Starting phenix.real_space_refine on Sun Jul 5 21:03:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wt8_32771/07_2026/7wt8_32771.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wt8_32771/07_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_32771/07_2026/7wt8_32771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wt8_32771/07_2026/7wt8_32771.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wt8_32771/07_2026/7wt8_32771.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wt8_32771/07_2026/7wt8_32771.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wt8_32771/07_2026/7wt8_32771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wt8_32771/07_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 11 Time building chain proxies: 7.13, 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: 2.87 Conformation dependent library (CDL) restraints added in 1.5 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: 1.14 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: 7.82 Time building geometry restraints manager: 3.77 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 - 17.65: 16015 17.65 - 35.29: 1600 35.29 - 52.94: 277 52.94 - 70.58: 47 70.58 - 88.23: 30 Dihedral angle restraints: 17969 sinusoidal: 7040 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 17966 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: 5.060 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: 0.030 Extract box with map and model: 0.660 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 31.070 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 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 : 14.237 88.231 10814 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/Z covalent geometry : bond 0.00601 / 0.37 (30934) covalent geometry : angle 0.99560 / 0.61 (42088) SS BOND : bond 0.00381 / 0.27 ( 43) SS BOND : angle 1.27024 / 0.90 ( 86) hydrogen bonds : bond 0.26125 / 17.07 ( 832) hydrogen bonds : angle 9.41494 / 6.44 ( 2298) Misc. bond : bond 0.00425 / 0.22 ( 2) link_BETA1-4 : bond 0.00680 / 0.39 ( 16) link_BETA1-4 : angle 1.70926 / 1.06 ( 48) link_NAG-ASN : bond 0.00992 / 0.64 ( 46) link_NAG-ASN : angle 2.71812 / 1.84 ( 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 : 1.078 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: 0.1683 time to fit residues: 77.4421 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 : 1.141 ------------------------------------------------------------------------------- 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... ** 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 = 0.147079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.102381 restraints weight = 74708.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.102580 restraints weight = 51591.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.102321 restraints weight = 40264.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.102499 restraints weight = 37986.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.102611 restraints weight = 36394.132| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31041 Z= 0.119 Angle : 0.612 15.512 42360 Z= 0.309 Chirality : 0.046 0.384 4922 Planarity : 0.005 0.078 5360 Dihedral : 5.754 59.698 4071 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.49 % Favored : 93.40 % 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: -1.41 (0.18), residues: 655 sheet: -0.43 (0.20), residues: 697 loop : -1.88 (0.12), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 316 TYR 0.023 0.001 TYR B 393 PHE 0.017 0.001 PHE B 397 TRP 0.025 0.001 TRP J 36 HIS 0.006 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (30934) covalent geometry : angle 0.60085 / 0.31 (42088) SS BOND : bond 0.00295 / 0.21 ( 43) SS BOND : angle 1.00435 / 0.70 ( 86) hydrogen bonds : bond 0.04782 / 3.16 ( 832) hydrogen bonds : angle 6.22728 / 4.25 ( 2298) Misc. bond : bond 0.00165 / 0.09 ( 2) link_BETA1-4 : bond 0.00464 / 0.29 ( 16) link_BETA1-4 : angle 1.26423 / 0.83 ( 48) link_NAG-ASN : bond 0.00461 / 0.26 ( 46) link_NAG-ASN : angle 1.96574 / 1.36 ( 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 228 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8083 (mm-40) REVERT: A 348 TYR cc_start: 0.6879 (p90) cc_final: 0.6663 (p90) REVERT: A 811 LYS cc_start: 0.8005 (mmtt) cc_final: 0.7706 (mmtt) REVERT: B 770 GLU cc_start: 0.7807 (tm-30) cc_final: 0.6941 (tm-30) REVERT: C 42 VAL cc_start: 0.8843 (t) cc_final: 0.8607 (t) REVERT: C 324 PHE cc_start: 0.5196 (OUTLIER) cc_final: 0.4960 (m-80) REVERT: C 938 SER cc_start: 0.7562 (OUTLIER) cc_final: 0.7105 (t) outliers start: 36 outliers final: 21 residues processed: 223 average time/residue: 0.1663 time to fit residues: 61.3045 Evaluate side-chains 181 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 141 LEU 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: 4.9990 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: 2.9990 chunk 301 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 211 optimal weight: 0.8980 chunk 228 optimal weight: 8.9990 chunk 265 optimal weight: 0.0980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 750 GLN C 997 GLN C1114 ASN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.144262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.098430 restraints weight = 74920.