Starting phenix.real_space_refine on Sun Jul 5 22:12:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cwm_30483/07_2026/7cwm_30483.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cwm_30483/07_2026/7cwm_30483.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 { model { file = "/net/cci-nas-00/data/ceres_data/7cwm_30483/07_2026/7cwm_30483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cwm_30483/07_2026/7cwm_30483.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7cwm_30483/07_2026/7cwm_30483.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cwm_30483/07_2026/7cwm_30483.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cwm_30483/07_2026/7cwm_30483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cwm_30483/07_2026/7cwm_30483.map" } 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= 0.000 sd= 0.001 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 19532 2.51 5 N 5120 2.21 5 O 5987 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 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: 30772 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 8253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8253 Classifications: {'peptide': 1056} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 48, 'TRANS': 1007} Chain breaks: 7 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 8351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1071, 8351 Classifications: {'peptide': 1071} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 50, 'TRANS': 1019} Chain breaks: 6 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 8350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1072, 8350 Classifications: {'peptide': 1072} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 51, 'TRANS': 1020} Chain breaks: 6 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3, 'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "G" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 814 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "K" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 7.15, per 1000 atoms: 0.23 Number of scatterers: 30772 At special positions: 0 Unit cell: (204.88, 147.68, 170.56, 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 5987 8.00 N 5120 7.00 C 19532 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 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.05 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.00 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 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 603 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG C1301 " - " ASN C 603 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C1074 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN A1098 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN C 234 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C 801 " " NAG V 1 " - " ASN C1098 " " NAG W 1 " - " ASN C1134 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.4 seconds 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7236 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 65 sheets defined 20.7% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 290 through 293 removed outlier: 3.893A pdb=" N LEU A 293 " --> pdb=" O ASP A 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 290 through 293' Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.697A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 364 through 372 removed outlier: 4.140A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.952A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.675A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.506A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.643A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.776A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 856 removed outlier: 4.023A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.548A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.545A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 940 removed outlier: 3.519A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 988 through 1032 removed outlier: 3.538A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.038A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 364 through 372 removed outlier: 4.140A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.910A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 385 through 389' Processing helix chain 'B' and resid 405 through 409 removed outlier: 3.952A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.674A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.505A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.643A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.501A pdb=" N ASP B 820 " --> pdb=" O SER B 816 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 856 removed outlier: 4.024A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.547A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.545A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 940 removed outlier: 3.518A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.612A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.542A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.039A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 304 removed outlier: 3.725A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 364 through 372 removed outlier: 4.141A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.323A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 409 removed outlier: 3.952A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.674A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.981A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.723A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.634A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 856 