633 helix: 1.99 (0.16), residues: 1055 sheet: 0.11 (0.20), residues: 602 loop : -0.27 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 518 TYR 0.021 0.001 TYR A1067 PHE 0.022 0.001 PHE B 140 TRP 0.025 0.001 TRP A 104 HIS 0.003 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00362 (30711) covalent geometry : angle 0.56950 (41764) SS BOND : bond 0.00246 ( 44) SS BOND : angle 0.98884 ( 88) hydrogen bonds : bond 0.03820 ( 1291) hydrogen bonds : angle 5.23012 ( 3735) Misc. bond : bond 0.00069 ( 1) link_BETA1-4 : bond 0.00265 ( 18) link_BETA1-4 : angle 1.15695 ( 54) link_NAG-ASN : bond 0.00468 ( 44) link_NAG-ASN : angle 2.31028 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 143 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6451 (m-80) cc_final: 0.6182 (m-80) REVERT: A 140 PHE cc_start: 0.5520 (p90) cc_final: 0.5128 (p90) REVERT: A 170 TYR cc_start: 0.7877 (t80) cc_final: 0.7608 (t80) REVERT: A 190 ARG cc_start: 0.7241 (mmt90) cc_final: 0.6913 (mmt90) REVERT: A 271 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8205 (mp10) REVERT: A 338 PHE cc_start: 0.6822 (m-10) cc_final: 0.6525 (m-80) REVERT: A 339 ASP cc_start: 0.6741 (m-30) cc_final: 0.6334 (t0) REVERT: A 342 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.7256 (t80) REVERT: A 759 PHE cc_start: 0.8368 (m-80) cc_final: 0.8093 (m-80) REVERT: A 985 ASP cc_start: 0.8221 (m-30) cc_final: 0.7716 (m-30) REVERT: A 988 GLU cc_start: 0.8245 (pm20) cc_final: 0.7593 (pm20) REVERT: B 324 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7849 (pm20) REVERT: B 759 PHE cc_start: 0.8163 (t80) cc_final: 0.7666 (t80) REVERT: B 1092 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8689 (mt-10) REVERT: C 88 ASP cc_start: 0.8520 (m-30) cc_final: 0.8048 (OUTLIER) REVERT: C 100 ILE cc_start: 0.7638 (mm) cc_final: 0.7423 (mp) REVERT: C 190 ARG cc_start: 0.8109 (mtt90) cc_final: 0.7816 (mtt180) REVERT: C 242 LEU cc_start: 0.6766 (tp) cc_final: 0.6479 (mt) REVERT: C 324 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8295 (pm20) REVERT: C 392 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.8382 (m-80) REVERT: C 586 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.8113 (m-30) REVERT: C 964 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8470 (mmmt) REVERT: D 383 MET cc_start: 0.5479 (mmm) cc_final: 0.5011 (ttt) REVERT: D 455 MET cc_start: 0.3596 (ttt) cc_final: 0.2803 (tpt) REVERT: D 555 LEU cc_start: 0.3858 (mt) cc_final: 0.3585 (tm) REVERT: D 557 MET cc_start: 0.0103 (tmm) cc_final: -0.1027 (ttp) outliers start: 61 outliers final: 35 residues processed: 192 average time/residue: 0.5459 time to fit residues: 129.1681 Evaluate side-chains 180 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 138 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 195 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 218 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 328 optimal weight: 0.0870 chunk 198 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 227 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 366 optimal weight: 1.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN C 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.157158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.094031 restraints weight = 59455.009| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.27 r_work: 0.3085 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30818 Z= 0.171 Angle : 0.590 12.414 42038 Z= 0.293 Chirality : 0.045 0.251 4843 Planarity : 0.004 0.054 5317 Dihedral : 5.437 59.314 5263 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.48 % Allowed : 13.74 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.14), residues: 3633 helix: 1.96 (0.16), residues: 1061 sheet: 0.04 (0.20), residues: 600 loop : -0.31 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 518 TYR 0.028 0.001 TYR D 454 PHE 0.020 0.001 PHE C 392 TRP 0.037 0.001 TRP A 104 HIS 0.004 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00400 (30711) covalent geometry : angle 0.57425 (41764) SS BOND : bond 0.00253 ( 44) SS BOND : angle 0.93815 ( 88) hydrogen bonds : bond 0.03902 ( 1291) hydrogen bonds : angle 5.28339 ( 3735) Misc. bond : bond 0.00072 ( 1) link_BETA1-4 : bond 0.00288 ( 18) link_BETA1-4 : angle 1.13512 ( 54) link_NAG-ASN : bond 0.00463 ( 44) link_NAG-ASN : angle 2.35003 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7266 Ramachandran restraints generated. 