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.098961 restraints weight = 50888.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.098506 restraints weight = 38023.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.098604 restraints weight = 37519.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.098910 restraints weight = 35231.555| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 31041 Z= 0.169 Angle : 0.616 10.278 42360 Z= 0.310 Chirality : 0.046 0.401 4922 Planarity : 0.004 0.071 5360 Dihedral : 5.397 62.824 4053 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.22 % Favored : 92.68 % Rotamer: Outliers : 1.49 % Allowed : 11.26 % Favored : 87.25 % 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: -2.03 (0.13), residues: 3714 helix: -0.88 (0.19), residues: 661 sheet: -0.45 (0.20), residues: 721 loop : -1.87 (0.13), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1104 TYR 0.024 0.001 TYR B 393 PHE 0.017 0.002 PHE C 901 TRP 0.022 0.001 TRP B 149 HIS 0.004 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (30934) covalent geometry : angle 0.60426 / 0.31 (42088) SS BOND : bond 0.00246 / 0.18 ( 43) SS BOND : angle 1.11788 / 0.80 ( 86) hydrogen bonds : bond 0.04507 / 2.98 ( 832) hydrogen bonds : angle 5.83962 / 3.99 ( 2298) Misc. bond : bond 0.00156 / 0.08 ( 2) link_BETA1-4 : bond 0.00390 / 0.21 ( 16) link_BETA1-4 : angle 1.20110 / 0.78 ( 48) link_NAG-ASN : bond 0.00397 / 0.22 ( 46) link_NAG-ASN : angle 1.96753 / 1.36 ( 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 219 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 170 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8077 (mm-40) REVERT: A 348 TYR cc_start: 0.6957 (p90) cc_final: 0.6731 (p90) REVERT: B 462 GLU cc_start: 0.7400 (pm20) cc_final: 0.7113 (pm20) REVERT: B 899 MET cc_start: 0.8924 (tpt) cc_final: 0.8639 (tpt) REVERT: C 539 ASN cc_start: 0.8139 (t0) cc_final: 0.7741 (t0) REVERT: J 28 ILE cc_start: 0.4246 (mp) cc_final: 0.3872 (pt) outliers start: 49 outliers final: 36 residues processed: 211 average time/residue: 0.1644 time to fit residues: 58.7254 Evaluate side-chains 189 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 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 884 THR 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 53 ASP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 311 SER 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 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: 5.9990 chunk 226 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 241 optimal weight: 7.9990 chunk 60 optimal weight: 0.4980 chunk 103 optimal weight: 0.9980 chunk 238 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 224 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 908 GLN C1114 ASN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.144349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.096858 restraints weight = 74497.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.097951 restraints weight = 53768.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.098036 restraints weight = 41738.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.098434 restraints weight = 35255.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.098675 restraints weight = 34882.469| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31041 Z= 0.134 Angle : 0.580 9.559 42360 Z= 0.291 Chirality : 0.045 0.392 4922 Planarity : 0.004 0.067 5360 Dihedral : 5.145 63.459 4048 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.68 % Favored : 93.21 % Rotamer: Outliers : 1.83 % Allowed : 13.33 % Favored : 84.84 % 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: -1.95 (0.13), residues: 3714 helix: -0.65 (0.20), residues: 670 sheet: -0.47 (0.20), residues: 712 loop : -1.84 (0.13), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1102 TYR 0.018 0.001 TYR B 393 PHE 0.017 0.001 PHE C1116 TRP 0.022 0.001 TRP B 149 HIS 0.003 0.001 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (30934) covalent geometry : angle 0.56769 / 0.29 (42088) SS BOND : bond 0.00253 / 0.18 ( 43) SS BOND : angle 1.03021 / 0.73 ( 86) hydrogen bonds : bond 0.03950 / 2.61 ( 832) hydrogen bonds : angle 5.55127 / 3.79 ( 2298) Misc. bond : bond 0.00152 / 0.08 ( 2) link_BETA1-4 : bond 0.00415 / 0.23 ( 16) link_BETA1-4 : angle 1.15877 / 0.75 ( 48) link_NAG-ASN : bond 0.00396 / 0.21 ( 46) link_NAG-ASN : angle 1.92591 / 1.32 ( 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 226 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 166 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8135 (mm-40) REVERT: A 348 TYR cc_start: 0.6979 (p90) cc_final: 0.6721 (p90) REVERT: A 811 LYS cc_start: 