Starting phenix.real_space_refine on Fri Mar 6 10:52:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wt8_32771/03_2026/7wt8_32771.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wt8_32771/03_2026/7wt8_32771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wt8_32771/03_2026/7wt8_32771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wt8_32771/03_2026/7wt8_32771.map" model { file = "/net/cci-nas-00/data/ceres_data/7wt8_32771/03_2026/7wt8_32771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wt8_32771/03_2026/7wt8_32771.cif" } resolution = 3.6 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= -0.002 sd= 0.076 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 133 5.16 5 C 19238 2.51 5 N 4959 2.21 5 O 5910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s 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: 30240 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Chain: "B" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Chain: "C" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Chain: "D" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 900 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "J" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 900 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 7.31, per 1000 atoms: 0.24 Number of scatterers: 30240 At special positions: 0 Unit cell: (147.66, 147.66, 246.1, 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 133 16.00 O 5910 8.00 N 4959 7.00 C 19238 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, 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 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.04 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.04 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.04 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 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.04 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.04 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.04 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.04 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " 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 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 286 " - pdb=" SG CYS C 296 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 356 " distance=2.03 Simple disulfide: pdb=" SG CYS C 374 " - pdb=" SG CYS C 427 " distance=2.03 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 520 " distance=2.04 Simple disulfide: pdb=" SG CYS C 475 " - pdb=" SG CYS C 483 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 644 " distance=2.03 Simple disulfide: pdb=" SG CYS C 657 " - pdb=" SG CYS C 666 " distance=2.03 Simple disulfide: pdb=" SG CYS C 733 " - pdb=" SG CYS C 755 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 744 " distance=2.03 Simple disulfide: pdb=" SG CYS C1027 " - pdb=" SG CYS C1038 " distance=2.03 Simple disulfide: pdb=" SG CYS C1077 " - pdb=" SG CYS C1121 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 95 " 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=2, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG 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 17 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 162 " " NAG A1304 " - " ASN A 340 " " NAG A1305 " - " ASN A 600 " " NAG A1306 " - " ASN A 613 " " NAG A1307 " - " ASN A 654 " " NAG A1308 " - " ASN A 706 " " NAG A1309 " - " ASN A1071 " " NAG B1301 " - " ASN B 17 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 122 " " NAG B1304 " - " ASN B 162 " " NAG B1306 " - " ASN B 328 " " NAG B1307 " - " ASN B 600 " " NAG B1308 " - " ASN B 613 " " NAG B1309 " - " ASN B 654 " " NAG B1310 " - " ASN B 706 " " NAG B1311 " - " ASN B1071 " " NAG C1301 " - " ASN C 17 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 162 " " NAG C1305 " - " ASN C 277 " " NAG C1306 " - " ASN C 338 " " NAG C1307 " - " ASN C 598 " " NAG C1308 " - " ASN C 611 " " NAG C1309 " - " ASN C 652 " " NAG C1310 " - " ASN C 704 " " NAG C1311 " - " ASN C1069 " " NAG E 1 " - " ASN A 279 " " NAG F 1 " - " ASN A 328 " " NAG G 1 " - " ASN A 714 " " NAG K 1 " - " ASN A 798 " " NAG L 1 " - " ASN A1095 " " NAG M 1 " - " ASN A1131 " " NAG N 1 " - " ASN B 340 " " NAG O 1 " - " ASN B 714 " " NAG P 1 " - " ASN B 798 " " NAG Q 1 " - " ASN B1095 " " NAG R 1 " - " ASN B1131 " " NAG S 1 " - " ASN C 326 " " NAG T 1 " - " ASN C 712 " " NAG U 1 " - " ASN C 796 " " NAG V 1 " - " ASN C1093 " " NAG W 1 " - " ASN C1129 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 1.2 seconds 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7026 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 58 sheets defined 20.0% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.853A pdb=" N LEU A 365 " --> pdb=" O TYR A 362 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A 366 " --> pdb=" O SER A 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 366' Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.942A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 3.682A pdb=" N ILE A 407 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A 408 " --> pdb=" O ARG A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 632 through 636 removed outlier: 3.724A pdb=" N THR A 635 " --> pdb=" O VAL A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 744 through 749 removed outlier: 3.573A pdb=" N ASN A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 749 " --> pdb=" O GLU A 745 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 744 through 749' Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 763 through 779 removed outlier: 3.738A pdb=" N GLU A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A 771 " --> pdb=" O ILE A 767 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 824 removed outlier: 3.857A pdb=" N VAL A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 879 removed outlier: 3.710A pdb=" N ILE A 879 " --> pdb=" O LEU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 887 Processing helix chain 'A' and resid 894 through 899 Processing helix chain 'A' and resid 900 through 902 No H-bonds generated for 'chain 'A' and resid 900 through 902' Processing helix chain 'A' and resid 913 through 915 No H-bonds generated for 'chain 'A' and resid 913 through 915' Processing helix chain 'A' and resid 916 through 938 removed outlier: 3.597A pdb=" N ILE A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 936 " --> pdb=" O GLN A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.603A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU A 956 " --> pdb=" O ASN A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 removed outlier: 3.747A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1027 removed outlier: 3.645A pdb=" N ALA A 986 " --> pdb=" O ASP A 982 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG A 992 " --> pdb=" O VAL A 988 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A1003 " --> pdb=" O GLN A 999 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR A1004 " --> pdb=" O SER A1000 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A1017 " --> pdb=" O ALA A1013 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A1021 " --> pdb=" O ALA A1017 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A1024 " --> pdb=" O ASN A1020 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A1027 " --> pdb=" O ALA A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1147 removed outlier: 4.082A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A1145 " --> pdb=" O GLU A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1156 Processing helix chain 'B' and resid 291 through 300 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.800A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 4.405A pdb=" N ALA B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 382 No H-bonds generated for 'chain 'B' and resid 380 through 382' Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.611A pdb=" N LEU B 387 " --> pdb=" O LYS B 383 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N CYS B 388 " --> pdb=" O LEU B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 383 through 388' Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.793A pdb=" N ILE B 407 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 