Starting phenix.real_space_refine on Fri Mar 6 23:14:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mjm_23878/03_2026/7mjm_23878.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mjm_23878/03_2026/7mjm_23878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mjm_23878/03_2026/7mjm_23878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mjm_23878/03_2026/7mjm_23878.map" model { file = "/net/cci-nas-00/data/ceres_data/7mjm_23878/03_2026/7mjm_23878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mjm_23878/03_2026/7mjm_23878.cif" } resolution = 2.83 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= 0.000 sd= 0.030 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 169 5.16 5 C 22366 2.51 5 N 5743 2.21 5 O 6818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35096 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 8140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8140 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8140 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8140 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} 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: "W" 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 9.17, per 1000 atoms: 0.26 Number of scatterers: 35096 At special positions: 0 Unit cell: (142, 164, 235, 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 169 16.00 O 6818 8.00 N 5743 7.00 C 22366 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 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=0, symmetry=0 Links applied BETA1-4 " 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 W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 90 " " NAG D 703 " - " ASN D 322 " " NAG D 704 " - " ASN D 546 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 90 " " NAG E 703 " - " ASN E 322 " " NAG E 704 " - " ASN E 546 " " NAG F 1 " - " ASN A 17 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 17 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN B1074 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 17 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C 801 " " NAG U 1 " - " ASN C1074 " " NAG V 1 " - " ASN C1098 " " NAG W 1 " - " ASN C1134 " Time building additional restraints: 3.17 Conformation dependent library (CDL) restraints added in 1.5 seconds 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8106 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 59 sheets defined 37.6% alpha, 32.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.656A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.898A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.179A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.561A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.631A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.134A 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: 3.682A 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: 3.899A 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 removed outlier: 3.516A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) 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: 4.098A 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: 3.591A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.905A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.040A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.558A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.629A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (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: 3.608A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.503A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.616A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.891A 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: 3.530A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.073A 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: 3.986A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.724A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.919A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.589A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.944A 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: 3.666A 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: 3.919A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.567A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.258A 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 20 through 53 removed outlier: 3.565A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN D 53 " --> pdb=" O ASN D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 80 Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.907A pdb=" N GLU D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) removed outlier: 3.518A 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 102 removed outlier: 3.938A pdb=" N ALA D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU D 100 " --> pdb=" O GLN D 96 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.627A pdb=" N SER D 106 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 154 Processing helix chain 'D' and resid 158 through 194 Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 221 through 249 removed outlier: 3.976A pdb=" N GLU D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.649A pdb=" N MET D 249 " --> pdb=" O ARG D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.684A 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 removed outlier: 3.524A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.584A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.686A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.685A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 4.473A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.702A 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 432 through 447 removed outlier: 4.047A pdb=" N PHE D 438 " --> pdb=" O THR D 434 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS D 441 " --> pdb=" O ASN D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 503 removed outlier: 3.546A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 509 removed outlier: 3.836A pdb=" N ASP D 509 " --> pdb=" O VAL D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.558A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.592A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 564 removed outlier: 4.213A pdb=" N GLU D 564 " --> pdb=" O GLY D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 removed outlier: 3.744A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.559A pdb=" N GLN E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 80 Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.858A pdb=" N GLU E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.965A pdb=" N ALA E 99 " --> pdb=" O LEU E 95 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU E 100 " --> pdb=" O GLN E 96 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.619A pdb=" N SER E 106 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 147 through 154 Processing helix chain 'E' and resid 158 through 194 Proline residue: E 178 - end of helix Processing helix chain 'E' and resid 198 through 204 Processing helix chain 'E' and resid 205 through 207 No H-bonds generated for 'chain 'E' and resid 205 through 207' Processing helix chain 'E' and resid 221 through 249 removed outlier: 3.996A pdb=" N GLU E 227 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.588A pdb=" N MET E 249 " --> pdb=" O ARG E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.661A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.508A pdb=" N VAL E 318 " --> pdb=" O PHE E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.583A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.682A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 removed outlier: 3.665A pdb=" N ARG E 393 " --> pdb=" O PHE E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 413 removed outlier: 4.515A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU E 406 " --> pdb=" O GLU E 402 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA E 413 " --> pdb=" O SER E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 432 through 447 removed outlier: 4.069A pdb=" N PHE E 438 " --> pdb=" O THR E 434 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS E 441 " --> pdb=" O ASN E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 466 Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 499 through 503 removed outlier: 3.546A pdb=" N SER E 502 " --> pdb=" O ASP E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 509 removed outlier: 3.831A pdb=" N ASP E 509 " --> pdb=" O VAL E 506 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 533 removed outlier: 3.601A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.575A pdb=" N GLY E 551 " --> pdb=" O SER E 547 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 564 removed outlier: 4.229A pdb=" N GLU E 564 " --> pdb=" O GLY E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 575 removed outlier: 3.746A pdb=" N VAL E 573 " --> pdb=" O ALA E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.048A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.994A 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: 3.547A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.774A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 12.732A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 13.029A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.730A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.442A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 11.422A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.169A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.196A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.451A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.536A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.474A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.547A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 11.422A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.169A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.196A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.451A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.536A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.474A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 154 through 172 removed outlier: 9.474A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.536A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.451A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.196A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 11.169A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.422A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 12.774A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 12.732A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 13.029A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.730A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.442A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 154 through 172 removed outlier: 9.474A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.536A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.451A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.196A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 11.169A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.422A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 12.774A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 12.732A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 13.029A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.730A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.442A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 154 through 172 removed outlier: 9.474A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.536A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.451A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.196A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 11.169A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.422A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 154 through 172 removed outlier: 9.474A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.536A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.451A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.196A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 11.169A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.422A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 259 through 260 removed outlier: 12.774A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 12.732A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 13.029A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.730A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.442A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 11.422A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.169A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.196A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.451A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.536A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.474A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 259 through 260 removed outlier: 3.749A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 11.422A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.169A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.196A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.451A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.536A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.474A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.628A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.122A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB6, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB7, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.129A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.785A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.590A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.590A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.392A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.710A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC6, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AC7, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.280A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.092A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.750A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 