0.7851 (mmtt) cc_final: 0.7504 (tttt) REVERT: A 899 MET cc_start: 0.9281 (tpt) cc_final: 0.9038 (tpt) REVERT: B 546 THR cc_start: 0.8924 (m) cc_final: 0.8702 (m) REVERT: C 150 MET cc_start: 0.4574 (tmm) cc_final: 0.4220 (tmm) REVERT: C 271 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6560 (tt) REVERT: I 45 LYS cc_start: 0.6739 (mtmm) cc_final: 0.6357 (tptp) outliers start: 60 outliers final: 38 residues processed: 213 average time/residue: 0.1715 time to fit residues: 61.3408 Evaluate side-chains 190 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 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 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 425 ASP 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 987 GLU 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 271 LEU Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 655 TYR Chi-restraints excluded: chain C residue 758 LEU 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: 0.7980 chunk 143 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 42 optimal weight: 30.0000 chunk 132 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 77 optimal weight: 0.0980 chunk 277 optimal weight: 10.0000 chunk 193 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN C 750 GLN C 908 GLN C 987 GLN C 997 GLN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.144273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.098228 restraints weight = 76443.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.097292 restraints weight = 57862.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.097350 restraints weight = 54778.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.097689 restraints weight = 44857.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.097950 restraints weight = 40320.805| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 31041 Z= 0.105 Angle : 0.558 9.275 42360 Z= 0.280 Chirality : 0.045 0.376 4922 Planarity : 0.004 0.063 5360 Dihedral : 4.927 64.588 4045 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.44 % Favored : 93.46 % Rotamer: Outliers : 1.77 % Allowed : 13.91 % Favored : 84.32 % 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: -1.78 (0.14), residues: 3714 helix: -0.38 (0.20), residues: 670 sheet: -0.39 (0.19), residues: 742 loop : -1.79 (0.13), residues: 2302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 316 TYR 0.016 0.001 TYR C 197 PHE 0.017 0.001 PHE A 79 TRP 0.026 0.001 TRP B 149 HIS 0.003 0.000 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (30934) covalent geometry : angle 0.54547 / 0.28 (42088) SS BOND : bond 0.00241 / 0.17 ( 43) SS BOND : angle 1.22160 / 0.88 ( 86) hydrogen bonds : bond 0.03604 / 2.36 ( 832) hydrogen bonds : angle 5.31947 / 3.64 ( 2298) Misc. bond : bond 0.00153 / 0.08 ( 2) link_BETA1-4 : bond 0.00406 / 0.23 ( 16) link_BETA1-4 : angle 1.14034 / 0.73 ( 48) link_NAG-ASN : bond 0.00413 / 0.23 ( 46) link_NAG-ASN : angle 1.87496 / 1.28 ( 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 227 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 169 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8154 (mm-40) REVERT: A 300 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7927 (tt) REVERT: A 348 TYR cc_start: 0.7214 (p90) cc_final: 0.6893 (p90) REVERT: A 811 LYS cc_start: 0.7920 (mmtt) cc_final: 0.7544 (tttt) REVERT: B 913 LEU cc_start: 0.7529 (tp) cc_final: 0.7291 (tp) REVERT: C 226 VAL cc_start: 0.8746 (OUTLIER) cc_final: 0.8475 (m) REVERT: I 45 LYS cc_start: 0.6792 (mtmm) cc_final: 0.6376 (tptp) outliers start: 58 outliers final: 39 residues processed: 218 average time/residue: 0.1621 time to fit residues: 60.4970 Evaluate side-chains 195 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 149 TRP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 300 LEU 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 543 LEU Chi-restraints excluded: chain A residue 584 ILE 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 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 726 VAL Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1101 VAL 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 906 VAL 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: 9.9990 chunk 358 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 199 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 44 optimal weight: 30.0000 chunk 352 optimal weight: 10.0000 chunk 313 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 280 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN C 750 GLN C 908 GLN C1114 ASN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.141203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.093209 restraints weight = 76407.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.093924 restraints weight = 57975.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.093861 restraints weight = 41951.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.094229 restraints weight = 38222.