630 through 635 removed outlier: 4.127A pdb=" N TYR B 633 " --> pdb=" O TRP B 630 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR B 635 " --> pdb=" O VAL B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 754 removed outlier: 3.564A pdb=" N SER B 747 " --> pdb=" O SER B 743 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY B 754 " --> pdb=" O LEU B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 780 removed outlier: 4.134A pdb=" N GLN B 759 " --> pdb=" O SER B 755 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 760 " --> pdb=" O PHE B 756 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR B 775 " --> pdb=" O GLN B 771 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN B 776 " --> pdb=" O ASP B 772 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 777 " --> pdb=" O LYS B 773 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL B 778 " --> pdb=" O ASN B 774 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B 780 " --> pdb=" O GLN B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 removed outlier: 3.599A pdb=" N LEU B 818 " --> pdb=" O PRO B 814 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN B 821 " --> pdb=" O ASP B 817 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL B 823 " --> pdb=" O LEU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 881 removed outlier: 3.604A pdb=" N ALA B 876 " --> pdb=" O SER B 872 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 879 " --> pdb=" O LEU B 875 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR B 880 " --> pdb=" O ALA B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 887 Processing helix chain 'B' and resid 909 through 913 removed outlier: 4.086A pdb=" N VAL B 912 " --> pdb=" O THR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 removed outlier: 4.129A pdb=" N ILE B 920 " --> pdb=" O ASN B 916 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 962 removed outlier: 4.160A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B 962 " --> pdb=" O THR B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 974 through 980 removed outlier: 3.596A pdb=" N PHE B 978 " --> pdb=" O LEU B 974 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER B 979 " --> pdb=" O ASN B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1024 removed outlier: 3.536A pdb=" N ASP B 991 " --> pdb=" O GLU B 987 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 993 " --> pdb=" O GLN B 989 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR B1004 " --> pdb=" O SER B1000 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B1017 " --> pdb=" O ALA B1013 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B1021 " --> pdb=" O ALA B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1155 removed outlier: 3.681A pdb=" N PHE B1145 " --> pdb=" O GLU B1141 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B1151 " --> pdb=" O GLU B1147 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN B1155 " --> pdb=" O LYS B1151 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 333 through 338 removed outlier: 3.900A pdb=" N PHE C 337 " --> pdb=" O PHE C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 364 removed outlier: 3.512A pdb=" N LEU C 363 " --> pdb=" O TYR C 360 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TYR C 364 " --> pdb=" O SER C 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 360 through 364' Processing helix chain 'C' and resid 412 through 417 Processing helix chain 'C' and resid 611 through 613 No H-bonds generated for 'chain 'C' and resid 611 through 613' Processing helix chain 'C' and resid 614 through 620 removed outlier: 3.600A pdb=" N ALA C 618 " --> pdb=" O GLU C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 738 removed outlier: 3.623A pdb=" N TYR C 736 " --> pdb=" O ASP C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 752 removed outlier: 3.664A pdb=" N LEU C 747 " --> pdb=" O GLU C 743 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU C 749 " --> pdb=" O SER C 745 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN C 750 " --> pdb=" O ASN C 746 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR C 751 " --> pdb=" O LEU C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 760 Processing helix chain 'C' and resid 764 through 777 removed outlier: 4.725A pdb=" N ASP C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR C 773 " --> pdb=" O GLN C 769 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN C 774 " --> pdb=" O ASP C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 821 Processing helix chain 'C' and resid 861 through 876 removed outlier: 3.502A pdb=" N GLY C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 885 removed outlier: 3.520A pdb=" N GLY C 884 " --> pdb=" O TRP C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 892 through 900 removed outlier: 4.627A pdb=" N MET C 897 " --> pdb=" O PRO C 894 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA C 898 " --> pdb=" O MET C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 913 removed outlier: 3.585A pdb=" N LEU C 911 " --> pdb=" O GLN C 908 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TYR C 912 " --> pdb=" O ASN C 909 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU C 913 " --> pdb=" O VAL C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 934 removed outlier: 3.647A pdb=" N ILE C 929 " --> pdb=" O ALA C 925 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN C 930 " --> pdb=" O ILE C 926 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP C 931 " --> pdb=" O GLY C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 960 removed outlier: 3.561A pdb=" N VAL C 946 " --> pdb=" O LYS C 942 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN C 950 " --> pdb=" O VAL C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 963 No H-bonds generated for 'chain 'C' and resid 961 through 963' Processing helix chain 'C' and resid 971 through 979 removed outlier: 4.339A pdb=" N ILE C 975 " --> pdb=" O VAL C 971 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE C 976 " --> pdb=" O LEU C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 980 through 1027 removed outlier: 3.656A pdb=" N VAL C 986 " --> pdb=" O PRO C 982 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG C 990 " --> pdb=" O VAL C 986 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C1011 " --> pdb=" O LEU C1007 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER C1016 " --> pdb=" O GLU C1012 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C1019 " --> pdb=" O ALA C1015 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER C1025 " --> pdb=" O ALA C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1135 through 1153 removed outlier: 3.511A pdb=" N GLU C1139 " --> pdb=" O PRO C1135 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE C1143 " --> pdb=" O GLU C1139 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLU C1146 " --> pdb=" O SER C1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.585A pdb=" N ASP D 82 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 79 through 83' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.645A pdb=" N ILE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.280A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR A 63 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL A 264 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR A 262 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 67 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 260 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N SER A 202 " --> pdb=" O PRO A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 54 removed outlier: 3.733A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.044A pdb=" N GLY A 103 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.585A pdb=" N GLN A 134 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 311 Processing sheet with id=AA6, first strand: chain 'A' and resid 321 through 322 removed outlier: 7.021A pdb=" N GLU A 321 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N ASN A 539 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 540 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.633A pdb=" N SER A 396 