3633 Oldfield, 0 Emsley, 3633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 147 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.5765 (m-80) cc_final: 0.5522 (m-80) REVERT: A 133 PHE cc_start: 0.6498 (m-80) cc_final: 0.6145 (m-80) REVERT: A 170 TYR cc_start: 0.7936 (t80) cc_final: 0.7644 (t80) REVERT: A 190 ARG cc_start: 0.7285 (mmt90) cc_final: 0.7023 (mmt90) REVERT: A 271 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8256 (mp10) REVERT: A 338 PHE cc_start: 0.6850 (m-10) cc_final: 0.6550 (m-80) REVERT: A 339 ASP cc_start: 0.6770 (m-30) cc_final: 0.6363 (t0) REVERT: A 342 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.7226 (t80) REVERT: A 759 PHE cc_start: 0.8391 (m-80) cc_final: 0.8124 (m-80) REVERT: A 985 ASP cc_start: 0.8222 (m-30) cc_final: 0.7697 (m-30) REVERT: A 988 GLU cc_start: 0.8249 (pm20) cc_final: 0.7605 (pm20) REVERT: B 324 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7832 (pm20) REVERT: B 759 PHE cc_start: 0.8171 (t80) cc_final: 0.7717 (t80) REVERT: B 1092 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8594 (mt-10) REVERT: C 88 ASP cc_start: 0.8548 (m-30) cc_final: 0.8065 (p0) REVERT: C 100 ILE cc_start: 0.7748 (mm) cc_final: 0.7533 (mp) REVERT: C 196 ASN cc_start: 0.5570 (m-40) cc_final: 0.4947 (p0) REVERT: C 242 LEU cc_start: 0.6729 (tp) cc_final: 0.6468 (mt) REVERT: C 324 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8253 (pm20) REVERT: C 964 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8457 (mmmt) REVERT: D 383 MET cc_start: 0.5605 (mmm) cc_final: 0.5083 (ttm) REVERT: D 455 MET cc_start: 0.3231 (ttt) cc_final: 0.2421 (tpt) REVERT: D 483 GLU cc_start: 0.3673 (OUTLIER) cc_final: 0.3350 (pt0) REVERT: D 555 LEU cc_start: 0.3417 (mt) cc_final: 0.3145 (tm) REVERT: D 557 MET cc_start: 0.0363 (tmm) cc_final: -0.0802 (ttp) outliers start: 48 outliers final: 33 residues processed: 187 average time/residue: 0.5415 time to fit residues: 123.6216 Evaluate side-chains 180 residues out of total 3239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 483 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 259 optimal weight: 0.9990 chunk 43 optimal weight: 20.0000 chunk 268 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 309 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 99 optimal weight: 0.2980 chunk 227 optimal weight: 7.9990 chunk 238 optimal weight: 0.0470 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.157721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.094434 restraints weight = 60002.582| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 3.24 r_work: 0.3113 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30818 Z= 0.132 Angle : 0.578 12.151 42038 Z= 0.285 Chirality : 0.044 0.256 4843 Planarity : 0.004 0.076 5317 Dihedral : 5.359 59.045 5263 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.27 % Allowed : 13.99 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.14), residues: 3633 helix: 2.01 (0.16), residues: 1055 sheet: 0.04 (0.20), residues: 591 loop : -0.27 (0.14), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 190 TYR 0.020 0.001 TYR A1067 PHE 0.033 0.001 PHE A 194 TRP 0.041 0.001 TRP A 104 HIS 0.003 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00303 (30711) covalent geometry : angle 0.56257 (41764) SS BOND : bond 0.00215 ( 44) SS BOND : angle 0.87529 ( 88) hydrogen bonds : bond 0.03708 ( 1291) hydrogen bonds : angle 5.21586 ( 3735) Misc. bond : bond 0.00060 ( 1) link_BETA1-4 : bond 0.00330 ( 18) link_BETA1-4 : angle 1.08664 ( 54) link_NAG-ASN : bond 0.00441 ( 44) link_NAG-ASN : angle 2.27485 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22109.38 seconds wall clock time: 374 minutes 1.87 seconds (22441.87 seconds total)