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.094311 restraints weight = 37994.883| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 31041 Z= 0.236 Angle : 0.663 10.984 42360 Z= 0.334 Chirality : 0.048 0.447 4922 Planarity : 0.005 0.057 5360 Dihedral : 5.285 65.328 4045 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.05 % Favored : 91.84 % Rotamer: Outliers : 2.22 % Allowed : 14.64 % Favored : 83.14 % 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: -1.99 (0.13), residues: 3714 helix: -0.57 (0.20), residues: 668 sheet: -0.57 (0.20), residues: 698 loop : -1.88 (0.13), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1104 TYR 0.021 0.002 TYR C1062 PHE 0.023 0.002 PHE A 55 TRP 0.032 0.002 TRP J 36 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.24 (30934) covalent geometry : angle 0.64970 / 0.33 (42088) SS BOND : bond 0.00328 / 0.23 ( 43) SS BOND : angle 1.36304 / 0.99 ( 86) hydrogen bonds : bond 0.04354 / 2.89 ( 832) hydrogen bonds : angle 5.57797 / 3.81 ( 2298) Misc. bond : bond 0.00152 / 0.08 ( 2) link_BETA1-4 : bond 0.00388 / 0.20 ( 16) link_BETA1-4 : angle 1.28074 / 0.84 ( 48) link_NAG-ASN : bond 0.00385 / 0.22 ( 46) link_NAG-ASN : angle 2.10303 / 1.45 ( 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 230 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 157 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8195 (mm-40) REVERT: A 238 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.7003 (tt0) REVERT: A 348 TYR cc_start: 0.7209 (p90) cc_final: 0.6979 (p90) REVERT: B 350 TRP cc_start: 0.8820 (OUTLIER) cc_final: 0.8374 (p-90) REVERT: B 770 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7949 (tm-30) REVERT: B 1001 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9159 (tp) REVERT: C 150 MET cc_start: 0.4195 (tmm) cc_final: 0.3825 (tmm) REVERT: C 226 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8411 (m) REVERT: J 28 ILE cc_start: 0.4438 (mp) cc_final: 0.3994 (pt) outliers start: 73 outliers final: 53 residues processed: 221 average time/residue: 0.1539 time to fit residues: 58.5740 Evaluate side-chains 203 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 145 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 SER 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 633 TYR 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 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 425 ASP 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 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 884 THR Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1116 ASN 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 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 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: 0.5980 chunk 347 optimal weight: 50.0000 chunk 155 optimal weight: 7.9990 chunk 323 optimal weight: 0.9980 chunk 259 optimal weight: 40.0000 chunk 241 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 GLN C 750 GLN C 997 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 = 0.4246 r_free = 0.4246 target = 0.141398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.093232 restraints weight = 77295.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.093579 restraints weight = 64379.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.094072 restraints weight = 45530.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.094296 restraints weight = 39966.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.094483 restraints weight = 38529.381| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 31041 Z= 0.199 Angle : 0.636 9.837 42360 Z= 0.320 Chirality : 0.047 0.427 4922 Planarity : 0.004 0.062 5360 Dihedral : 5.274 67.129 4045 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.84 % Favored : 92.03 % Rotamer: Outliers : 2.47 % Allowed : 15.53 % Favored : 82.01 % 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: -2.02 (0.13), residues: 3714 helix: -0.57 (0.20), residues: 675 sheet: -0.63 (0.19), residues: 706 loop : -1.89 (0.13), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 316 TYR 0.020 0.001 TYR C1062 PHE 0.018 0.002 PHE B1118 TRP 0.030 0.001 TRP B 149 HIS 0.003 0.001 HIS C1043 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (30934) covalent geometry : angle 0.62271 / 0.32 (42088) SS BOND : bond 0.00312 / 0.23 ( 43) SS BOND : angle 1.23712 / 0.90 ( 86) hydrogen bonds : bond 0.04117 / 2.74 ( 832) hydrogen bonds : angle 5.47438 / 3.74 ( 2298) Misc. bond : bond 0.00159 / 0.08 ( 2) link_BETA1-4 : bond 0.00382 / 0.20 ( 16) link_BETA1-4 : angle 1.25735 / 0.83 ( 48) link_NAG-ASN : bond 0.00383 / 0.21 ( 46) link_NAG-ASN : angle 2.06903 / 1.42 ( 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 230 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 149 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7842 (OUTLIER) cc_final: 0.7531 (t60) REVERT: A 115 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8199 (mm-40) REVERT: A 238 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.6942 (tt0) REVERT: A 348 