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS A 353 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A 394 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE A 355 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 392 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ASN A 391 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLU A 513 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A 511 " --> pdb=" O TYR A 393 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 399 " --> pdb=" O TYR A 505 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA9, first strand: chain 'A' and resid 470 through 471 removed outlier: 3.553A pdb=" N TYR A 470 " --> pdb=" O TYR A 486 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 562 through 563 removed outlier: 6.760A pdb=" N PHE A 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 572 through 574 removed outlier: 7.034A pdb=" N VAL A 573 " --> pdb=" O LEU A 582 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 661 through 662 removed outlier: 3.552A pdb=" N ILE A 690 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN A 672 " --> pdb=" O SER A 688 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 688 " --> pdb=" O GLN A 672 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 715 through 724 removed outlier: 7.183A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 724 Processing sheet with id=AB6, first strand: chain 'A' and resid 731 through 733 Processing sheet with id=AB7, first strand: chain 'A' and resid 1078 through 1079 Processing sheet with id=AB8, first strand: chain 'A' and resid 1086 through 1087 Processing sheet with id=AB9, first strand: chain 'A' and resid 1091 through 1092 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.756A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA B 261 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N SER B 202 " --> pdb=" O PRO B 224 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.971A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.604A pdb=" N GLY B 107 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY B 103 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 130 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 133 through 135 removed outlier: 4.151A pdb=" N GLN B 134 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N SER B 159 " --> pdb=" O GLN B 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 308 through 313 removed outlier: 5.871A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER B 313 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 608 " --> pdb=" O SER B 593 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 322 through 323 removed outlier: 3.662A pdb=" N GLY B 545 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 390 through 393 removed outlier: 5.203A pdb=" N ASN B 391 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU B 513 " --> pdb=" O ASN B 391 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE B 399 " --> pdb=" O TYR B 505 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE B 397 " --> pdb=" O VAL B 507 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 390 through 393 removed outlier: 5.203A pdb=" N ASN B 391 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU B 513 " --> pdb=" O ASN B 391 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP B 433 " --> pdb=" O ARG B 506 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 508 " --> pdb=" O ILE B 431 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AD1, first strand: chain 'B' and resid 470 through 471 removed outlier: 3.536A pdb=" N TYR B 470 " --> pdb=" O TYR B 486 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR B 486 " --> pdb=" O TYR B 470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.138A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN B 672 " --> pdb=" O SER B 688 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 708 through 709 removed outlier: 3.555A pdb=" N THR B1073 " --> pdb=" O SER B1094 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 715 through 725 removed outlier: 3.536A pdb=" N ALA B1053 " --> pdb=" O GLY B1056 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET B1047 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 732 through 733 Processing sheet with id=AD6, first strand: chain 'B' and resid 1078 through 1079 removed outlier: 3.572A pdb=" N CYS B1079 " --> pdb=" O VAL B1130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 1086 through 1087 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.574A pdb=" N ASN C 61 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TYR C 264 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA C 259 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N SER C 202 " --> pdb=" O PRO C 224 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.847A pdb=" N ASP C 282 " --> pdb=" O LYS C 273 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.744A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N PHE C 133 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR C 114 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N CYS C 131 " --> pdb=" O THR C 114 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N SER C 116 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS C 129 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU C 118 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL C 127 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL C 120 " --> pdb=" O ASN C 125 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASN C 125 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL C 126 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL C 168 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE C 128 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU C 166 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL C 130 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 349 through 351 removed outlier: 3.591A pdb=" N ALA C 392 " --> pdb=" O LYS C 351 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ASN C 389 " --> pdb=" O GLU C 511 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU C 511 " --> pdb=" O ASN C 389 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 447 through 449 Processing sheet with id=AE4, first strand: chain 'C' and resid 533 through 534 Processing sheet with id=AE5, first strand: chain 'C' and resid 590 through 591 Processing sheet with id=AE6, first strand: chain 'C' and resid 649 through 655 removed outlier: 6.380A pdb=" N GLU C 649 " --> pdb=" O ALA C 689 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N THR C 691 " --> pdb=" O GLU C 649 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N VAL C 651 " --> pdb=" O THR C 691 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 706 through 710 Processing sheet with id=AE8, first strand: chain 'C' and resid 713 through 723 removed outlier: 3.510A pdb=" N SER C 716 " --> pdb=" O THR C1061 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU C 720 " --> pdb=" O PHE C1057 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL C1060 " --> pdb=" O LEU C1044 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 713 through 723 removed outlier: 3.510A pdb=" N SER C 716 " --> pdb=" O THR C1061 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU C 720 " --> pdb=" O PHE C1057 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA C1051 " --> pdb=" O GLY C1054 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 730 through 731 Processing sheet with id=AF2, first strand: chain 'C' and resid 1115 through 1117 removed outlier: 3.877A pdb=" N CYS C1077 " --> pdb=" O VAL C1128 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AF4, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.600A pdb=" N GLN D 90 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 21 through 23 removed outlier: 3.704A pdb=" N THR D 74 " --> pdb=" O SER D 63 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER D 63 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.670A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.632A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 10 through 11 Processing sheet with id=AF9, first strand: chain 'I' and resid 19 through 24 removed outlier: 3.700A pdb=" N ILE I 75 " --> pdb=" O VAL I 19 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 45 through 46 removed outlier: 3.807A pdb=" N GLN I 90 " --> pdb=" O THR I 97 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 48 through 49 Processing sheet with id=AG3, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AG4, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.680A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N MET J 34 " --> pdb=" O VAL J 50 " (cutoff:3.500A) 855 hydrogen bonds defined for protein. 