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.706A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.881A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 941 removed outlier: 3.518A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.539A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.618A pdb=" N ALA C 989 " --> pdb=" O ASP C 985 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.920A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 74 through 76 No H-bonds generated for 'chain 'I' and resid 74 through 76' Processing helix chain 'I' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.095A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 205 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 55 removed outlier: 3.646A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 70 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 101 through 104 removed outlier: 6.015A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 120 removed outlier: 6.403A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 278 through 279 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.840A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.685A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.009A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.389A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.847A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.169A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.768A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 31 removed outlier: 7.848A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA B 263 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 205 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC6, first strand: chain 'B' and resid 101 through 104 removed outlier: 6.015A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.403A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.843A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.847A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 removed outlier: 4.009A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.388A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.450A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.843A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.166A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.768A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.509A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.275A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 205 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.585A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE5, first strand: chain 'C' and resid 101 through 104 removed outlier: 6.015A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 116 through 120 removed outlier: 6.403A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.933A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.804A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.009A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'C' and resid 553 through 554 removed outlier: 3.840A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.350A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.870A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.235A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF9, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AG1, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.551A pdb=" N THR G 113 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AG3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.550A pdb=" N THR H 113 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AG5, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.551A pdb=" N THR I 113 " --> pdb=" O TYR I 94 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 4 through 7 removed outlier: 11.870A pdb=" N CYS L 23 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 10.398A pdb=" N THR L 74 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N ALA L 25 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 11.277A pdb=" N THR L 72 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.346A pdb=" N GLN L 27 " --> pdb=" O ASP L 70 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ASP L 70 " --> pdb=" O GLN L 27 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.605A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 4 through 7 removed outlier: 11.871A pdb=" N CYS J 23 " --> pdb=" O THR J 74 " (cutoff:3.500A) removed outlier: 10.397A pdb=" N THR J 74 " --> pdb=" O CYS J 23 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N ALA J 25 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 11.277A pdb=" N THR J 72 " --> pdb=" O ALA J 25 " (cutoff:3.500A) removed outlier: 10.345A pdb=" N GLN J 27 " --> pdb=" O ASP J 70 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ASP J 70 " --> pdb=" O GLN J 27 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.605A pdb=" N GLU J 105 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 4 through 7 removed outlier: 11.870A pdb=" N CYS K 23 " --> pdb=" O THR K 74 " (cutoff:3.500A) removed outlier: 10.397A pdb=" N THR K 74 " --> pdb=" O CYS K 23 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N ALA K 25 " --> pdb=" O THR K 72 " (cutoff:3.500A) removed outlier: 11.277A pdb=" N THR K 72 " --> pdb=" O ALA K 25 " (cutoff:3.500A) removed outlier: 10.346A pdb=" N GLN K 27 " --> pdb=" O ASP K 70 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ASP K 70 " --> pdb=" O GLN K 27 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.605A pdb=" N GLU K 105 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 1033 hydrogen bonds defined for protein. 