TYR cc_start: 0.7278 (p90) cc_final: 0.6991 (p90) REVERT: A 811 LYS cc_start: 0.7987 (mmtt) cc_final: 0.7629 (tttt) REVERT: B 350 TRP cc_start: 0.8794 (OUTLIER) cc_final: 0.8351 (p-90) REVERT: B 770 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7916 (tm-30) REVERT: B 1001 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9133 (tp) REVERT: C 150 MET cc_start: 0.4398 (tmm) cc_final: 0.4021 (tmm) REVERT: I 45 LYS cc_start: 0.6646 (mtmm) cc_final: 0.6209 (tptt) REVERT: J 28 ILE cc_start: 0.4183 (mp) cc_final: 0.3717 (pt) outliers start: 81 outliers final: 61 residues processed: 221 average time/residue: 0.1671 time to fit residues: 63.6662 Evaluate side-chains 212 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 146 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR 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 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 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 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 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 726 VAL Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1001 LEU 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 312 ASN Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 655 TYR Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 813 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 38 optimal weight: 8.9990 chunk 47 optimal weight: 30.0000 chunk 225 optimal weight: 7.9990 chunk 217 optimal weight: 8.9990 chunk 241 optimal weight: 6.9990 chunk 362 optimal weight: 7.9990 chunk 272 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.140089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.093310 restraints weight = 75071.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.092850 restraints weight = 60745.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.092814 restraints weight = 47056.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.093128 restraints weight = 41319.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.093310 restraints weight = 39042.817| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 31041 Z= 0.314 Angle : 0.765 12.938 42360 Z= 0.387 Chirality : 0.051 0.501 4922 Planarity : 0.005 0.068 5360 Dihedral : 5.842 69.942 4045 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.04 % Favored : 89.82 % Rotamer: Outliers : 2.80 % Allowed : 15.80 % Favored : 81.40 % 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: -2.36 (0.13), residues: 3714 helix: -0.86 (0.19), residues: 668 sheet: -0.96 (0.19), residues: 743 loop : -2.09 (0.13), residues: 2303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 352 TYR 0.025 0.002 TYR C1062 PHE 0.025 0.002 PHE A 55 TRP 0.063 0.002 TRP C 348 HIS 0.006 0.001 HIS C1043 Details of bonding type rmsd/Z covalent geometry : bond 0.00746 / 0.31 (30934) covalent geometry : angle 0.75002 / 0.38 (42088) SS BOND : bond 0.00402 / 0.29 ( 43) SS BOND : angle 1.51223 / 1.10 ( 86) hydrogen bonds : bond 0.04976 / 3.31 ( 832) hydrogen bonds : angle 5.87208 / 4.01 ( 2298) Misc. bond : bond 0.00171 / 0.09 ( 2) link_BETA1-4 : bond 0.00457 / 0.23 ( 16) link_BETA1-4 : angle 1.51238 / 1.02 ( 48) link_NAG-ASN : bond 0.00462 / 0.28 ( 46) link_NAG-ASN : angle 2.38294 / 1.64 ( 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 236 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 144 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8060 (OUTLIER) cc_final: 0.7781 (t60) REVERT: A 238 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: A 348 TYR cc_start: 0.7414 (p90) cc_final: 0.7121 (p90) REVERT: B 350 TRP cc_start: 0.8897 (OUTLIER) cc_final: 0.8521 (p-90) REVERT: B 770 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8027 (tm-30) REVERT: B 1001 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9229 (tp) REVERT: B 1119 VAL cc_start: 0.8248 (OUTLIER) cc_final: 0.7992 (m) REVERT: C 150 MET cc_start: 0.4327 (tmm) cc_final: 0.3999 (tmm) REVERT: C 779 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.7074 (mp10) REVERT: C 868 TYR cc_start: 0.8770 (OUTLIER) cc_final: 0.8423 (m-10) REVERT: D 30 ASN cc_start: -0.0170 (OUTLIER) cc_final: -0.1088 (m-40) REVERT: H 105 ASN cc_start: 0.6042 (t0) cc_final: 0.5516 (m-40) REVERT: I 45 LYS cc_start: 0.6349 (mtmm) cc_final: 0.5950 (tptt) REVERT: J 28 ILE cc_start: 0.4290 (mp) cc_final: 0.3823 (pt) outliers start: 92 outliers final: 64 residues processed: 227 average time/residue: 0.1597 time to fit residues: 61.9838 Evaluate side-chains 211 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 139 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR 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 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 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 390 THR 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 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 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 1001 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 