2298 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.13 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 4882 1.30 - 1.43: 8455 1.43 - 1.57: 17425 1.57 - 1.70: 1 1.70 - 1.84: 171 Bond restraints: 30934 Sorted by residual: bond pdb=" C PRO C 892 " pdb=" O PRO C 892 " ideal model delta sigma weight residual 1.233 1.162 0.071 1.23e-02 6.61e+03 3.32e+01 bond pdb=" N VAL B1065 " pdb=" CA VAL B1065 " ideal model delta sigma weight residual 1.454 1.494 -0.039 7.70e-03 1.69e+04 2.58e+01 bond pdb=" CA SER A 813 " pdb=" CB SER A 813 " ideal model delta sigma weight residual 1.536 1.474 0.062 1.23e-02 6.61e+03 2.57e+01 bond pdb=" C PRO B 894 " pdb=" O PRO B 894 " ideal model delta sigma weight residual 1.235 1.169 0.066 1.30e-02 5.92e+03 2.56e+01 bond pdb=" C PRO B1066 " pdb=" O PRO B1066 " ideal model delta sigma weight residual 1.233 1.174 0.059 1.21e-02 6.83e+03 2.41e+01 ... (remaining 30929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 40522 2.43 - 4.86: 1317 4.86 - 7.30: 186 7.30 - 9.73: 47 9.73 - 12.16: 16 Bond angle restraints: 42088 Sorted by residual: angle pdb=" CA PRO A 894 " pdb=" C PRO A 894 " pdb=" O PRO A 894 " ideal model delta sigma weight residual 121.27 111.60 9.67 1.05e+00 9.07e-01 8.48e+01 angle pdb=" N PRO C 892 " pdb=" CA PRO C 892 " pdb=" CB PRO C 892 " ideal model delta sigma weight residual 103.27 95.10 8.17 9.00e-01 1.23e+00 8.24e+01 angle pdb=" N THR C 763 " pdb=" CA THR C 763 " pdb=" C THR C 763 " ideal model delta sigma weight residual 114.31 102.73 11.58 1.29e+00 6.01e-01 8.05e+01 angle pdb=" N PRO B 896 " pdb=" CA PRO B 896 " pdb=" C PRO B 896 " ideal model delta sigma weight residual 114.68 105.43 9.25 1.04e+00 9.25e-01 7.91e+01 angle pdb=" N GLN C 896 " pdb=" CA GLN C 896 " pdb=" C GLN C 896 " ideal model delta sigma weight residual 112.68 100.95 11.73 1.33e+00 5.65e-01 7.78e+01 ... (remaining 42083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.90: 17850 22.90 - 45.80: 1211 45.80 - 68.71: 148 68.71 - 91.61: 34 91.61 - 114.51: 49 Dihedral angle restraints: 19292 sinusoidal: 8363 harmonic: 10929 Sorted by residual: dihedral pdb=" CA ASP B 142 " pdb=" C ASP B 142 " pdb=" N HIS B 143 " pdb=" CA HIS B 143 " ideal model delta harmonic sigma weight residual -180.00 -112.00 -68.00 0 5.00e+00 4.00e-02 1.85e+02 dihedral pdb=" CA ASP C 142 " pdb=" C ASP C 142 " pdb=" N HIS C 143 " pdb=" CA HIS C 143 " ideal model delta harmonic sigma weight residual -180.00 -118.19 -61.81 0 5.00e+00 4.00e-02 1.53e+02 dihedral pdb=" CA LEU C 215 " pdb=" C LEU C 215 " pdb=" N PRO C 216 " pdb=" CA PRO C 216 " ideal model delta harmonic sigma weight residual 180.00 131.67 48.33 0 5.00e+00 4.00e-02 9.34e+01 ... (remaining 19289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 4477 0.100 - 0.199: 380 0.199 - 0.299: 54 0.299 - 0.399: 7 0.399 - 0.498: 4 Chirality restraints: 4922 Sorted by residual: chirality pdb=" CB ILE C 95 " pdb=" CA ILE C 95 " pdb=" CG1 ILE C 95 " pdb=" CG2 ILE C 95 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.21e+00 chirality pdb=" CA PHE B 326 " pdb=" N PHE B 326 " pdb=" C PHE B 326 " pdb=" CB PHE B 326 " both_signs ideal model delta sigma weight residual False 2.51 2.99 -0.48 2.00e-01 2.50e+01 5.75e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN A 798 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.49e+00 ... (remaining 4919 not shown) Planarity restraints: 5406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 324 " 0.021 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C VAL B 324 " -0.070 2.00e-02 2.50e+03 pdb=" O VAL B 324 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG B 325 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 886 " -0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C GLY B 886 " 0.065 2.00e-02 2.50e+03 pdb=" O GLY B 886 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA B 887 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 333 " 0.060 5.00e-02 4.00e+02 9.15e-02 1.34e+01 pdb=" N PRO B 334 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 334 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 334 " 0.049 5.00e-02 4.00e+02 ... (remaining 5403 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2458 2.74 - 3.28: 28734 3.28 - 3.82: 47473 3.82 - 4.36: 54597 4.36 - 4.90: 94182 Nonbonded interactions: 227444 Sorted by model distance: nonbonded pdb=" O GLU C 656 " pdb=" OH TYR C 690 " model vdw 2.200 3.040 nonbonded pdb=" O GLY B 877 " pdb=" OG SER B 881 " model vdw 2.219 3.040 nonbonded pdb=" O TYR I 86 " pdb=" OG1 THR I 102 " model vdw 2.250 3.040 nonbonded pdb=" O GLU B 658 " pdb=" OH TYR B 692 " model vdw 2.252 3.040 nonbonded pdb=" OD1 ASP D 50 " pdb=" OH TYR D 91 " model vdw 2.265 3.040 ... (remaining 227439 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 14 through 1309) selection = (chain 'C' and resid 14 through 1309) } ncs_group { reference = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' 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' } ncs_group { reference = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.790 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 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 : 0.006 0.131 31041 Z= 0.368 Angle : 1.008 12.160 42360 Z= 0.607 Chirality : 0.063 0.498 4922 Planarity : 0.006 0.091 5360 Dihedral : 15.740 114.512 12137 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.62 % Favored : 92.03 % Rotamer: Outliers : 1.00 % Allowed : 1.40 % Favored : 97.60 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.11 % 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: -2.76 (0.13), residues: 3714 helix: -2.74 (0.15), residues: 624 sheet: -0.63 (0.20), residues: 689 loop : -2.04 (0.12), residues: 2401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 316 TYR 0.018 0.002 TYR C 260 PHE 0.025 0.002 PHE C 893 TRP 0.028 0.002 TRP A 883 HIS 0.007 0.001 HIS C1043 Details of bonding type rmsd covalent geometry : bond 0.00601 (30934) covalent geometry : angle 0.99560 (42088) SS BOND : bond 0.00381 ( 43) SS BOND : angle 1.27024 ( 86) hydrogen bonds : bond 0.26125 ( 832) hydrogen bonds : angle 9.41494 ( 2298) Misc. bond : bond 0.00425 ( 2) link_BETA1-4 : bond 0.00680 ( 16) link_BETA1-4 : angle 1.70926 ( 48) link_NAG-ASN : bond 0.00992 ( 46) link_NAG-ASN : angle 2.71812 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 244 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 ARG cc_start: 0.5917 (OUTLIER) cc_final: 0.5684 (ttt180) REVERT: B 462 GLU cc_start: 0.7190 (pm20) cc_final: 0.6978 (pm20) REVERT: B 770 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7596 (tm-30) REVERT: C 217 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6238 (tm-30) REVERT: C 324 PHE cc_start: 0.4825 (OUTLIER) cc_final: 0.4284 (t80) REVERT: C 447 LEU cc_start: 0.6264 (mm) cc_final: 0.5912 (mm) REVERT: C 899 TYR cc_start: 0.7468 (m-10) cc_final: 0.7188 (m-10) REVERT: J 28 ILE cc_start: 0.3266 (mp) cc_final: 0.2864 (pt) outliers start: 33 outliers final: 13 residues processed: 275 average time/residue: 0.1756 time to fit residues: 80.6624 Evaluate side-chains 174 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 761 LYS Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain C residue 217 GLN Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 800 ILE Chi-restraints excluded: chain C residue 938 SER Chi-restraints excluded: chain C residue 940 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.0020 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 GLN B 916 ASN C 143 HIS C 217 GLN C 750 GLN C 890 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.147049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.102259 restraints weight = 74292.