2757 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: 7.99 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7469 1.33 - 1.45: 7902 1.45 - 1.58: 15906 1.58 - 1.70: 0 1.70 - 1.83: 169 Bond restraints: 31446 Sorted by residual: bond pdb=" CA SER C 60 " pdb=" CB SER C 60 " ideal model delta sigma weight residual 1.533 1.476 0.058 1.51e-02 4.39e+03 1.46e+01 bond pdb=" N THR C 588 " pdb=" CA THR C 588 " ideal model delta sigma weight residual 1.456 1.493 -0.037 9.80e-03 1.04e+04 1.44e+01 bond pdb=" N LEU C 24 " pdb=" CA LEU C 24 " ideal model delta sigma weight residual 1.455 1.490 -0.035 9.60e-03 1.09e+04 1.36e+01 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.337 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" N GLU C 324 " pdb=" CA GLU C 324 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.16e-02 7.43e+03 1.10e+01 ... (remaining 31441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 40354 2.17 - 4.34: 2104 4.34 - 6.51: 247 6.51 - 8.68: 39 8.68 - 10.85: 10 Bond angle restraints: 42754 Sorted by residual: angle pdb=" N ILE C 100 " pdb=" CA ILE C 100 " pdb=" C ILE C 100 " ideal model delta sigma weight residual 113.20 102.85 10.35 9.60e-01 1.09e+00 1.16e+02 angle pdb=" N ILE A 100 " pdb=" CA ILE A 100 " pdb=" C ILE A 100 " ideal model delta sigma weight residual 113.20 102.85 10.35 9.60e-01 1.09e+00 1.16e+02 angle pdb=" N CYS B 301 " pdb=" CA CYS B 301 " pdb=" C CYS B 301 " ideal model delta sigma weight residual 113.23 102.38 10.85 1.24e+00 6.50e-01 7.65e+01 angle pdb=" CA GLY A 283 " pdb=" C GLY A 283 " pdb=" O GLY A 283 " ideal model delta sigma weight residual 122.56 116.30 6.26 1.03e+00 9.43e-01 3.70e+01 angle pdb=" N LEU A 849 " pdb=" CA LEU A 849 " pdb=" C LEU A 849 " ideal model delta sigma weight residual 113.16 106.11 7.05 1.24e+00 6.50e-01 3.23e+01 ... (remaining 42749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 17491 16.86 - 33.71: 674 33.71 - 50.57: 128 50.57 - 67.43: 40 67.43 - 84.28: 9 Dihedral angle restraints: 18342 sinusoidal: 7072 harmonic: 11270 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -159.01 73.01 1 1.00e+01 1.00e-02 6.79e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -158.90 72.90 1 1.00e+01 1.00e-02 6.78e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -158.30 72.30 1 1.00e+01 1.00e-02 6.68e+01 ... (remaining 18339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.315: 4951 0.315 - 0.630: 10 0.630 - 0.945: 0 0.945 - 1.260: 0 1.260 - 1.575: 1 Chirality restraints: 4962 Sorted by residual: chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.83 -1.57 2.00e-01 2.50e+01 6.20e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.12e+01 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.78e+01 ... (remaining 4959 not shown) Planarity restraints: 5493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " -0.333 2.00e-02 2.50e+03 2.81e-01 9.87e+02 pdb=" C7 NAG N 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " 0.489 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 1 " 0.262 2.00e-02 2.50e+03 2.24e-01 6.25e+02 pdb=" C7 NAG W 1 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG W 1 " -0.027 2.00e-02 2.50e+03 pdb=" N2 NAG W 1 " -0.373 2.00e-02 2.50e+03 pdb=" O7 NAG W 1 " 0.195 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " -0.019 2.00e-02 2.50e+03 1.16e-01 1.67e+02 pdb=" CG ASN C 234 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " 0.119 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " -0.192 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " 0.121 2.00e-02 2.50e+03 ... (remaining 5490 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 29 2.19 - 2.87: 11789 2.87 - 3.54: 42943 3.54 - 4.22: 72440 4.22 - 4.90: 122122 Nonbonded interactions: 249323 Sorted by model distance: nonbonded pdb=" CG ARG B 408 " pdb=" OG SER L 65 " model vdw 1.512 3.440 nonbonded pdb=" CD ARG B 408 " pdb=" OG SER L 65 " model vdw 1.614 3.440 nonbonded pdb=" NE ARG B 408 " pdb=" OG SER L 65 " model vdw 1.769 3.120 nonbonded pdb=" CD1 LEU B 48 " pdb=" O LYS B 304 " model vdw 1.804 3.460 nonbonded pdb=" OE2 GLU B 324 " pdb=" CG2 VAL B 534 " model vdw 1.847 3.460 ... (remaining 249318 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' and (resid 14 through 20 or (resid 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 through 356 or (resid 357 and (name N or n \ ame CA or name C or name O or name CB )) or resid 358 through 518 or (resid 519 \ through 520 and (name N or name CA or name C or name O or name CB )) or resid 52 \ 1 or resid 531 through 698 or (resid 699 and (name N or name CA or name C or nam \ e O or name CB )) or resid 700 through 1305)) selection = (chain 'B' and (resid 14 through 356 or (resid 357 and (name N or name CA or nam \ e C or name O or name CB )) or resid 358 through 378 or resid 389 through 518 or \ (resid 519 through 520 and (name N or name CA or name C or name O or name CB )) \ or resid 521 or resid 523 or resid 532 through 698 or (resid 699 and (name N or \ name CA or name C or name O or name CB )) or resid 700 through 1305)) selection = (chain 'C' and (resid 14 through 20 or (resid 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 through 329 or resid 334 through 378 or re \ sid 389 through 521 or resid 523 or resid 532 through 1305)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' 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 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = (chain 'J' and (resid 0 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 107)) selection = (chain 'K' and (resid 0 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 107)) selection = chain 'L' } 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: 6.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 29.800 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.090 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 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 : 0.009 0.393 31533 Z= 0.477 Angle : 1.080 25.661 42969 Z= 0.654 Chirality : 0.068 1.575 4962 Planarity : 0.008 0.281 5464 Dihedral : 9.927 84.284 10977 Min Nonbonded Distance : 1.512 Molprobity Statistics. All-atom Clashscore : 22.