228 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 270 PHE 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 758 LEU Chi-restraints excluded: chain C residue 779 GLN 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 907 THR 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 D residue 30 ASN Chi-restraints excluded: chain H residue 119 SER 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: 10.0000 chunk 96 optimal weight: 0.7980 chunk 208 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 233 optimal weight: 0.0980 chunk 154 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 284 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 329 optimal weight: 50.0000 chunk 193 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 ASN ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.143479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.097980 restraints weight = 75501.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.096603 restraints weight = 54613.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.097228 restraints weight = 52382.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.097487 restraints weight = 41353.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.097787 restraints weight = 37424.907| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31041 Z= 0.114 Angle : 0.603 11.020 42360 Z= 0.302 Chirality : 0.046 0.388 4922 Planarity : 0.004 0.093 5360 Dihedral : 5.214 71.235 4045 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.41 % Favored : 93.46 % Rotamer: Outliers : 1.98 % Allowed : 16.68 % Favored : 81.34 % 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: -1.97 (0.13), residues: 3714 helix: -0.31 (0.20), residues: 675 sheet: -0.64 (0.19), residues: 719 loop : -1.93 (0.13), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 316 TYR 0.019 0.001 TYR D 32 PHE 0.020 0.001 PHE C 55 TRP 0.038 0.002 TRP C 348 HIS 0.003 0.001 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (30934) covalent geometry : angle 0.59021 / 0.30 (42088) SS BOND : bond 0.00306 / 0.22 ( 43) SS BOND : angle 1.06336 / 0.76 ( 86) hydrogen bonds : bond 0.03543 / 2.36 ( 832) hydrogen bonds : angle 5.25394 / 3.58 ( 2298) Misc. bond : bond 0.00183 / 0.09 ( 2) link_BETA1-4 : bond 0.00459 / 0.25 ( 16) link_BETA1-4 : angle 1.26231 / 0.82 ( 48) link_NAG-ASN : bond 0.00434 / 0.24 ( 46) link_NAG-ASN : angle 2.02224 / 1.37 ( 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 236 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 171 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7805 (OUTLIER) cc_final: 0.7464 (t60) REVERT: A 115 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8201 (mm-40) REVERT: A 348 TYR cc_start: 0.7341 (p90) cc_final: 0.7032 (p90) REVERT: A 811 LYS cc_start: 0.7920 (mmtt) cc_final: 0.7461 (tttt) REVERT: A 874 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8903 (mm) REVERT: B 913 LEU cc_start: 0.7732 (tp) cc_final: 0.7475 (tp) REVERT: B 960 VAL cc_start: 0.9583 (OUTLIER) cc_final: 0.9321 (t) REVERT: B 1119 VAL cc_start: 0.8192 (OUTLIER) cc_final: 0.7972 (m) REVERT: C 150 MET cc_start: 0.4310 (tmm) cc_final: 0.3949 (tmm) REVERT: C 779 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7219 (mp10) REVERT: C 868 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.8340 (m-10) REVERT: H 105 ASN cc_start: 0.5930 (t0) cc_final: 0.5429 (m-40) REVERT: I 45 LYS cc_start: 0.6354 (mtmm) cc_final: 0.6002 (tptt) outliers start: 65 outliers final: 48 residues processed: 224 average time/residue: 0.1694 time to fit residues: 63.4406 Evaluate side-chains 207 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 152 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 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 489 LEU 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 B residue 329 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 390 THR 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 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 884 THR Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 228 LEU 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 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 868 TYR Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1143 PHE 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: 30.0000 chunk 43 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 chunk 297 optimal weight: 0.4980 chunk 156 optimal weight: 20.0000 chunk 294 optimal weight: 0.9980 chunk 41 optimal weight: 40.0000 chunk 260 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 305 optimal weight: 0.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 ASN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 ASN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.142306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.095914 restraints weight = 77236.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.096298 restraints weight = 54027.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.096042 restraints weight = 41068.