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.101066 restraints weight = 55707.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.101540 restraints weight = 44757.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.101864 restraints weight = 37501.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.102103 restraints weight = 34886.662| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31041 Z= 0.120 Angle : 0.630 15.606 42360 Z= 0.315 Chirality : 0.046 0.360 4922 Planarity : 0.005 0.079 5360 Dihedral : 11.301 101.629 5394 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.60 % Favored : 93.30 % Rotamer: Outliers : 1.10 % Allowed : 8.01 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.13), residues: 3714 helix: -1.39 (0.18), residues: 653 sheet: -0.44 (0.20), residues: 693 loop : -1.89 (0.12), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 316 TYR 0.023 0.001 TYR B 393 PHE 0.016 0.001 PHE B 397 TRP 0.024 0.001 TRP J 36 HIS 0.004 0.001 HIS C 143 Details of bonding type rmsd covalent geometry : bond 0.00265 (30934) covalent geometry : angle 0.61791 (42088) SS BOND : bond 0.00302 ( 43) SS BOND : angle 0.99744 ( 86) hydrogen bonds : bond 0.04870 ( 832) hydrogen bonds : angle 6.26271 ( 2298) Misc. bond : bond 0.00261 ( 2) link_BETA1-4 : bond 0.00448 ( 16) link_BETA1-4 : angle 1.34585 ( 48) link_NAG-ASN : bond 0.00451 ( 46) link_NAG-ASN : angle 2.01098 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8094 (mm-40) REVERT: A 348 TYR cc_start: 0.6940 (p90) cc_final: 0.6701 (p90) REVERT: A 811 LYS cc_start: 0.8004 (mmtt) cc_final: 0.7706 (mmtt) REVERT: B 770 GLU cc_start: 0.7812 (tm-30) cc_final: 0.6937 (tm-30) REVERT: C 42 VAL cc_start: 0.8858 (t) cc_final: 0.8623 (t) REVERT: C 324 PHE cc_start: 0.5114 (OUTLIER) cc_final: 0.4826 (m-80) REVERT: C 938 SER cc_start: 0.7547 (OUTLIER) cc_final: 0.7031 (t) REVERT: I 45 LYS cc_start: 0.6632 (mtmm) cc_final: 0.6387 (tptp) outliers start: 36 outliers final: 20 residues processed: 220 average time/residue: 0.1856 time to fit residues: 67.4273 Evaluate side-chains 179 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 149 TRP Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain C residue 655 TYR Chi-restraints excluded: chain C residue 755 CYS Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 938 SER Chi-restraints excluded: chain C residue 1143 PHE Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain J residue 68 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 41 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 chunk 163 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 310 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 211 optimal weight: 0.5980 chunk 228 optimal weight: 9.9990 chunk 265 optimal weight: 1.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN B 952 ASN C 66 HIS C 750 GLN C 908 GLN C 997 GLN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.144266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.097736 restraints weight = 75172.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.098874 restraints weight = 50203.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.098720 restraints weight = 37080.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.098789 restraints weight = 35610.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.098782 restraints weight = 36554.444| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 31041 Z= 0.193 Angle : 0.649 10.217 42360 Z= 0.324 Chirality : 0.047 0.366 4922 Planarity : 0.005 0.072 5360 Dihedral : 9.930 106.030 5376 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.00 % Favored : 91.90 % Rotamer: Outliers : 1.55 % Allowed : 11.57 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.13), residues: 3714 helix: -0.94 (0.19), residues: 663 sheet: -0.52 (0.19), residues: 715 loop : -1.89 (0.13), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1104 TYR 0.025 0.001 TYR B 393 PHE 0.020 0.002 PHE C 901 TRP 0.021 0.001 TRP B 149 HIS 0.004 0.001 HIS C 143 Details of bonding type rmsd covalent geometry : bond 0.00457 (30934) covalent geometry : angle 0.63629 (42088) SS BOND : bond 0.00293 ( 43) SS BOND : angle 1.18716 ( 86) hydrogen bonds : bond 0.04690 ( 832) hydrogen bonds : angle 5.91841 ( 2298) Misc. bond : bond 0.00233 ( 2) link_BETA1-4 : bond 0.00422 ( 16) link_BETA1-4 : angle 1.41609 ( 48) link_NAG-ASN : bond 0.00405 ( 46) link_NAG-ASN : angle 2.08541 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 170 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 TYR cc_start: 0.6770 (p90) cc_final: 0.6546 (p90) REVERT: B 462 GLU cc_start: 0.7424 (pm20) cc_final: 0.7123 (pm20) REVERT: C 539 ASN cc_start: 0.8144 (t0) cc_final: 0.7720 (t0) REVERT: J 28 ILE cc_start: 0.4226 (mp) cc_final: 0.3846 (pt) outliers start: 51 outliers final: 38 residues processed: 213 average time/residue: 0.1681 time to fit residues: 61.2834 Evaluate side-chains 189 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 149 TRP Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 952 ASN Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 655 TYR Chi-restraints excluded: chain C residue 750 GLN Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 813 ILE Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain C residue 1114 ASN Chi-restraints excluded: chain C residue 1143 PHE Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain J residue 68 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 257 optimal weight: 30.0000 chunk 94 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 226 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 241 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 238 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 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 = 0.4276 r_free = 0.4276 target = 0.142923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.095072 restraints weight = 74375.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.096780 restraints weight = 50136.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.096715 restraints weight = 32309.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.096934 restraints weight = 32991.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.097059 restraints weight = 31108.766| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 31041 Z= 0.188 Angle : 0.634 9.575 42360 Z= 0.316 Chirality : 0.047 0.370 4922 Planarity : 0.004 0.069 5360 Dihedral : 9.425 109.013 5371 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.65 % Favored : 92.25 % Rotamer: Outliers : 2.16 % Allowed : 13.27 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.13), residues: 3714 helix: -0.80 (0.20), residues: 662 sheet: -0.62 (0.19), residues: 705 loop : -1.90 (0.13), residues: 2347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1104 TYR 0.021 0.001 TYR B 393 PHE 0.017 0.002 PHE C1116 TRP 0.023 0.001 TRP B 149 HIS 0.003 0.001 HIS B 951 Details of bonding type rmsd covalent geometry : bond 0.00447 (30934) covalent geometry : angle 0.62076 (42088) SS BOND : bond 0.00268 ( 43) SS BOND : angle 1.15798 ( 86) hydrogen bonds : bond 0.04283 ( 832) hydrogen bonds : angle 5.70840 ( 2298) Misc. bond : bond 0.00238 ( 2) link_BETA1-4 : bond 0.00370 ( 16) link_BETA1-4 : angle 1.42792 ( 48) link_NAG-ASN : bond 0.00389 ( 46) link_NAG-ASN : angle 2.07709 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 160 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8143 (mm-40) REVERT: A 348 TYR cc_start: 0.7098 (p90) cc_final: 0.6831 (p90) REVERT: A 811 LYS cc_start: 0.7766 (mmtt) cc_final: 0.7423 (tttt) REVERT: A 899 MET cc_start: 0.9271 (tpt) cc_final: 0.9032 (tpt) REVERT: C 150 MET cc_start: 0.4614 (tmm) cc_final: 0.4214 (tmm) REVERT: C 226 VAL cc_start: 0.8656 (OUTLIER) cc_final: 0.8388 (m) REVERT: C 539 ASN cc_start: 0.8108 (t0) cc_final: 0.7629 (t0) REVERT: I 45 LYS cc_start: 0.6497 (mtmm) cc_final: 0.6156 (tptp) REVERT: I 87 TYR cc_start: 0.6563 (m-80) cc_final: 0.6325 (m-80) REVERT: J 28 ILE cc_start: 0.4152 (mp) cc_final: 0.3723 (pt) outliers start: 71 outliers final: 49 residues processed: 219 average time/residue: 0.1689 time to fit residues: 63.2037 Evaluate side-chains 200 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 149 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 149 TRP Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1060 LEU Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 655 TYR Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 1114 ASN Chi-restraints excluded: chain C residue 1143 PHE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain J residue 68 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 290 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 188 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 277 optimal weight: 20.0000 chunk 193 optimal weight: 0.7980 chunk 208 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 GLN C 987 GLN C 997 GLN ** I 89 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 = 0.4294 r_free = 0.4294 target = 0.144236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.097675 restraints weight = 74866.