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.66 % Favored : 92.29 % Rotamer: Outliers : 0.54 % Allowed : 1.86 % Favored : 97.61 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -3.56 (0.11), residues: 3827 helix: -3.19 (0.15), residues: 587 sheet: -2.01 (0.16), residues: 816 loop : -2.37 (0.10), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 61 TYR 0.030 0.003 TYR G 94 PHE 0.035 0.003 PHE C 392 TRP 0.026 0.003 TRP G 47 HIS 0.011 0.002 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00834 / 0.45 (31446) covalent geometry : angle 1.05673 / 0.65 (42754) SS BOND : bond 0.00887 / 0.53 ( 43) SS BOND : angle 1.34215 / 0.98 ( 86) hydrogen bonds : bond 0.25403 / 16.98 ( 1029) hydrogen bonds : angle 11.56923 / 7.99 ( 2757) Misc. bond : bond 0.16534 / 8.70 ( 1) link_BETA1-4 : bond 0.00728 / 0.46 ( 14) link_BETA1-4 : angle 3.17061 / 2.06 ( 42) link_NAG-ASN : bond 0.07388 / 5.12 ( 29) link_NAG-ASN : angle 4.58423 / 2.92 ( 87) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 256 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 203 ILE cc_start: 0.7526 (mt) cc_final: 0.7194 (tt) REVERT: B 902 MET cc_start: 0.8075 (mmm) cc_final: 0.7869 (mmm) REVERT: C 221 SER cc_start: 0.6465 (m) cc_final: 0.6195 (p) REVERT: L 79 GLN cc_start: 0.6293 (mm-40) cc_final: 0.5924 (mm110) outliers start: 18 outliers final: 9 residues processed: 272 average time/residue: 0.2264 time to fit residues: 94.8286 Evaluate side-chains 116 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 524 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 121 ASN A 234 ASN A 317 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN A 519 HIS A 655 HIS ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN B 121 ASN B 122 ASN B 317 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 564 GLN B 779 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN C 66 HIS C 146 HIS C 148 ASN C 282 ASN C 317 ASN C 498 GLN C 501 ASN C 655 HIS C 901 GLN C 913 GLN C 935 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 ASN G 104 ASN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN H 104 ASN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 ASN I 104 ASN I 105 ASN L 38 GLN J 38 GLN ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.069502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.050236 restraints weight = 213875.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.051644 restraints weight = 105358.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.052396 restraints weight = 67620.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.052940 restraints weight = 51837.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.053281 restraints weight = 43579.996| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31533 Z= 0.184 Angle : 0.725 16.727 42969 Z= 0.371 Chirality : 0.047 0.607 4962 Planarity : 0.005 0.052 5464 Dihedral : 6.622 58.491 4186 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.51 % Favored : 94.46 % Rotamer: Outliers : 1.11 % Allowed : 4.70 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.03 % Twisted Proline : 0.00 % 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: -2.53 (0.12), residues: 3827 helix: -0.91 (0.18), residues: 637 sheet: -1.69 (0.16), residues: 887 loop : -1.94 (0.12), residues: 2303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 408 TYR 0.029 0.002 TYR I 53 PHE 0.035 0.002 PHE B 106 TRP 0.036 0.002 TRP I 109 HIS 0.009 0.002 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (31446) covalent geometry : angle 0.71201 / 0.37 (42754) SS BOND : bond 0.00279 / 0.18 ( 43) SS BOND : angle 1.10495 / 0.74 ( 86) hydrogen bonds : bond 0.05281 / 3.48 ( 1029) hydrogen bonds : angle 7.58594 / 5.26 ( 2757) Misc. bond : bond 0.00636 / 0.33 ( 1) link_BETA1-4 : bond 0.00787 / 0.55 ( 14) link_BETA1-4 : angle 2.16983 / 1.44 ( 42) link_NAG-ASN : bond 0.00438 / 0.29 ( 29) link_NAG-ASN : angle 2.69487 / 1.62 ( 87) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5247 (tpt) cc_final: 0.5028 (tpt) REVERT: B 239 GLN cc_start: 0.6961 (tt0) cc_final: 0.6243 (tp40) REVERT: B 869 MET cc_start: 0.7965 (mtp) cc_final: 0.7755 (mtm) REVERT: B 1029 MET cc_start: 0.8732 (tpp) cc_final: 0.8496 (tpp) REVERT: C 221 SER cc_start: 0.7042 (m) cc_final: 0.6631 (p) REVERT: C 740 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7970 (tpp) REVERT: H 34 MET cc_start: 0.8352 (tpp) cc_final: 0.8145 (tpp) REVERT: I 103 MET cc_start: 0.7581 (tpt) cc_final: 0.7313 (tpt) REVERT: L 90 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.8029 (pp30) REVERT: L 92 TYR cc_start: 0.8972 (t80) cc_final: 0.8447 (t80) REVERT: K 34 ASN cc_start: 0.4616 (m-40) cc_final: 0.4144 (m-40) outliers start: 37 outliers final: 13 residues processed: 159 average time/residue: 0.2039 time to fit residues: 52.1115 Evaluate side-chains 113 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain I residue 105 ASN Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain K residue 22 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 28 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 chunk 195 optimal weight: 9.9990 chunk 208 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 315 optimal weight: 0.9980 chunk 329 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 381 optimal weight: 40.0000 chunk 181 optimal weight: 0.8980 chunk 233 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A 498 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C 935 GLN C 992 GLN C1002 GLN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 ASN I 104 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN J 55 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.069074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.050046 restraints weight = 212716.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.051458 restraints weight = 105026.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.052223 restraints weight = 68314.