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.096239 restraints weight = 40408.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.096411 restraints weight = 38427.115| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31041 Z= 0.129 Angle : 0.606 10.068 42360 Z= 0.302 Chirality : 0.046 0.413 4922 Planarity : 0.005 0.100 5360 Dihedral : 5.115 72.033 4045 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.95 % Favored : 92.92 % Rotamer: Outliers : 1.89 % Allowed : 17.08 % Favored : 81.04 % 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: -1.87 (0.14), residues: 3714 helix: -0.14 (0.20), residues: 673 sheet: -0.58 (0.19), residues: 729 loop : -1.89 (0.13), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 325 TYR 0.016 0.001 TYR J 79 PHE 0.020 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/Z covalent geometry : bond 0.00301 / 0.13 (30934) covalent geometry : angle 0.59321 / 0.30 (42088) SS BOND : bond 0.00323 / 0.23 ( 43) SS BOND : angle 1.08970 / 0.78 ( 86) hydrogen bonds : bond 0.03575 / 2.38 ( 832) hydrogen bonds : angle 5.17899 / 3.53 ( 2298) Misc. bond : bond 0.00174 / 0.09 ( 2) link_BETA1-4 : bond 0.00392 / 0.21 ( 16) link_BETA1-4 : angle 1.27616 / 0.82 ( 48) link_NAG-ASN : bond 0.00411 / 0.23 ( 46) link_NAG-ASN : angle 2.00079 / 1.36 ( 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 224 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 162 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7835 (OUTLIER) cc_final: 0.7526 (t60) REVERT: A 115 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8210 (mm-40) REVERT: A 348 TYR cc_start: 0.7371 (p90) cc_final: 0.7060 (p90) REVERT: A 811 LYS cc_start: 0.7992 (mmtt) cc_final: 0.7461 (tttt) REVERT: A 874 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8937 (mm) REVERT: B 770 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7802 (tm-30) REVERT: B 960 VAL cc_start: 0.9574 (OUTLIER) cc_final: 0.9332 (t) REVERT: C 150 MET cc_start: 0.4213 (tmm) cc_final: 0.3869 (tmm) REVERT: I 45 LYS cc_start: 0.6252 (mtmm) cc_final: 0.5910 (tptt) outliers start: 62 outliers final: 50 residues processed: 215 average time/residue: 0.1694 time to fit residues: 61.8003 Evaluate side-chains 208 residues out of total 3289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 154 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 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 489 LEU 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 B residue 329 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 425 ASP 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 884 THR Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 228 LEU 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 655 TYR Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 800 ILE Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1143 PHE 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: 0.9990 chunk 147 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 200 optimal weight: 0.5980 chunk 370 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 251 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 275 optimal weight: 6.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN H 105 ASN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.142117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.094284 restraints weight = 77741.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.095730 restraints weight = 53629.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.095433 restraints weight = 38183.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.095712 restraints weight = 38367.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.095713 restraints weight = 37826.440| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31041 Z= 0.141 Angle : 0.609 9.978 42360 Z= 0.304 Chirality : 0.046 0.420 4922 Planarity : 0.004 0.071 5360 Dihedral : 5.082 74.069 4045 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.05 % Favored : 92.81 % Rotamer: Outliers : 1.95 % Allowed : 17.05 % 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: -1.85 (0.14), residues: 3714 helix: -0.10 (0.20), residues: 673 sheet: -0.61 (0.19), residues: 745 loop : -1.88 (0.13), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 325 TYR 0.026 0.001 TYR B 393 PHE 0.021 0.001 PHE C 165 TRP 0.036 0.001 TRP B 149 HIS 0.003 0.001 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (30934) covalent geometry : angle 0.59604 / 0.30 (42088) SS BOND : bond 0.00308 / 0.22 ( 43) SS BOND : angle 1.10167 / 0.79 ( 86) hydrogen bonds : bond 0.03609 / 2.40 ( 832) hydrogen bonds : angle 5.13699 / 3.50 ( 2298) Misc. bond : bond 0.00172 / 0.09 ( 2) link_BETA1-4 : bond 0.00409 / 0.22 ( 16) link_BETA1-4 : angle 1.26584 / 0.83 ( 48) link_NAG-ASN : bond 0.00394 / 0.21 ( 46) link_NAG-ASN : angle 2.00016 / 1.36 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4954.15 seconds wall clock time: 86 minutes 42.02 seconds (5202.02 seconds total)