154 through 163 removed outlier: 5.286A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 9.988A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 10.255A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 13.027A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 11.942A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.482A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.603A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.530A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.063A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.830A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.554A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.554A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.396A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE4, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AE5, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.197A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.156A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.919A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 154 through 163 removed outlier: 9.409A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.316A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.339A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.222A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.266A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.874A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.923A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.667A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.205A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.543A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.543A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.374A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AG2, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.242A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.132A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.154A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.128A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1692 hydrogen bonds defined for protein. 4731 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: 9.47 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10161 1.34 - 1.46: 8978 1.46 - 1.58: 16563 1.58 - 1.71: 0 1.71 - 1.83: 238 Bond restraints: 35940 Sorted by residual: bond pdb=" C1 NAG R 1 " pdb=" O5 NAG R 1 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.53e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.21e+00 ... (remaining 35935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 47865 2.39 - 4.77: 918 4.77 - 7.16: 99 7.16 - 9.55: 13 9.55 - 11.94: 4 Bond angle restraints: 48899 Sorted by residual: angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.28 -5.58 1.22e+00 6.72e-01 2.10e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.24 -5.54 1.22e+00 6.72e-01 2.06e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.06 -5.36 1.22e+00 6.72e-01 1.93e+01 angle pdb=" CB MET D 474 " pdb=" CG MET D 474 " pdb=" SD MET D 474 " ideal model delta sigma weight residual 112.70 124.64 -11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" CB MET E 474 " pdb=" CG MET E 474 " pdb=" SD MET E 474 " ideal model delta sigma weight residual 112.70 124.44 -11.74 3.00e+00 1.11e-01 1.53e+01 ... (remaining 48894 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 20390 18.00 - 35.99: 1504 35.99 - 53.99: 248 53.99 - 71.98: 73 71.98 - 89.97: 40 Dihedral angle restraints: 22255 sinusoidal: 9666 harmonic: 12589 Sorted by residual: dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual 180.00 154.17 25.83 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA PHE C 515 " pdb=" C PHE C 515 " pdb=" N GLU C 516 " pdb=" CA GLU C 516 " ideal model delta harmonic sigma weight residual 180.00 157.25 22.75 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA TRP E 606 " pdb=" C TRP E 606 " pdb=" N SER E 607 " pdb=" CA SER E 607 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 22252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4399 0.061 - 0.123: 1023 0.123 - 0.184: 172 0.184 - 0.245: 21 0.245 - 0.307: 4 Chirality restraints: 5619 Sorted by residual: chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CG LEU C 277 " pdb=" CB LEU C 277 " pdb=" CD1 LEU C 277 " pdb=" CD2 LEU C 277 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 5616 not shown) Planarity restraints: 6295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 524 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C GLN D 524 " 0.056 2.00e-02 2.50e+03 pdb=" O GLN D 524 " -0.021 2.00e-02 2.50e+03 pdb=" N PHE D 525 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 902 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C MET C 902 " 0.055 2.00e-02 2.50e+03 pdb=" O MET C 902 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA C 903 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 524 " 0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C GLN E 524 " -0.055 2.00e-02 2.50e+03 pdb=" O GLN E 524 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE E 525 " 0.019 2.00e-02 2.50e+03 ... (remaining 6292 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 9225 2.81 - 3.33: 30262 3.33 - 3.85: 59257 3.85 - 4.38: 68778 4.38 - 4.90: 118276 Nonbonded interactions: 285798 Sorted by model distance: nonbonded pdb=" OE1 GLN C 115 " pdb=" OG1 THR C 167 " model vdw 2.285 3.040 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.285 3.040 nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.307 3.040 nonbonded pdb=" O ASP A 80 " pdb=" OH TYR A 265 " model vdw 2.317 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.324 3.040 ... (remaining 285793 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = 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' selection = chain 'W' } 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: 4.670 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: 0.040 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 36.320 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.110 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:7.