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.052802 restraints weight = 52691.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.052882 restraints weight = 44422.748| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31533 Z= 0.153 Angle : 0.623 15.578 42969 Z= 0.314 Chirality : 0.044 0.538 4962 Planarity : 0.004 0.043 5464 Dihedral : 5.803 59.784 4181 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.02 % Favored : 94.96 % Rotamer: Outliers : 1.11 % Allowed : 6.26 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.03 % 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: -1.88 (0.13), residues: 3827 helix: 0.42 (0.20), residues: 646 sheet: -1.41 (0.16), residues: 933 loop : -1.71 (0.12), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 408 TYR 0.024 0.001 TYR A 170 PHE 0.030 0.002 PHE C 106 TRP 0.023 0.001 TRP I 109 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (31446) covalent geometry : angle 0.60847 / 0.31 (42754) SS BOND : bond 0.00506 / 0.23 ( 43) SS BOND : angle 0.91390 / 0.61 ( 86) hydrogen bonds : bond 0.04226 / 2.80 ( 1029) hydrogen bonds : angle 6.49453 / 4.51 ( 2757) Misc. bond : bond 0.00057 / 0.03 ( 1) link_BETA1-4 : bond 0.00579 / 0.39 ( 14) link_BETA1-4 : angle 2.32018 / 1.56 ( 42) link_NAG-ASN : bond 0.00474 / 0.31 ( 29) link_NAG-ASN : angle 2.47668 / 1.47 ( 87) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5216 (tpt) cc_final: 0.4923 (tpt) REVERT: A 902 MET cc_start: 0.9177 (mmm) cc_final: 0.8920 (mmm) REVERT: B 153 MET cc_start: 0.4352 (tpp) cc_final: 0.4140 (tpp) REVERT: B 239 GLN cc_start: 0.7045 (tt0) cc_final: 0.6357 (tp40) REVERT: B 315 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8358 (p) REVERT: C 63 THR cc_start: 0.8770 (OUTLIER) cc_final: 0.8520 (p) REVERT: C 221 SER cc_start: 0.6866 (m) cc_final: 0.6491 (p) REVERT: C 740 MET cc_start: 0.8463 (tpp) cc_final: 0.7965 (tpp) REVERT: I 103 MET cc_start: 0.6782 (tpt) cc_final: 0.6352 (tpt) REVERT: L 92 TYR cc_start: 0.8935 (t80) cc_final: 0.8439 (t80) REVERT: K 34 ASN cc_start: 0.4088 (m-40) cc_final: 0.3858 (m-40) REVERT: K 92 TYR cc_start: 0.8038 (t80) cc_final: 0.7818 (t80) outliers start: 37 outliers final: 16 residues processed: 145 average time/residue: 0.1845 time to fit residues: 44.4578 Evaluate side-chains 117 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 105 ASN Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 208 optimal weight: 0.7980 chunk 232 optimal weight: 6.9990 chunk 239 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 161 optimal weight: 0.9990 chunk 328 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 209 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN A 935 GLN B 121 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 HIS I 104 ASN L 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.068662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.049614 restraints weight = 212146.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.050984 restraints weight = 105533.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.051937 restraints weight = 68469.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.052467 restraints weight = 52097.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.052694 restraints weight = 43669.183| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31533 Z= 0.142 Angle : 0.584 14.076 42969 Z= 0.293 Chirality : 0.043 0.479 4962 Planarity : 0.003 0.044 5464 Dihedral : 5.329 58.913 4179 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.91 % Favored : 95.06 % Rotamer: Outliers : 1.26 % Allowed : 7.24 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.03 % 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: -1.57 (0.13), residues: 3827 helix: 1.03 (0.21), residues: 640 sheet: -1.26 (0.16), residues: 933 loop : -1.60 (0.12), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 408 TYR 0.022 0.001 TYR I 53 PHE 0.027 0.001 PHE A 133 TRP 0.014 0.001 TRP I 109 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (31446) covalent geometry : angle 0.57081 / 0.29 (42754) SS BOND : bond 0.00665 / 0.24 ( 43) SS BOND : angle 1.04844 / 0.67 ( 86) hydrogen bonds : bond 0.03777 / 2.50 ( 1029) hydrogen bonds : angle 6.00202 / 4.18 ( 2757) Misc. bond : bond 0.00070 / 0.04 ( 1) link_BETA1-4 : bond 0.00677 / 0.48 ( 14) link_BETA1-4 : angle 2.09970 / 1.41 ( 42) link_NAG-ASN : bond 0.00394 / 0.26 ( 29) link_NAG-ASN : angle 2.24114 / 1.32 ( 87) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 104 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5105 (tpt) cc_final: 0.4826 (tpt) REVERT: A 902 MET cc_start: 0.9208 (mmm) cc_final: 0.8890 (tpp) REVERT: B 239 GLN cc_start: 0.7130 (tt0) cc_final: 0.6458 (tp40) REVERT: C 740 MET cc_start: 0.8496 (tpp) cc_final: 0.7934 (tpp) REVERT: C 1145 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7601 (tt) REVERT: L 92 TYR cc_start: 0.8984 (t80) cc_final: 0.8409 (t80) REVERT: K 34 ASN cc_start: 0.3852 (m-40) cc_final: 0.3362 (m-40) outliers start: 42 outliers final: 23 residues processed: 141 average time/residue: 0.1942 time to fit residues: 45.6841 Evaluate side-chains 115 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 13 optimal weight: 0.6980 chunk 342 optimal weight: 50.0000 chunk 216 optimal weight: 8.9990 chunk 270 optimal weight: 3.9990 chunk 302 optimal weight: 0.0980 chunk 20 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 352 optimal weight: 8.9990 chunk 290 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.068566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.049814 restraints weight = 211164.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.050978 restraints weight = 104418.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.051827 restraints weight = 68031.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.052381 restraints weight = 51943.