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.098259 restraints weight = 56295.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.098291 restraints weight = 40350.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.098490 restraints weight = 36181.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.098805 restraints weight = 33842.794| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 31041 Z= 0.117 Angle : 0.583 9.261 42360 Z= 0.290 Chirality : 0.045 0.346 4922 Planarity : 0.004 0.065 5360 Dihedral : 8.811 109.607 5371 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.62 % Favored : 93.27 % Rotamer: Outliers : 1.86 % Allowed : 14.43 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.14), residues: 3714 helix: -0.48 (0.20), residues: 671 sheet: -0.42 (0.19), residues: 728 loop : -1.85 (0.13), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 316 TYR 0.019 0.001 TYR B 393 PHE 0.016 0.001 PHE A 79 TRP 0.026 0.001 TRP J 36 HIS 0.003 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00269 (30934) covalent geometry : angle 0.56818 (42088) SS BOND : bond 0.00334 ( 43) SS BOND : angle 1.31214 ( 86) hydrogen bonds : bond 0.03705 ( 832) hydrogen bonds : angle 5.39225 ( 2298) Misc. bond : bond 0.00250 ( 2) link_BETA1-4 : bond 0.00422 ( 16) link_BETA1-4 : angle 1.39044 ( 48) link_NAG-ASN : bond 0.00422 ( 46) link_NAG-ASN : angle 1.99566 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 167 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8101 (mm-40) REVERT: A 238 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.6641 (tt0) REVERT: A 348 TYR cc_start: 0.7271 (p90) cc_final: 0.6951 (p90) REVERT: A 811 LYS cc_start: 0.7761 (mmtt) cc_final: 0.7425 (tttt) REVERT: B 462 GLU cc_start: 0.7286 (pm20) cc_final: 0.7012 (pm20) REVERT: B 913 LEU cc_start: 0.7652 (tp) cc_final: 0.7419 (tp) REVERT: C 226 VAL cc_start: 0.8756 (OUTLIER) cc_final: 0.8470 (m) REVERT: I 45 LYS cc_start: 0.6675 (mtmm) cc_final: 0.6271 (tptp) outliers start: 61 outliers final: 38 residues processed: 216 average time/residue: 0.1748 time to fit residues: 64.1824 Evaluate side-chains 188 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 149 TRP Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 655 TYR Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 1143 PHE Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 68 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 273 optimal weight: 10.0000 chunk 358 optimal weight: 30.0000 chunk 187 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 199 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 352 optimal weight: 9.9990 chunk 313 optimal weight: 0.5980 chunk 77 optimal weight: 0.1980 chunk 280 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN A1002 GLN B 850 GLN ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 GLN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.141820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.095954 restraints weight = 77317.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.094948 restraints weight = 53473.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.094721 restraints weight = 45888.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.095062 restraints weight = 42749.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.095127 restraints weight = 40900.470| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31041 Z= 0.180 Angle : 0.626 9.511 42360 Z= 0.311 Chirality : 0.047 0.369 4922 Planarity : 0.004 0.061 5360 Dihedral : 8.551 113.121 5368 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.59 % Favored : 92.30 % Rotamer: Outliers : 2.56 % Allowed : 14.95 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: -1.94 (0.14), residues: 3714 helix: -0.46 (0.20), residues: 669 sheet: -0.55 (0.19), residues: 716 loop : -1.87 (0.13), residues: 2329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1104 TYR 0.019 0.001 TYR B 393 PHE 0.018 0.001 PHE A 55 TRP 0.026 0.001 TRP B 149 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00428 (30934) covalent geometry : angle 0.61187 (42088) SS BOND : bond 0.00458 ( 43) SS BOND : angle 1.24819 ( 86) hydrogen bonds : bond 0.04011 ( 832) hydrogen bonds : angle 5.43753 ( 2298) Misc. bond : bond 0.00238 ( 2) link_BETA1-4 : bond 0.00408 ( 16) link_BETA1-4 : angle 1.52871 ( 48) link_NAG-ASN : bond 0.00386 ( 46) link_NAG-ASN : angle 2.07877 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 152 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7853 (OUTLIER) cc_final: 0.7634 (t60) REVERT: A 115 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8170 (mm-40) REVERT: A 238 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.6886 (tt0) REVERT: A 273 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7591 (tt) REVERT: A 348 TYR cc_start: 0.7314 (p90) cc_final: 0.7011 (p90) REVERT: A 811 LYS cc_start: 0.7816 (mmtt) cc_final: 0.7385 (tttt) REVERT: B 350 TRP cc_start: 0.8788 (OUTLIER) cc_final: 0.8345 (p-90) REVERT: B 462 GLU cc_start: 0.7496 (pm20) cc_final: 0.7274 (pm20) REVERT: B 770 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7894 (tm-30) REVERT: C 150 MET cc_start: 0.4295 (tmm) cc_final: 0.3919 (tmm) REVERT: C 226 VAL cc_start: 0.8731 (OUTLIER) cc_final: 0.8442 (m) REVERT: C 779 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7244 (mp10) REVERT: J 28 ILE cc_start: 0.4284 (mp) cc_final: 0.3859 (pt) outliers start: 84 outliers final: 60 residues processed: 228 average time/residue: 0.1635 time to fit residues: 64.5783 Evaluate side-chains 209 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 142 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 149 TRP Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 TRP Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1060 LEU Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 655 TYR Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 750 GLN Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1114 ASN Chi-restraints excluded: chain C residue 1143 PHE Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 68 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 64 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 347 optimal weight: 50.0000 chunk 155 optimal weight: 10.0000 chunk 323 optimal weight: 0.9990 chunk 259 optimal weight: 40.0000 chunk 241 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 195 optimal weight: 0.8980 chunk 37 optimal weight: 30.0000 chunk 62 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 ASN ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN C 750 GLN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 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 = 0.4243 r_free = 0.4243 target = 0.141220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.095119 restraints weight = 77611.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.094118 restraints weight = 56632.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.094029 restraints weight = 50547.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.094100 restraints weight = 47219.