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 36054 Z= 0.219 Angle : 0.807 15.026 49195 Z= 0.421 Chirality : 0.054 0.307 5619 Planarity : 0.007 0.104 6245 Dihedral : 13.353 89.975 14011 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.11), residues: 4260 helix: -0.55 (0.12), residues: 1390 sheet: 0.15 (0.18), residues: 703 loop : -0.87 (0.12), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG B 357 TYR 0.028 0.002 TYR E 385 PHE 0.040 0.002 PHE B 135 TRP 0.019 0.002 TRP D 566 HIS 0.012 0.001 HIS E 493 Details of bonding type rmsd covalent geometry : bond 0.00445 (35940) covalent geometry : angle 0.78110 (48899) SS BOND : bond 0.00200 ( 46) SS BOND : angle 1.32849 ( 92) hydrogen bonds : bond 0.12617 ( 1576) hydrogen bonds : angle 7.18371 ( 4731) link_BETA1-4 : bond 0.00623 ( 18) link_BETA1-4 : angle 1.69401 ( 54) link_NAG-ASN : bond 0.00530 ( 50) link_NAG-ASN : angle 3.54810 ( 150) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.7558 (m-80) cc_final: 0.7264 (m-80) REVERT: A 515 PHE cc_start: 0.8162 (m-80) cc_final: 0.7511 (m-80) REVERT: B 197 ILE cc_start: 0.8773 (mm) cc_final: 0.8483 (mm) REVERT: B 258 TRP cc_start: 0.1184 (p-90) cc_final: 0.0344 (p90) REVERT: C 244 LEU cc_start: 0.5165 (mt) cc_final: 0.4939 (mp) REVERT: C 351 TYR cc_start: 0.8262 (p90) cc_final: 0.8030 (p90) REVERT: C 389 ASP cc_start: 0.8906 (m-30) cc_final: 0.8555 (t0) REVERT: C 565 PHE cc_start: 0.8436 (p90) cc_final: 0.8215 (p90) REVERT: C 572 THR cc_start: 0.8561 (p) cc_final: 0.8348 (p) REVERT: C 1029 MET cc_start: 0.8954 (tpp) cc_final: 0.8677 (tpp) REVERT: C 1141 LEU cc_start: 0.8657 (tt) cc_final: 0.8381 (tm) REVERT: D 83 TYR cc_start: 0.3360 (m-80) cc_final: 0.3070 (m-80) REVERT: D 98 GLN cc_start: 0.4293 (mt0) cc_final: 0.3444 (pp30) REVERT: D 152 MET cc_start: -0.2036 (mmm) cc_final: -0.3164 (pp-130) REVERT: D 165 TRP cc_start: 0.1566 (t60) cc_final: 0.0496 (m-10) REVERT: D 297 MET cc_start: 0.0542 (ttt) cc_final: 0.0002 (tmm) REVERT: D 327 PHE cc_start: -0.2513 (t80) cc_final: -0.2788 (t80) REVERT: D 332 MET cc_start: 0.3481 (ttp) cc_final: 0.3255 (tmm) REVERT: D 365 THR cc_start: 0.1884 (m) cc_final: 0.1079 (p) REVERT: D 366 MET cc_start: 0.2065 (ttp) cc_final: 0.1315 (pmt) REVERT: D 383 MET cc_start: 0.4193 (mtp) cc_final: 0.3575 (mtp) REVERT: D 468 ILE cc_start: -0.1686 (mt) cc_final: -0.2018 (mm) REVERT: D 474 MET cc_start: -0.1471 (mmp) cc_final: -0.2218 (ppp) REVERT: D 480 MET cc_start: 0.2737 (ttm) cc_final: 0.2486 (tpp) REVERT: E 95 LEU cc_start: 0.6243 (mt) cc_final: 0.5907 (mt) REVERT: E 162 LEU cc_start: 0.5092 (tp) cc_final: 0.4820 (pp) REVERT: E 182 GLU cc_start: 0.6537 (mt-10) cc_final: 0.6062 (tp30) REVERT: E 192 ARG cc_start: 0.8297 (mtm110) cc_final: 0.8042 (tmm160) REVERT: E 270 MET cc_start: -0.0106 (tpt) cc_final: -0.0345 (tmt) REVERT: E 271 TRP cc_start: 0.3182 (m-90) cc_final: 0.2483 (p90) REVERT: E 273 ARG cc_start: 0.4811 (ttt90) cc_final: 0.4589 (ptt180) REVERT: E 303 ASP cc_start: 0.6473 (t0) cc_final: 0.6253 (p0) REVERT: E 309 LYS cc_start: 0.7449 (mmtt) cc_final: 0.7130 (ptpp) REVERT: E 332 MET cc_start: 0.2861 (ttp) cc_final: 0.2442 (ppp) REVERT: E 552 GLN cc_start: 0.7382 (mm-40) cc_final: 0.7067 (pp30) REVERT: E 583 PRO cc_start: 0.2421 (Cg_exo) cc_final: 0.1342 (Cg_endo) REVERT: E 594 TRP cc_start: 0.0241 (t60) cc_final: -0.0311 (m100) outliers start: 0 outliers final: 2 residues processed: 348 average time/residue: 0.8234 time to fit residues: 338.3122 Evaluate side-chains 172 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 170 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain D residue 28 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 0.2980 chunk 424 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 856 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 370 ASN ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 HIS D 493 HIS D 599 ASN E 121 ASN E 175 GLN E 325 GLN E 599 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.144783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.092253 restraints weight = 109535.124| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 5.65 r_work: 0.3125 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 36054 Z= 0.211 Angle : 0.619 10.914 49195 Z= 0.315 Chirality : 0.045 0.258 5619 Planarity : 0.005 0.064 6245 Dihedral : 5.984 57.760 6059 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.14 % Allowed : 6.44 % Favored : 92.42 % 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 are not related in a simple way. whole: -0.05 (0.12), residues: 4260 helix: 0.85 (0.13), residues: 1395 sheet: 0.29 (0.18), residues: 749 loop : -0.70 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 245 TYR 0.033 0.002 TYR B 453 PHE 0.024 0.002 PHE D 512 TRP 0.015 0.001 TRP D 203 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00468 (35940) covalent geometry : angle 0.60166 (48899) SS BOND : bond 0.00198 ( 46) SS BOND : angle 0.78322 ( 92) hydrogen bonds : bond 0.04514 ( 1576) hydrogen bonds : angle 5.44745 ( 4731) link_BETA1-4 : bond 0.00228 ( 18) link_BETA1-4 : angle 1.03509 ( 54) link_NAG-ASN : bond 0.00569 ( 50) link_NAG-ASN : angle 2.62666 ( 150) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 179 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7710 (OUTLIER) cc_final: 0.7507 (t80) REVERT: A 515 PHE cc_start: 0.7744 (m-80) cc_final: 0.7512 (m-80) REVERT: B 258 TRP cc_start: 0.1784 (p-90) cc_final: 0.0661 (p90) REVERT: B 950 ASP cc_start: 0.8718 (p0) cc_final: 0.8513 (p0) REVERT: B 983 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8400 (ttp80) REVERT: C 1141 LEU cc_start: 0.8498 (tt) cc_final: 0.8268 (tm) REVERT: D 98 GLN cc_start: 0.4353 (mt0) cc_final: 0.3651 (pp30) REVERT: D 152 MET cc_start: -0.1176 (mmm) cc_final: -0.2049 (pp-130) REVERT: D 270 MET cc_start: -0.1342 (tpt) cc_final: -0.2115 (tpt) REVERT: D 323 MET cc_start: 0.2862 (OUTLIER) cc_final: 0.2149 (tpp) REVERT: D 383 MET cc_start: 0.3583 (mtp) cc_final: 0.3382 (mtp) REVERT: D 444 LEU cc_start: -0.0652 (OUTLIER) cc_final: -0.0913 (tp) REVERT: E 98 GLN cc_start: 0.6941 (mt0) cc_final: 0.6300 (tp-100) REVERT: E 151 ILE cc_start: 0.4418 (mm) cc_final: 0.4134 (pp) REVERT: E 152 MET cc_start: -0.1482 (mtt) cc_final: -0.2290 (mtt) REVERT: E 162 LEU cc_start: 0.5411 (tp) cc_final: 0.5033 (pp) REVERT: E 182 GLU cc_start: 0.6205 (mt-10) cc_final: 0.5802 (tp30) REVERT: E 192 ARG cc_start: 0.8281 (mtm110) cc_final: 0.7986 (tmm160) REVERT: E 271 TRP cc_start: 0.3252 (m-90) cc_final: 0.2730 (m-90) REVERT: E 274 PHE cc_start: 0.5410 (m-10) cc_final: 0.5118 (m-10) REVERT: E 292 ASP cc_start: 0.4115 (t70) cc_final: 0.3663 (p0) REVERT: E 297 MET cc_start: -0.0152 (ttm) cc_final: -0.0406 (ptm) REVERT: E 309 LYS cc_start: 0.7328 (mmtt) cc_final: 0.7074 (ptmm) REVERT: E 455 MET cc_start: 0.3793 (tmm) cc_final: 0.3549 (mmm) REVERT: E 474 MET cc_start: 0.0242 (mmm) cc_final: -0.0001 (mmt) REVERT: E 552 GLN cc_start: 0.7564 (mm-40) cc_final: 0.7274 (pp30) outliers start: 43 outliers final: 8 residues processed: 205 average time/residue: 0.8053 time to fit residues: 195.9917 Evaluate side-chains 156 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 505 HIS Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 46 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 413 optimal weight: 20.0000 chunk 424 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 305 optimal weight: 1.9990 chunk 373 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 206 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN A 955 ASN A 965 GLN A1011 GLN B 14 GLN B 901 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN D 81 GLN E 493 HIS ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.153372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.099015 restraints weight = 94716.161| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 7.17 r_work: 0.3083 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36054 Z= 0.142 Angle : 0.555 10.663 49195 Z= 0.279 Chirality : 0.043 0.260 5619 Planarity : 0.004 0.038 6245 Dihedral : 5.605 57.971 6057 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.95 % Allowed : 8.26 % Favored : 90.79 % 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 are not related in a simple way. whole: 0.30 (0.12), residues: 4260 helix: 1.34 (0.14), residues: 1401 sheet: 0.29 (0.19), residues: 724 loop : -0.57 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 169 TYR 0.021 0.001 TYR C1067 PHE 0.018 0.001 PHE D 555 TRP 0.025 0.001 TRP D 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00313 (35940) covalent geometry : angle 0.53840 (48899) SS BOND : bond 0.00146 ( 46) SS BOND : angle 0.64127 ( 92) hydrogen bonds : bond 0.04058 ( 1576) hydrogen bonds : angle 5.17400 ( 4731) link_BETA1-4 : bond 0.00264 ( 18) link_BETA1-4 : angle 0.93979 ( 54) link_NAG-ASN : bond 0.00493 ( 50) link_NAG-ASN : angle 2.42364 ( 150) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 258 TRP cc_start: 0.2022 (p-90) cc_final: 0.0860 (p90) REVERT: B 950 ASP cc_start: 0.8792 (p0) cc_final: 0.8590 (p0) REVERT: B 983 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8363 (ttp80) REVERT: C 423 TYR cc_start: 0.7719 (t80) cc_final: 0.7409 (t80) REVERT: C 1142 GLN cc_start: 0.8495 (tp40) cc_final: 0.7931 (tp40) REVERT: D 98 GLN cc_start: 0.4160 (mt0) cc_final: 0.3457 (pp30) REVERT: D 152 MET cc_start: -0.0624 (mmm) cc_final: -0.1801 (pp-130) REVERT: D 270 MET cc_start: -0.1145 (tpt) cc_final: -0.1807 (tpt) REVERT: E 98 GLN cc_start: 0.7082 (mt0) cc_final: 0.6428 (tp-100) REVERT: E 151 ILE cc_start: 0.4418 (OUTLIER) cc_final: 0.4107 (pp) REVERT: E 162 LEU cc_start: 0.5510 (tp) cc_final: 0.5103 (pp) REVERT: E 182 GLU cc_start: 0.6086 (mt-10) cc_final: 0.5732 (mm-30) REVERT: E 192 ARG cc_start: 0.8195 (mtm110) cc_final: 0.7870 (tmm160) REVERT: E 270 MET cc_start: 0.1616 (OUTLIER) cc_final: 0.1301 (tpp) REVERT: E 309 LYS cc_start: 0.7298 (mmtt) cc_final: 0.7012 (tptp) REVERT: E 552 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7320 (pp30) outliers start: 36 outliers final: 8 residues processed: 189 average time/residue: 0.7747 time to fit residues: 175.1291 Evaluate side-chains 153 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 505 HIS Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 175 optimal weight: 0.7980 chunk 243 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 30 optimal weight: 40.0000 chunk 155 optimal weight: 0.7980 chunk 309 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 288 optimal weight: 0.5980 chunk 424 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN A 955 ASN A1011 GLN B 14 GLN B 321 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 HIS E 531 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.154923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.098201 restraints weight = 106752.147| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 6.75 r_work: 0.3095 rms_B_bonded: 5.75 restraints_weight: 2.0000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36054 Z= 0.135 Angle : 0.538 10.594 49195 Z= 0.270 Chirality : 0.043 0.259 5619 Planarity : 0.004 0.036 6245 Dihedral : 5.296 58.904 6057 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.29 % Allowed : 8.87 % Favored : 89.84 % 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 are not related in a simple way. whole: 0.44 (0.13), residues: 4260 helix: 1.52 (0.14), residues: 1401 sheet: 0.22 (0.19), residues: 690 loop : -0.46 (0.13), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 567 TYR 0.022 0.001 TYR D 516 PHE 0.029 0.001 PHE C 515 TRP 0.036 0.001 TRP D 473 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00298 (35940) covalent geometry : angle 0.52197 (48899) SS BOND : bond 0.00134 ( 46) SS BOND : angle 0.57916 ( 92) hydrogen bonds : bond 0.03845 ( 1576) hydrogen bonds : angle 4.98797 ( 4731) link_BETA1-4 : bond 0.00231 ( 18) link_BETA1-4 : angle 0.96972 ( 54) link_NAG-ASN : bond 0.00484 ( 50) link_NAG-ASN : angle 2.33650 ( 150) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 161 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 856 ASN cc_start: 0.6112 (OUTLIER) cc_final: 0.5462 (p0) REVERT: A 1002 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8286 (tm-30) REVERT: B 950 ASP cc_start: 0.8761 (p0) cc_final: 0.8554 (p0) REVERT: B 983 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8408 (ttp80) REVERT: B 1111 GLU cc_start: 0.8933 (tt0) cc_final: 0.8726 (tt0) REVERT: C 423 TYR cc_start: 0.7797 (t80) cc_final: 0.7490 (t80) REVERT: C 1142 GLN cc_start: 0.8507 (tp40) cc_final: 0.7951 (tp40) REVERT: D 98 GLN cc_start: 0.4144 (mt0) cc_final: 0.3381 (pp30) REVERT: D 152 MET cc_start: -0.0598 (mmm) cc_final: -0.1946 (pp-130) REVERT: D 270 MET cc_start: -0.1730 (tpt) cc_final: -0.2334 (tpt) REVERT: E 98 GLN cc_start: 0.7145 (mt0) cc_final: 0.6578 (tp-100) REVERT: E 151 ILE cc_start: 0.4236 (mm) cc_final: 0.3950 (pp) REVERT: E 162 LEU cc_start: 0.5401 (tp) cc_final: 0.4862 (pp) REVERT: E 165 TRP cc_start: -0.1471 (t60) cc_final: -0.2009 (t60) REVERT: E 182 GLU cc_start: 0.6123 (mt-10) cc_final: 0.5832 (mm-30) REVERT: E 192 ARG cc_start: 0.8250 (mtm110) cc_final: 0.8038 (tmm160) REVERT: E 309 LYS cc_start: 0.7326 (mmtt) cc_final: 0.7091 (tptp) REVERT: E 455 MET cc_start: 0.4243 (tmm) cc_final: 0.3990 (mmm) REVERT: E 552 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7401 (pp30) outliers start: 49 outliers final: 11 residues processed: 197 average time/residue: 0.7160 time to fit residues: 170.0085 Evaluate side-chains 158 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 168 optimal weight: 3.9990 chunk 241 optimal weight: 8.9990 chunk 198 optimal weight: 2.9990 chunk 290 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 chunk 396 optimal weight: 30.0000 chunk 162 optimal weight: 0.9990 chunk 313 optimal weight: 30.0000 chunk 84 optimal weight: 3.9990 chunk 235 optimal weight: 0.9990 chunk 193 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 755 GLN B 14 GLN B 824 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.154667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.099640 restraints weight = 107411.991| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 5.69 r_work: 0.3071 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 36054 Z= 0.181 Angle : 0.561 10.540 49195 Z= 0.279 Chirality : 0.043 0.257 5619 Planarity : 0.004 0.037 6245 Dihedral : 5.229 57.176 6057 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.14 % Allowed : 10.03 % Favored : 88.83 % 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 are not related in a simple way. whole: 0.51 (0.13), residues: 4260 helix: 1.67 (0.14), residues: 1393 sheet: 0.16 (0.19), residues: 698 loop : -0.44 (0.13), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 