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.052703 restraints weight = 43727.653| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 31533 Z= 0.124 Angle : 0.560 13.397 42969 Z= 0.279 Chirality : 0.043 0.454 4962 Planarity : 0.003 0.047 5464 Dihedral : 5.130 58.916 4179 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.65 % Favored : 95.32 % Rotamer: Outliers : 1.20 % Allowed : 7.66 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.03 % 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: -1.42 (0.13), residues: 3827 helix: 1.17 (0.21), residues: 654 sheet: -1.14 (0.16), residues: 924 loop : -1.54 (0.12), residues: 2249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.022 0.001 TYR I 53 PHE 0.016 0.001 PHE B 106 TRP 0.011 0.001 TRP I 109 HIS 0.015 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (31446) covalent geometry : angle 0.54691 / 0.28 (42754) SS BOND : bond 0.00255 / 0.18 ( 43) SS BOND : angle 0.93547 / 0.65 ( 86) hydrogen bonds : bond 0.03615 / 2.38 ( 1029) hydrogen bonds : angle 5.73431 / 3.99 ( 2757) Misc. bond : bond 0.00051 / 0.03 ( 1) link_BETA1-4 : bond 0.00582 / 0.41 ( 14) link_BETA1-4 : angle 2.12697 / 1.43 ( 42) link_NAG-ASN : bond 0.00368 / 0.24 ( 29) link_NAG-ASN : angle 2.15152 / 1.27 ( 87) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 101 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5135 (tpt) cc_final: 0.4837 (tpt) REVERT: A 906 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8600 (m-10) REVERT: B 239 GLN cc_start: 0.7130 (tt0) cc_final: 0.6457 (tp40) REVERT: B 315 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8594 (p) REVERT: C 63 THR cc_start: 0.8770 (OUTLIER) cc_final: 0.8555 (p) REVERT: C 740 MET cc_start: 0.8527 (tpp) cc_final: 0.7961 (tpp) REVERT: C 1145 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7462 (tt) REVERT: I 103 MET cc_start: 0.6919 (tpt) cc_final: 0.6529 (tpt) REVERT: L 92 TYR cc_start: 0.8983 (t80) cc_final: 0.8392 (t80) outliers start: 40 outliers final: 21 residues processed: 135 average time/residue: 0.1945 time to fit residues: 43.6004 Evaluate side-chains 111 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 112 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 368 optimal weight: 30.0000 chunk 379 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 224 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 284 optimal weight: 6.9990 chunk 339 optimal weight: 20.0000 chunk 75 optimal weight: 7.9990 chunk 281 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 125 ASN C 762 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 GLN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.066321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.047251 restraints weight = 210883.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.048380 restraints weight = 106067.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.049106 restraints weight = 70203.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.049530 restraints weight = 54154.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.049925 restraints weight = 46789.418| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 31533 Z= 0.298 Angle : 0.717 16.915 42969 Z= 0.358 Chirality : 0.046 0.388 4962 Planarity : 0.004 0.048 5464 Dihedral : 5.471 50.622 4178 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.38 % Favored : 93.60 % Rotamer: Outliers : 1.62 % Allowed : 8.23 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.03 % 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: -1.65 (0.13), residues: 3827 helix: 0.73 (0.20), residues: 674 sheet: -1.33 (0.17), residues: 821 loop : -1.60 (0.12), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 72 TYR 0.027 0.002 TYR A 269 PHE 0.042 0.002 PHE C 855 TRP 0.020 0.002 TRP I 36 HIS 0.036 0.002 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.30 (31446) covalent geometry : angle 0.70379 / 0.36 (42754) SS BOND : bond 0.00315 / 0.22 ( 43) SS BOND : angle 1.09971 / 0.74 ( 86) hydrogen bonds : bond 0.04296 / 2.83 ( 1029) hydrogen bonds : angle 6.05990 / 4.24 ( 2757) Misc. bond : bond 0.00082 / 0.04 ( 1) link_BETA1-4 : bond 0.00932 / 0.64 ( 14) link_BETA1-4 : angle 2.25325 / 1.50 ( 42) link_NAG-ASN : bond 0.00878 / 0.51 ( 29) link_NAG-ASN : angle 2.65317 / 1.70 ( 87) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 89 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5099 (tpt) cc_final: 0.4751 (tpt) REVERT: A 1089 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8374 (m-80) REVERT: C 740 MET cc_start: 0.8667 (tpp) cc_final: 0.8084 (tpp) REVERT: C 1145 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7655 (tt) REVERT: I 35 HIS cc_start: 0.5632 (m90) cc_final: 0.5296 (m170) REVERT: I 103 MET cc_start: 0.6247 (tpt) cc_final: 0.5584 (tpt) REVERT: L 92 TYR cc_start: 0.8955 (t80) cc_final: 0.8389 (t80) outliers start: 54 outliers final: 30 residues processed: 138 average time/residue: 0.1943 time to fit residues: 45.0581 Evaluate side-chains 112 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 80 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain K residue 22 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 38 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 171 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 146 optimal weight: 9.9990 chunk 356 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 211 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 256 optimal weight: 20.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN C 641 ASN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** 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 = 0.4047 r_free = 0.4047 target = 0.067498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.048425 restraints weight = 210886.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.049793 restraints weight = 104679.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.050465 restraints weight = 67625.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.051084 restraints weight = 53636.