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.094367 restraints weight = 41611.135| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 31041 Z= 0.204 Angle : 0.650 9.905 42360 Z= 0.324 Chirality : 0.047 0.358 4922 Planarity : 0.004 0.059 5360 Dihedral : 8.371 114.983 5368 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.19 % Favored : 91.68 % Rotamer: Outliers : 3.07 % Allowed : 15.46 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: -2.04 (0.13), residues: 3714 helix: -0.54 (0.20), residues: 669 sheet: -0.67 (0.19), residues: 721 loop : -1.92 (0.13), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1104 TYR 0.020 0.002 TYR B 393 PHE 0.019 0.002 PHE B1118 TRP 0.030 0.001 TRP B 149 HIS 0.003 0.001 HIS C1043 Details of bonding type rmsd covalent geometry : bond 0.00484 (30934) covalent geometry : angle 0.63565 (42088) SS BOND : bond 0.00308 ( 43) SS BOND : angle 1.26794 ( 86) hydrogen bonds : bond 0.04133 ( 832) hydrogen bonds : angle 5.47832 ( 2298) Misc. bond : bond 0.00250 ( 2) link_BETA1-4 : bond 0.00423 ( 16) link_BETA1-4 : angle 1.58941 ( 48) link_NAG-ASN : bond 0.00387 ( 46) link_NAG-ASN : angle 2.14509 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 150 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7865 (OUTLIER) cc_final: 0.7588 (t60) REVERT: A 115 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8179 (mm-40) REVERT: A 238 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.6962 (tt0) REVERT: A 273 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7657 (tt) REVERT: A 348 TYR cc_start: 0.7317 (p90) cc_final: 0.7043 (p90) REVERT: B 350 TRP cc_start: 0.8807 (OUTLIER) cc_final: 0.8375 (p-90) REVERT: B 462 GLU cc_start: 0.7460 (pm20) cc_final: 0.7208 (pm20) REVERT: B 770 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7953 (tm-30) REVERT: B 960 VAL cc_start: 0.9571 (OUTLIER) cc_final: 0.9309 (t) REVERT: B 1060 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7836 (tt) REVERT: C 150 MET cc_start: 0.4297 (tmm) cc_final: 0.3935 (tmm) REVERT: C 226 VAL cc_start: 0.8743 (OUTLIER) cc_final: 0.8457 (m) REVERT: C 779 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7174 (mp10) REVERT: C 868 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.8310 (m-10) REVERT: J 28 ILE cc_start: 0.4170 (mp) cc_final: 0.3702 (pt) outliers start: 101 outliers final: 75 residues processed: 241 average time/residue: 0.1591 time to fit residues: 65.8900 Evaluate side-chains 228 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 143 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 TRP Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 TRP Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 638 ASN Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1060 LEU Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 655 TYR Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 800 ILE Chi-restraints excluded: chain C residue 813 ILE Chi-restraints excluded: chain C residue 868 TYR Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1114 ASN Chi-restraints excluded: chain C residue 1143 PHE Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 68 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 38 optimal weight: 0.4980 chunk 47 optimal weight: 30.0000 chunk 225 optimal weight: 0.7980 chunk 217 optimal weight: 7.9990 chunk 241 optimal weight: 9.9990 chunk 362 optimal weight: 7.9990 chunk 272 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN C 750 GLN I 34 ASN ** I 89 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 = 0.4263 r_free = 0.4263 target = 0.142656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.096694 restraints weight = 77234.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.096565 restraints weight = 54890.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.095851 restraints weight = 45576.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.096174 restraints weight = 47684.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.096428 restraints weight = 42030.580| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31041 Z= 0.119 Angle : 0.595 9.282 42360 Z= 0.294 Chirality : 0.045 0.339 4922 Planarity : 0.004 0.066 5360 Dihedral : 7.928 113.962 5368 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.79 % Favored : 93.08 % Rotamer: Outliers : 2.59 % Allowed : 16.10 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: -1.85 (0.14), residues: 3714 helix: -0.23 (0.20), residues: 668 sheet: -0.51 (0.19), residues: 737 loop : -1.87 (0.13), residues: 2309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 316 TYR 0.020 0.001 TYR B 393 PHE 0.020 0.001 PHE C 55 TRP 0.063 0.002 TRP C 348 HIS 0.003 0.000 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00275 (30934) covalent geometry : angle 0.58032 (42088) SS BOND : bond 0.00271 ( 43) SS BOND : angle 1.04218 ( 86) hydrogen bonds : bond 0.03551 ( 832) hydrogen bonds : angle 5.20566 ( 2298) Misc. bond : bond 0.00265 ( 2) link_BETA1-4 : bond 0.00390 ( 16) link_BETA1-4 : angle 1.55458 ( 48) link_NAG-ASN : bond 0.00411 ( 46) link_NAG-ASN : angle 2.08278 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 159 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7762 (OUTLIER) cc_final: 0.7463 (t60) REVERT: A 115 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8157 (mm-40) REVERT: A 238 GLN cc_start: 0.7223 (OUTLIER) cc_final: 0.6559 (tt0) REVERT: A 273 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7532 (tt) REVERT: A 348 TYR cc_start: 0.7434 (p90) cc_final: 0.7081 (p90) REVERT: A 811 LYS cc_start: 0.7876 (mmtt) cc_final: 0.7607 (tttt) REVERT: A 874 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9004 (mm) REVERT: A 899 MET cc_start: 0.9306 (tpt) cc_final: 0.9071 (tpt) REVERT: B 350 TRP cc_start: 0.8709 (OUTLIER) cc_final: 0.8307 (p-90) REVERT: B 462 GLU cc_start: 0.7317 (pm20) cc_final: 0.7107 (pm20) REVERT: B 770 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7771 (tm-30) REVERT: B 913 LEU cc_start: 0.7673 (tp) cc_final: 0.7425 (tp) REVERT: B 960 VAL cc_start: 0.9585 (OUTLIER) cc_final: 0.9325 (t) REVERT: C 150 MET cc_start: 0.4449 (tmm) cc_final: 0.4062 (tmm) REVERT: C 779 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7230 (mp10) REVERT: C 868 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.8198 (m-10) REVERT: I 45 LYS cc_start: 0.6531 (mtmm) cc_final: 0.6158 (tptt) outliers start: 85 outliers final: 61 residues processed: 235 average time/residue: 0.1707 time to fit residues: 68.7184 Evaluate side-chains 215 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 145 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 TRP Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 TRP Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 655 TYR Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 800 ILE Chi-restraints excluded: chain C residue 868 TYR Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain C residue 1143 PHE Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain J residue 68 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 62 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 208 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 233 optimal weight: 9.9990 chunk 154 optimal weight: 0.4980 chunk 49 optimal weight: 10.0000 chunk 284 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 329 optimal weight: 9.9990 chunk 193 optimal weight: 0.0980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 GLN ** I 89 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 = 0.4259 r_free = 0.4259 target = 0.142332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.096408 restraints weight = 77123.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.096219 restraints weight = 53079.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.095679 restraints weight = 43464.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.096060 restraints weight = 40587.