567 TYR 0.020 0.001 TYR C1067 PHE 0.031 0.001 PHE C 392 TRP 0.030 0.001 TRP D 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00404 (35940) covalent geometry : angle 0.54517 (48899) SS BOND : bond 0.00157 ( 46) SS BOND : angle 0.63962 ( 92) hydrogen bonds : bond 0.03947 ( 1576) hydrogen bonds : angle 4.97413 ( 4731) link_BETA1-4 : bond 0.00154 ( 18) link_BETA1-4 : angle 1.03553 ( 54) link_NAG-ASN : bond 0.00505 ( 50) link_NAG-ASN : angle 2.37379 ( 150) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 155 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1002 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8229 (tm-30) REVERT: B 197 ILE cc_start: 0.8566 (mp) cc_final: 0.8016 (mm) REVERT: B 950 ASP cc_start: 0.8826 (p0) cc_final: 0.8624 (p0) REVERT: B 983 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8419 (ttp80) REVERT: C 214 ARG cc_start: 0.8869 (tmm-80) cc_final: 0.8523 (ttp80) REVERT: C 423 TYR cc_start: 0.7869 (t80) cc_final: 0.7370 (t80) REVERT: C 1142 GLN cc_start: 0.8541 (tp40) cc_final: 0.7965 (tp40) REVERT: D 98 GLN cc_start: 0.4119 (mt0) cc_final: 0.3466 (pp30) REVERT: D 152 MET cc_start: -0.0271 (mmm) cc_final: -0.1963 (pp-130) REVERT: D 270 MET cc_start: -0.1223 (tpt) cc_final: -0.2021 (tpt) REVERT: D 366 MET cc_start: 0.1831 (ttp) cc_final: 0.1063 (pmm) REVERT: D 474 MET cc_start: -0.0510 (mmm) cc_final: -0.1989 (pp-130) REVERT: E 98 GLN cc_start: 0.7130 (mt0) cc_final: 0.6570 (tp-100) REVERT: E 151 ILE cc_start: 0.4294 (mm) cc_final: 0.3993 (pp) REVERT: E 162 LEU cc_start: 0.5377 (tp) cc_final: 0.4880 (pp) REVERT: E 165 TRP cc_start: -0.1510 (t60) cc_final: -0.2020 (t60) REVERT: E 192 ARG cc_start: 0.8208 (mtm110) cc_final: 0.7891 (tmm160) REVERT: E 309 LYS cc_start: 0.7381 (mmtt) cc_final: 0.7127 (tptp) REVERT: E 455 MET cc_start: 0.4531 (tmm) cc_final: 0.4240 (mtp) REVERT: E 552 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7664 (pp30) outliers start: 43 outliers final: 16 residues processed: 188 average time/residue: 0.6770 time to fit residues: 154.6287 Evaluate side-chains 159 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 505 HIS Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 202 optimal weight: 0.9990 chunk 216 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 chunk 240 optimal weight: 3.9990 chunk 416 optimal weight: 8.9990 chunk 187 optimal weight: 10.0000 chunk 306 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 370 optimal weight: 1.9990 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 824 ASN A 856 ASN B 14 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 535 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.144258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.090659 restraints weight = 111724.241| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 5.12 r_work: 0.3104 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 36054 Z= 0.142 Angle : 0.535 10.531 49195 Z= 0.268 Chirality : 0.043 0.259 5619 Planarity : 0.003 0.037 6245 Dihedral : 5.084 55.410 6057 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.19 % Allowed : 10.72 % Favored : 88.09 % 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 are not related in a simple way. whole: 0.59 (0.13), residues: 4260 helix: 1.72 (0.14), residues: 1401 sheet: 0.11 (0.19), residues: 701 loop : -0.36 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 567 TYR 0.020 0.001 TYR C1067 PHE 0.030 0.001 PHE D 523 TRP 0.035 0.001 TRP D 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00316 (35940) covalent geometry : angle 0.51977 (48899) SS BOND : bond 0.00141 ( 46) SS BOND : angle 0.55766 ( 92) hydrogen bonds : bond 0.03767 ( 1576) hydrogen bonds : angle 4.88716 ( 4731) link_BETA1-4 : bond 0.00246 ( 18) link_BETA1-4 : angle 0.96372 ( 54) link_NAG-ASN : bond 0.00461 ( 50) link_NAG-ASN : angle 2.30181 ( 150) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 144 time to evaluate : 1.260 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 1002 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8204 (tm-30) REVERT: B 197 ILE cc_start: 0.8649 (mp) cc_final: 0.8169 (mm) REVERT: B 983 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8444 (ttp80) REVERT: B 1050 MET cc_start: 0.9413 (OUTLIER) cc_final: 0.8894 (ptp) REVERT: C 214 ARG cc_start: 0.8820 (tmm-80) cc_final: 0.8506 (ttp80) REVERT: C 309 GLU cc_start: 0.8799 (mp0) cc_final: 0.8450 (pm20) REVERT: C 423 TYR cc_start: 0.7509 (t80) cc_final: 0.7255 (t80) REVERT: C 1142 GLN cc_start: 0.8628 (tp40) cc_final: 0.8183 (tp40) REVERT: D 98 GLN cc_start: 0.4131 (mt0) cc_final: 0.3387 (pp30) REVERT: D 152 MET cc_start: -0.0412 (mmm) cc_final: -0.2239 (pp-130) REVERT: D 165 TRP cc_start: 0.1579 (t60) cc_final: 0.0958 (m-10) REVERT: D 366 MET cc_start: 0.1538 (ttp) cc_final: 0.0917 (pmm) REVERT: D 474 MET cc_start: -0.1162 (mmm) cc_final: -0.2056 (pp-130) REVERT: E 98 GLN cc_start: 0.7102 (mt0) cc_final: 0.6442 (tp-100) REVERT: E 151 ILE cc_start: 0.4272 (mm) cc_final: 0.3974 (pp) REVERT: E 162 LEU cc_start: 0.5305 (tp) cc_final: 0.4532 (pp) REVERT: E 192 ARG cc_start: 0.8159 (mtm110) cc_final: 0.7799 (tmm160) REVERT: E 309 LYS cc_start: 0.7459 (mmtt) cc_final: 0.7133 (tptp) REVERT: E 455 MET cc_start: 0.4473 (tmm) cc_final: 0.4183 (ttm) REVERT: E 552 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7564 (pp30) outliers start: 45 outliers final: 15 residues processed: 178 average time/residue: 0.6753 time to fit residues: 145.5092 Evaluate side-chains 151 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 505 HIS Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 129 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 427 optimal weight: 8.9990 chunk 364 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 404 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 249 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN B 14 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.144756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.084149 restraints weight = 108471.385| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 5.08 r_work: 0.3075 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 36054 Z= 0.182 Angle : 0.556 10.945 49195 Z= 0.279 Chirality : 0.043 0.256 5619 Planarity : 0.004 0.044 6245 Dihedral : 5.082 56.323 6057 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.11 % Allowed : 10.93 % Favored : 87.96 % 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 are not related in a simple way. whole: 0.59 (0.13), residues: 4260 helix: 1.72 (0.14), residues: 1393 sheet: 0.02 (0.19), residues: 693 loop : -0.31 (0.13), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 567 TYR 0.020 0.001 TYR C1067 PHE 0.021 0.001 PHE D 523 TRP 0.033 0.001 TRP E 165 HIS 0.007 0.001 HIS E 265 Details of bonding type rmsd covalent geometry : bond 0.00407 (35940) covalent geometry : angle 0.54083 (48899) SS BOND : bond 0.00143 ( 46) SS BOND : angle 0.61835 ( 92) hydrogen bonds : bond 0.03928 ( 1576) hydrogen bonds : angle 4.90791 ( 4731) link_BETA1-4 : bond 0.00198 ( 18) link_BETA1-4 : angle 1.07607 ( 54) link_NAG-ASN : bond 0.00487 ( 50) link_NAG-ASN : angle 2.32931 ( 150) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 1.394 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 1002 GLN cc_start: 0.8803 (tm-30) cc_final: 0.8196 (tm-30) REVERT: B 197 ILE cc_start: 0.8640 (mp) cc_final: 0.8177 (mm) REVERT: B 983 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8420 (ttp80) REVERT: B 1050 MET cc_start: 0.9407 (OUTLIER) cc_final: 0.8941 (ptp) REVERT: C 126 VAL cc_start: 0.7977 (OUTLIER) cc_final: 0.7720 (t) REVERT: C 309 GLU cc_start: 0.8853 (mp0) cc_final: 0.8552 (pm20) REVERT: C 423 TYR cc_start: 0.7154 (t80) cc_final: 0.6934 (t80) REVERT: C 1142 GLN cc_start: 0.8654 (tp40) cc_final: 0.8218 (tp40) REVERT: D 98 GLN cc_start: 0.4122 (mt0) cc_final: 0.3516 (pp30) REVERT: D 152 MET cc_start: 0.1031 (mmm) cc_final: -0.2733 (pp-130) REVERT: D 249 MET cc_start: 0.1649 (mmp) cc_final: 0.1027 (ptt) REVERT: D 270 MET cc_start: -0.0633 (mmm) cc_final: -0.1837 (mmm) REVERT: D 366 MET cc_start: 0.1968 (ttp) cc_final: 0.1350 (pmm) REVERT: E 98 GLN cc_start: 0.7265 (mt0) cc_final: 0.6700 (tp-100) REVERT: E 162 LEU cc_start: 0.5055 (tp) cc_final: 0.4836 (tp) REVERT: E 163 TRP cc_start: 0.3078 (t60) cc_final: 0.2798 (m-10) REVERT: E 192 ARG cc_start: 0.8155 (mtm110) cc_final: 0.7934 (tmm160) REVERT: E 270 MET cc_start: 0.3270 (tmm) cc_final: 0.2883 (tpp) REVERT: E 309 LYS cc_start: 0.7272 (mmtt) cc_final: 0.7009 (tptp) REVERT: E 552 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7733 (pp30) outliers start: 42 outliers final: 18 residues processed: 173 average time/residue: 0.7006 time to fit residues: 146.0272 Evaluate side-chains 152 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 505 HIS Chi-restraints excluded: chain E residue 363 LYS Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 520 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 317 optimal weight: 9.9990 chunk 342 optimal weight: 0.7980 chunk 235 optimal weight: 8.9990 chunk 374 optimal weight: 20.0000 chunk 428 optimal weight: 0.9990 chunk 325 optimal weight: 20.0000 chunk 266 optimal weight: 5.9990 chunk 259 optimal weight: 5.9990 chunk 396 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN B 14 GLN B 218 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.144754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.083994 restraints weight = 108778.969| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 4.74 r_work: 0.3076 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 36054 Z= 0.173 Angle : 0.556 12.029 49195 Z= 0.277 Chirality : 0.043 0.260 5619 Planarity : 0.004 0.069 6245 Dihedral : 5.025 56.334 6057 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.06 % Allowed : 11.43 % Favored : 87.51 % 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 are not related in a simple way. whole: 0.63 (0.13), residues: 4260 helix: 1.78 (0.14), residues: 1397 sheet: -0.10 (0.19), residues: 708 loop : -0.25 (0.13), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 214 TYR 0.033 0.001 TYR D 237 PHE 0.019 0.001 PHE E 274 TRP 0.041 0.001 TRP D 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00388 (35940) covalent geometry : angle 0.54163 (48899) SS BOND : bond 0.00134 ( 46) SS BOND : angle 0.58755 ( 92) hydrogen bonds : bond 0.03856 ( 1576) hydrogen bonds : angle 4.88471 ( 4731) link_BETA1-4 : bond 0.00238 ( 18) link_BETA1-4 : angle 1.01519 ( 54) link_NAG-ASN : bond 0.00473 ( 50) link_NAG-ASN : angle 2.31352 ( 150) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 1.417 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 1002 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8225 (tm-30) REVERT: B 197 ILE cc_start: 0.8655 (mp) cc_final: 0.8196 (mm) REVERT: B 740 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8668 (ttp) REVERT: B 983 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8446 (ttp80) REVERT: B 1050 MET cc_start: 0.9425 (OUTLIER) cc_final: 0.8964 (ptp) REVERT: B 1142 GLN cc_start: 0.9067 (tp40) cc_final: 0.8644 (tm-30) REVERT: C 126 VAL cc_start: 0.8023 (OUTLIER) cc_final: 0.7736 (t) REVERT: C 309 GLU cc_start: 0.8812 (mp0) cc_final: 0.8521 (pm20) REVERT: C 423 TYR cc_start: 0.6846 (t80) cc_final: 0.6597 (t80) REVERT: C 1142 GLN cc_start: 0.8563 (tp40) cc_final: 0.8084 (tp40) REVERT: D 98 GLN cc_start: 0.4145 (mt0) cc_final: 0.3504 (pp30) REVERT: D 249 MET cc_start: 0.1903 (mmp) cc_final: 0.1254 (ptt) REVERT: D 366 MET cc_start: 0.1682 (ttp) cc_final: 0.1053 (pmm) REVERT: E 98 GLN cc_start: 0.7221 (mt0) cc_final: 0.6654 (tp-100) REVERT: E 162 LEU cc_start: 0.5170 (tp) cc_final: 0.4919 (pp) REVERT: E 192 ARG cc_start: 0.8158 (mtm110) cc_final: 0.7915 (tmm160) REVERT: E 270 MET cc_start: 0.3172 (tmm) cc_final: 0.2874 (tpp) REVERT: E 309 LYS cc_start: 0.7163 (mmtt) cc_final: 0.6882 (tptp) REVERT: E 455 MET cc_start: 0.4278 (tmm) cc_final: 0.3999 (mmm) REVERT: E 552 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7772 (pp30) outliers start: 40 outliers final: 17 residues processed: 171 average time/residue: 0.6781 time to fit residues: 140.8858 Evaluate side-chains 154 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 505 HIS Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 566 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 212 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 334 optimal weight: 40.0000 chunk 98 optimal weight: 1.9990 chunk 399 optimal weight: 10.0000 chunk 382 optimal weight: 0.4980 chunk 335 optimal weight: 0.0770 chunk 363 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN B 14 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN E 437 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.142337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.089788 restraints weight = 114961.351| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 6.27 r_work: 0.3078 rms_B_bonded: 5.32 restraints_weight: 2.0000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 36054 Z= 0.117 Angle : 0.538 10.651 49195 Z= 0.268 Chirality : 0.043 0.260 5619 Planarity : 0.004 0.037 6245 Dihedral : 4.849 55.596 6057 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.71 % Allowed : 12.01 % 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 are not related in a simple way. whole: 0.67 (0.13), residues: 4260 helix: 1.84 (0.14), residues: 1401 sheet: -0.11 (0.19), residues: 715 loop : -0.24 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 214 TYR 0.027 0.001 TYR D 521 PHE 0.016 0.001 PHE E 274 TRP 0.054 0.001 TRP D 165 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00259 (35940) covalent geometry : angle 0.52408 (48899) SS BOND : bond 0.00123 ( 46) SS BOND : angle 0.51511 ( 92) hydrogen bonds : bond 0.03602 ( 1576) hydrogen bonds : angle 4.77646 ( 4731) link_BETA1-4 : bond 0.00295 ( 18) link_BETA1-4 : angle 0.91854 ( 54) link_NAG-ASN : bond 0.00438 ( 50) link_NAG-ASN : angle 2.23663 ( 150) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 1.470 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 856 ASN cc_start: 0.6625 (OUTLIER) cc_final: 0.6330 (p0) REVERT: A 1002 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8203 (tm-30) REVERT: B 197 ILE cc_start: 0.8677 (mp) cc_final: 0.8285 (mm) REVERT: B 983 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8451 (ttp80) REVERT: B 1142 GLN cc_start: 0.9087 (tp40) cc_final: 0.8659 (tm-30) REVERT: C 126 VAL cc_start: 0.7874 (OUTLIER) cc_final: 0.7599 (t) REVERT: C 153 MET cc_start: 0.5760 (tpp) cc_final: 0.5403 (tmt) REVERT: C 423 TYR cc_start: 0.6398 (t80) cc_final: 0.6170 (t80) REVERT: C 1142 GLN cc_start: 0.8568 (tp40) cc_final: 0.8026 (tp40) REVERT: D 98 GLN cc_start: 0.4168 (mt0) cc_final: 0.3478 (pp30) REVERT: D 152 MET cc_start: 0.0504 (mmt) cc_final: -0.2269 (pp-130) REVERT: D 165 TRP cc_start: 0.1911 (t60) cc_final: 0.0961 (m-10) REVERT: D 249 MET cc_start: 0.1902 (mmp) cc_final: 0.1041 (ptt) REVERT: D 366 MET cc_start: 0.1672 (ttp) cc_final: 0.1011 (pmm) REVERT: D 423 LEU cc_start: 0.3858 (tp) cc_final: 0.3619 (tp) REVERT: D 499 ASP cc_start: 0.1979 (m-30) cc_final: 0.1621 (m-30) REVERT: E 98 GLN cc_start: 0.7087 (mt0) cc_final: 0.6578 (tp-100) REVERT: E 162 LEU cc_start: 0.5136 (tp) cc_final: 0.4833 (pp) REVERT: E 192 ARG cc_start: 0.8054 (mtm110) cc_final: 0.7766 (tmm160) REVERT: E 270 MET cc_start: 0.3045 (tmm) cc_final: 0.2751 (tpp) REVERT: E 309 LYS cc_start: 0.7147 (mmtt) cc_final: 0.6880 (tptp) REVERT: E 383 MET cc_start: 0.5588 (ttm) cc_final: 0.5287 (ptm) REVERT: E 455 MET cc_start: 0.4317 (tmm) cc_final: 0.4021 (ttp) REVERT: E 552 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7767 (pp30) outliers start: 27 outliers final: 13 residues processed: 164 average time/residue: 0.6753 time to fit residues: 133.7240 Evaluate side-chains 149 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 505 HIS Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 344 optimal weight: 0.5980 chunk 230 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 363 optimal weight: 7.9990 chunk 262 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 372 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 40 optimal weight: 40.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.141904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.090115 restraints weight = 115964.569| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 5.27 r_work: 0.3068 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.252 36054 Z= 0.194 Angle : 0.664 59.197 49195 Z= 0.348 Chirality : 0.047 1.000 5619 Planarity : 0.004 0.037 6245 Dihedral : 4.874 55.619 6057 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.58 % Allowed : 12.12 % Favored : 87.30 % Cbeta Deviations : 0.02 % 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 are not related in a simple way. whole: 0.68 (0.13), residues: 4260 helix: 1.85 (0.14), residues: 1395 sheet: -0.11 (0.19), residues: 715 loop : -0.23 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C 214 TYR 0.036 0.001 TYR A 904 PHE 0.029 0.001 PHE C 377 TRP 0.064 0.002 TRP B 258 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00435 (35940) covalent geometry : angle 0.65365 (48899) SS BOND : bond 0.00142 ( 46) SS BOND : angle 0.54767 ( 92) hydrogen bonds : bond 0.03633 ( 1576) hydrogen bonds : angle 4.77203 ( 4731) link_BETA1-4 : bond 0.00391 ( 18) link_BETA1-4 : angle 0.94018 ( 54) link_NAG-ASN : bond 0.00431 ( 50) link_NAG-ASN : angle 2.22860 ( 150) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 1.302 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 1002 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8206 (tm-30) REVERT: B 197 ILE cc_start: 0.8627 (mp) cc_final: 0.8184 (mm) REVERT: B 983 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8440 (ttp80) REVERT: B 1050 MET cc_start: 0.9404 (OUTLIER) cc_final: 0.8807 (ptp) REVERT: B 1142 GLN cc_start: 0.9119 (tp40) cc_final: 0.8691 (tm-30) REVERT: C 126 VAL cc_start: 0.7958 (OUTLIER) cc_final: 0.7682 (t) REVERT: C 423 TYR cc_start: 0.7040 (t80) cc_final: 0.6813 (t80) REVERT: C 1142 GLN cc_start: 0.8611 (tp40) cc_final: 0.8017 (tp40) REVERT: D 98 GLN cc_start: 0.4143 (mt0) cc_final: 0.3445 (pp30) REVERT: D 152 MET cc_start: 0.0661 (mmt) cc_final: -0.2143 (pp-130) REVERT: D 165 TRP cc_start: 0.1651 (t60) cc_final: 0.0716 (m-10) REVERT: D 249 MET cc_start: 0.1905 (mmp) cc_final: 0.1144 (ptt) REVERT: D 366 MET cc_start: 0.1580 (ttp) cc_final: 0.0901 (pmm) REVERT: D 423 LEU cc_start: 0.4072 (tp) cc_final: 0.3857 (tp) REVERT: D 499 ASP cc_start: 0.1892 (m-30) cc_final: 0.1499 (m-30) REVERT: E 98 GLN cc_start: 0.7157 (mt0) cc_final: 0.6619 (tp-100) REVERT: E 162 LEU cc_start: 0.5127 (tp) cc_final: 0.4857 (pp) REVERT: E 192 ARG cc_start: 0.8064 (mtm110) cc_final: 0.7812 (tmm160) REVERT: E 270 MET cc_start: 0.3158 (tmm) cc_final: 0.2814 (tpp) REVERT: E 309 LYS cc_start: 0.7160 (mmtt) cc_final: 0.6865 (tptp) REVERT: E 383 MET cc_start: 0.5595 (ttm) cc_final: 0.5278 (ptm) REVERT: E 455 MET cc_start: 0.4343 (tmm) cc_final: 0.4028 (mmm) REVERT: E 552 GLN cc_start: 0.7968 (mm-40) cc_final: 0.7707 (pp30) outliers start: 22 outliers final: 12 residues processed: 149 average time/residue: 0.7156 time to fit residues: 127.5726 Evaluate side-chains 147 residues out of total 3788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 505 HIS Chi-restraints excluded: chain E residue 446 ILE Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 201 optimal weight: 2.9990 chunk 401 optimal weight: 20.0000 chunk 63 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 381 optimal weight: 8.9990 chunk 315 optimal weight: 9.9990 chunk 367 optimal weight: 5.9990 chunk 266 optimal weight: 5.9990 chunk 379 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 277 optimal weight: 2.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.142006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.088977 restraints weight = 115733.133| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 6.22 r_work: 0.3091 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.252 36054 Z= 0.194 Angle : 0.664 59.197 49195 Z= 0.348 Chirality : 0.047 1.000 5619 Planarity : 0.004 0.037 6245 Dihedral : 4.825 55.619 6055 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.42 % Allowed : 12.28 % Favored : 87.30 % Cbeta Deviations : 0.02 % 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 are not related in a simple way. whole: 0.68 (0.13), residues: 4260 helix: 1.85 (0.14), residues: 1395 sheet: -0.11 (0.19), residues: 715 loop : -0.23 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C 214 TYR 0.036 0.001 TYR A 904 PHE 0.029 0.001 PHE C 377 TRP 0.064 0.002 TRP B 258 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00435 (35940) covalent geometry : angle 0.65365 (48899) SS BOND : bond 0.00142 ( 46) SS BOND : angle 0.54767 ( 92) hydrogen bonds : bond 0.03633 ( 1576) hydrogen bonds : angle 4.77203 ( 4731) link_BETA1-4 : bond 0.00391 ( 18) link_BETA1-4 : angle 0.94018 ( 54) link_NAG-ASN : bond 0.00431 ( 50) link_NAG-ASN : angle 2.22860 ( 150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22868.40 seconds wall clock time: 387 minutes 11.56 seconds (23231.56 seconds total)