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.051394 restraints weight = 45320.990| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 31533 Z= 0.123 Angle : 0.575 14.550 42969 Z= 0.287 Chirality : 0.043 0.394 4962 Planarity : 0.004 0.050 5464 Dihedral : 5.011 47.821 4176 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.73 % Favored : 95.24 % Rotamer: Outliers : 0.99 % Allowed : 9.10 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.03 % 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: -1.41 (0.13), residues: 3827 helix: 1.12 (0.21), residues: 659 sheet: -1.31 (0.16), residues: 897 loop : -1.43 (0.12), residues: 2271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 18 TYR 0.014 0.001 TYR A 279 PHE 0.024 0.001 PHE K 98 TRP 0.018 0.001 TRP I 36 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (31446) covalent geometry : angle 0.55996 / 0.28 (42754) SS BOND : bond 0.00401 / 0.23 ( 43) SS BOND : angle 1.78726 / 1.30 ( 86) hydrogen bonds : bond 0.03530 / 2.30 ( 1029) hydrogen bonds : angle 5.62334 / 3.91 ( 2757) Misc. bond : bond 0.00089 / 0.05 ( 1) link_BETA1-4 : bond 0.00608 / 0.43 ( 14) link_BETA1-4 : angle 2.06741 / 1.41 ( 42) link_NAG-ASN : bond 0.00356 / 0.24 ( 29) link_NAG-ASN : angle 1.97288 / 1.17 ( 87) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5092 (tpt) cc_final: 0.4796 (tpt) REVERT: A 902 MET cc_start: 0.8895 (tpp) cc_final: 0.8685 (mmm) REVERT: A 906 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8599 (m-10) REVERT: B 239 GLN cc_start: 0.7240 (tt0) cc_final: 0.6652 (tp40) REVERT: C 63 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8594 (p) REVERT: C 740 MET cc_start: 0.8584 (tpp) cc_final: 0.7999 (tpp) REVERT: C 1145 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7358 (tt) REVERT: I 34 MET cc_start: 0.6844 (tpp) cc_final: 0.6334 (tpp) REVERT: I 35 HIS cc_start: 0.5883 (OUTLIER) cc_final: 0.5203 (m170) REVERT: I 103 MET cc_start: 0.6352 (tpt) cc_final: 0.5877 (tpt) REVERT: L 92 TYR cc_start: 0.8964 (t80) cc_final: 0.8370 (t80) outliers start: 33 outliers final: 20 residues processed: 112 average time/residue: 0.1864 time to fit residues: 35.8649 Evaluate side-chains 105 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 261 optimal weight: 8.9990 chunk 342 optimal weight: 50.0000 chunk 331 optimal weight: 4.9990 chunk 121 optimal weight: 0.3980 chunk 236 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 287 optimal weight: 0.6980 chunk 190 optimal weight: 7.9990 chunk 289 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 268 optimal weight: 0.6980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** 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 = 0.4030 r_free = 0.4030 target = 0.066826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.047644 restraints weight = 212237.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.048860 restraints weight = 105783.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.049807 restraints weight = 69994.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.050128 restraints weight = 53251.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.050456 restraints weight = 46596.868| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 31533 Z= 0.172 Angle : 0.597 15.037 42969 Z= 0.298 Chirality : 0.043 0.363 4962 Planarity : 0.004 0.049 5464 Dihedral : 4.980 43.658 4175 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.38 % Favored : 94.59 % Rotamer: Outliers : 1.11 % Allowed : 9.04 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.03 % 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: -1.40 (0.13), residues: 3827 helix: 1.01 (0.21), residues: 674 sheet: -1.28 (0.17), residues: 871 loop : -1.41 (0.12), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 38 TYR 0.016 0.001 TYR A 269 PHE 0.019 0.001 PHE C 855 TRP 0.016 0.001 TRP I 36 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (31446) covalent geometry : angle 0.57870 / 0.29 (42754) SS BOND : bond 0.00538 / 0.45 ( 43) SS BOND : angle 2.22419 / 1.43 ( 86) hydrogen bonds : bond 0.03626 / 2.39 ( 1029) hydrogen bonds : angle 5.57242 / 3.89 ( 2757) Misc. bond : bond 0.00065 / 0.03 ( 1) link_BETA1-4 : bond 0.00612 / 0.43 ( 14) link_BETA1-4 : angle 2.08428 / 1.40 ( 42) link_NAG-ASN : bond 0.00507 / 0.31 ( 29) link_NAG-ASN : angle 2.13757 / 1.33 ( 87) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 79 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5298 (tpt) cc_final: 0.4992 (tpt) REVERT: A 697 MET cc_start: 0.7711 (mmm) cc_final: 0.7408 (mmm) REVERT: A 906 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8752 (m-10) REVERT: B 109 THR cc_start: 0.3947 (OUTLIER) cc_final: 0.3688 (p) REVERT: B 239 GLN cc_start: 0.7268 (tt0) cc_final: 0.6676 (tp40) REVERT: B 1050 MET cc_start: 0.8130 (mtm) cc_final: 0.7885 (ptp) REVERT: C 63 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8574 (p) REVERT: C 740 MET cc_start: 0.8145 (tpp) cc_final: 0.7519 (tpp) REVERT: C 1145 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7495 (tt) REVERT: I 34 MET cc_start: 0.6599 (tpp) cc_final: 0.6165 (tpp) REVERT: I 35 HIS cc_start: 0.6196 (OUTLIER) cc_final: 0.5533 (m170) REVERT: I 103 MET cc_start: 0.6531 (tpt) cc_final: 0.6052 (tpt) REVERT: L 92 TYR cc_start: 0.8962 (t80) cc_final: 0.8401 (t80) outliers start: 37 outliers final: 24 residues processed: 111 average time/residue: 0.1748 time to fit residues: 33.6192 Evaluate side-chains 105 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 144 optimal weight: 6.9990 chunk 262 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 13 optimal weight: 0.5980 chunk 238 optimal weight: 3.9990 chunk 351 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 205 optimal weight: 0.8980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN B1088 HIS C1002 GLN C1088 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 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 = 0.4028 r_free = 0.4028 target = 0.066733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.047729 restraints weight = 209593.