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.096097 restraints weight = 39310.631| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31041 Z= 0.140 Angle : 0.609 9.555 42360 Z= 0.302 Chirality : 0.046 0.342 4922 Planarity : 0.004 0.075 5360 Dihedral : 7.755 114.668 5368 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.16 % Favored : 92.70 % Rotamer: Outliers : 2.44 % Allowed : 16.44 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: -1.84 (0.14), residues: 3714 helix: -0.18 (0.20), residues: 668 sheet: -0.46 (0.19), residues: 737 loop : -1.89 (0.13), residues: 2309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 316 TYR 0.058 0.001 TYR C 201 PHE 0.021 0.001 PHE C 165 TRP 0.039 0.001 TRP C 348 HIS 0.003 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00331 (30934) covalent geometry : angle 0.59453 (42088) SS BOND : bond 0.00279 ( 43) SS BOND : angle 1.05520 ( 86) hydrogen bonds : bond 0.03647 ( 832) hydrogen bonds : angle 5.20844 ( 2298) Misc. bond : bond 0.00256 ( 2) link_BETA1-4 : bond 0.00439 ( 16) link_BETA1-4 : angle 1.64058 ( 48) link_NAG-ASN : bond 0.00387 ( 46) link_NAG-ASN : angle 2.10293 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 153 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7792 (OUTLIER) cc_final: 0.7528 (t60) REVERT: A 115 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8189 (mm-40) REVERT: A 238 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6729 (tt0) REVERT: A 273 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7542 (tt) REVERT: A 348 TYR cc_start: 0.7411 (p90) cc_final: 0.7065 (p90) REVERT: A 811 LYS cc_start: 0.7919 (mmtt) cc_final: 0.7500 (tttt) REVERT: A 874 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9027 (mm) REVERT: B 350 TRP cc_start: 0.8714 (OUTLIER) cc_final: 0.8273 (p-90) REVERT: B 770 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7884 (tm-30) REVERT: B 913 LEU cc_start: 0.7762 (tp) cc_final: 0.7553 (tp) REVERT: B 960 VAL cc_start: 0.9577 (OUTLIER) cc_final: 0.9332 (t) REVERT: C 150 MET cc_start: 0.4287 (tmm) cc_final: 0.3928 (tmm) REVERT: C 779 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7248 (mp10) REVERT: C 868 TYR cc_start: 0.8618 (OUTLIER) cc_final: 0.8241 (m-10) REVERT: I 45 LYS cc_start: 0.6398 (mtmm) cc_final: 0.6033 (tptp) outliers start: 80 outliers final: 65 residues processed: 224 average time/residue: 0.1706 time to fit residues: 65.2735 Evaluate side-chains 219 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 145 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 TRP Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 TRP Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 655 TYR Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 800 ILE Chi-restraints excluded: chain C residue 868 TYR Chi-restraints excluded: chain C residue 895 MET Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1143 PHE Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 356 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 123 optimal weight: 0.5980 chunk 297 optimal weight: 0.9990 chunk 156 optimal weight: 20.0000 chunk 294 optimal weight: 0.6980 chunk 41 optimal weight: 40.0000 chunk 260 optimal weight: 8.9990 chunk 226 optimal weight: 7.9990 chunk 305 optimal weight: 0.7980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.142542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.094269 restraints weight = 77019.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.095768 restraints weight = 56510.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.096055 restraints weight = 38397.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.096450 restraints weight = 34804.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.096537 restraints weight = 35359.396| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31041 Z= 0.133 Angle : 0.605 9.610 42360 Z= 0.300 Chirality : 0.046 0.342 4922 Planarity : 0.004 0.069 5360 Dihedral : 7.548 113.654 5368 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.84 % Favored : 93.03 % Rotamer: Outliers : 2.25 % Allowed : 16.74 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: -1.81 (0.14), residues: 3714 helix: -0.10 (0.20), residues: 674 sheet: -0.47 (0.19), residues: 737 loop : -1.88 (0.13), residues: 2303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 316 TYR 0.016 0.001 TYR C1062 PHE 0.021 0.001 PHE C 165 TRP 0.038 0.001 TRP B 149 HIS 0.003 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00315 (30934) covalent geometry : angle 0.59075 (42088) SS BOND : bond 0.00285 ( 43) SS BOND : angle 1.02747 ( 86) hydrogen bonds : bond 0.03549 ( 832) hydrogen bonds : angle 5.13678 ( 2298) Misc. bond : bond 0.00259 ( 2) link_BETA1-4 : bond 0.00443 ( 16) link_BETA1-4 : angle 1.65378 ( 48) link_NAG-ASN : bond 0.00394 ( 46) link_NAG-ASN : angle 2.10067 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7428 Ramachandran restraints generated. 3714 Oldfield, 0 Emsley, 3714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 154 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7788 (OUTLIER) cc_final: 0.7523 (t60) REVERT: A 115 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8174 (mm-40) REVERT: A 238 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.6674 (tt0) REVERT: A 273 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7451 (tt) REVERT: A 348 TYR cc_start: 0.7267 (p90) cc_final: 0.6944 (p90) REVERT: A 811 LYS cc_start: 0.7851 (mmtt) cc_final: 0.7425 (tttt) REVERT: A 874 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.9006 (mm) REVERT: B 350 TRP cc_start: 0.8635 (OUTLIER) cc_final: 0.8223 (p-90) REVERT: B 770 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7820 (tm-30) REVERT: B 913 LEU cc_start: 0.7764 (tp) cc_final: 0.7562 (tp) REVERT: B 960 VAL cc_start: 0.9571 (OUTLIER) cc_final: 0.9338 (t) REVERT: C 150 MET cc_start: 0.4316 (tmm) cc_final: 0.3959 (tmm) REVERT: C 779 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7250 (mp10) REVERT: C 868 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.8257 (m-10) outliers start: 74 outliers final: 61 residues processed: 219 average time/residue: 0.1857 time to fit residues: 68.3871 Evaluate side-chains 218 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 148 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 TRP Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 350 TRP Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 655 TYR Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 800 ILE Chi-restraints excluded: chain C residue 868 TYR Chi-restraints excluded: chain C residue 895 MET Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain C residue 1143 PHE Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain J residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 193 optimal weight: 0.1980 chunk 147 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 370 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 chunk 251 optimal weight: 20.0000 chunk 165 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 275 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 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 = 0.4258 r_free = 0.4258 target = 0.142239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.094179 restraints weight = 77492.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.095292 restraints weight = 58599.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.095412 restraints weight = 42978.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.095551 restraints weight = 38393.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.095826 restraints weight = 39463.239| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31041 Z= 0.145 Angle : 0.610 9.644 42360 Z= 0.303 Chirality : 0.046 0.340 4922 Planarity : 0.004 0.065 5360 Dihedral : 7.379 112.878 5365 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.46 % Favored : 92.41 % Rotamer: Outliers : 2.28 % Allowed : 16.86 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.01 % 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: -1.81 (0.14), residues: 3714 helix: -0.10 (0.20), residues: 671 sheet: -0.53 (0.19), residues: 752 loop : -1.86 (0.13), residues: 2291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 316 TYR 0.019 0.001 TYR I 86 PHE 0.021 0.001 PHE C 165 TRP 0.036 0.001 TRP B 149 HIS 0.002 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00342 (30934) covalent geometry : angle 0.59571 (42088) SS BOND : bond 0.00282 ( 43) SS BOND : angle 1.05189 ( 86) hydrogen bonds : bond 0.03621 ( 832) hydrogen bonds : angle 5.15379 ( 2298) Misc. bond : bond 0.00263 ( 2) link_BETA1-4 : bond 0.00468 ( 16) link_BETA1-4 : angle 1.69120 ( 48) link_NAG-ASN : bond 0.00388 ( 46) link_NAG-ASN : angle 2.11657 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5200.77 seconds wall clock time: 91 minutes 0.40 seconds (5460.40 seconds total)