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.048952 restraints weight = 104597.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.049833 restraints weight = 68974.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.050320 restraints weight = 52510.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.050597 restraints weight = 44414.881| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 31533 Z= 0.157 Angle : 0.583 15.201 42969 Z= 0.290 Chirality : 0.043 0.348 4962 Planarity : 0.004 0.055 5464 Dihedral : 4.852 37.546 4175 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.02 % Favored : 94.96 % Rotamer: Outliers : 1.14 % Allowed : 8.95 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.03 % 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: -1.25 (0.13), residues: 3827 helix: 1.12 (0.21), residues: 668 sheet: -1.13 (0.17), residues: 923 loop : -1.32 (0.13), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 38 TYR 0.051 0.001 TYR K 36 PHE 0.021 0.001 PHE A 898 TRP 0.032 0.001 TRP I 36 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (31446) covalent geometry : angle 0.56867 / 0.29 (42754) SS BOND : bond 0.00261 / 0.18 ( 43) SS BOND : angle 1.77312 / 1.13 ( 86) hydrogen bonds : bond 0.03486 / 2.29 ( 1029) hydrogen bonds : angle 5.45474 / 3.81 ( 2757) Misc. bond : bond 0.00073 / 0.04 ( 1) link_BETA1-4 : bond 0.00579 / 0.40 ( 14) link_BETA1-4 : angle 2.04806 / 1.39 ( 42) link_NAG-ASN : bond 0.00421 / 0.27 ( 29) link_NAG-ASN : angle 1.95772 / 1.20 ( 87) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 86 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5046 (tpt) cc_final: 0.4782 (tpt) REVERT: A 697 MET cc_start: 0.7812 (mmm) cc_final: 0.7600 (mmm) REVERT: A 906 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.8639 (m-10) REVERT: B 109 THR cc_start: 0.3958 (OUTLIER) cc_final: 0.3664 (p) REVERT: C 63 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8603 (p) REVERT: C 740 MET cc_start: 0.8118 (tpp) cc_final: 0.7526 (tpp) REVERT: C 1145 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7360 (tt) REVERT: I 34 MET cc_start: 0.6761 (tpp) cc_final: 0.6537 (tpp) REVERT: L 92 TYR cc_start: 0.8976 (t80) cc_final: 0.8400 (t80) outliers start: 38 outliers final: 26 residues processed: 118 average time/residue: 0.1686 time to fit residues: 33.7128 Evaluate side-chains 107 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 312 optimal weight: 3.9990 chunk 257 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 332 optimal weight: 30.0000 chunk 166 optimal weight: 3.9990 chunk 320 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 326 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS G 2 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.065203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.045667 restraints weight = 209669.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.046885 restraints weight = 107928.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.047685 restraints weight = 72237.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.048105 restraints weight = 55746.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.048229 restraints weight = 48301.176| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 31533 Z= 0.298 Angle : 0.738 18.142 42969 Z= 0.367 Chirality : 0.046 0.302 4962 Planarity : 0.004 0.053 5464 Dihedral : 5.428 30.356 4175 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.24 % Favored : 92.74 % Rotamer: Outliers : 1.05 % Allowed : 9.16 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.03 % 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: -1.58 (0.13), residues: 3827 helix: 0.61 (0.20), residues: 697 sheet: -1.36 (0.17), residues: 901 loop : -1.47 (0.13), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 38 TYR 0.027 0.002 TYR B 269 PHE 0.026 0.002 PHE B 135 TRP 0.019 0.002 TRP I 36 HIS 0.010 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00646 / 0.30 (31446) covalent geometry : angle 0.72220 / 0.36 (42754) SS BOND : bond 0.00393 / 0.28 ( 43) SS BOND : angle 1.91031 / 1.23 ( 86) hydrogen bonds : bond 0.04249 / 2.83 ( 1029) hydrogen bonds : angle 5.96490 / 4.18 ( 2757) Misc. bond : bond 0.00082 / 0.04 ( 1) link_BETA1-4 : bond 0.00656 / 0.44 ( 14) link_BETA1-4 : angle 2.26188 / 1.51 ( 42) link_NAG-ASN : bond 0.00947 / 0.55 ( 29) link_NAG-ASN : angle 2.61888 / 1.73 ( 87) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 83 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8016 (mmm) cc_final: 0.7719 (mmm) REVERT: B 109 THR cc_start: 0.4354 (OUTLIER) cc_final: 0.4040 (p) REVERT: C 556 ASN cc_start: 0.7716 (p0) cc_final: 0.7415 (p0) REVERT: C 740 MET cc_start: 0.8317 (tpp) cc_final: 0.7795 (tpp) REVERT: C 1145 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7692 (tp) REVERT: I 34 MET cc_start: 0.5689 (tpp) cc_final: 0.5453 (tpp) REVERT: I 103 MET cc_start: 0.7453 (tpt) cc_final: 0.6970 (tpt) REVERT: L 92 TYR cc_start: 0.8999 (t80) cc_final: 0.8382 (t80) outliers start: 35 outliers final: 27 residues processed: 113 average time/residue: 0.1769 time to fit residues: 34.2125 Evaluate side-chains 107 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain K residue 22 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 233 optimal weight: 0.9980 chunk 0 optimal weight: 40.0000 chunk 365 optimal weight: 4.9990 chunk 245 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 43 optimal weight: 0.0370 chunk 334 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 322 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN ** K 34 ASN ** 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 = 0.4005 r_free = 0.4005 target = 0.065805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.046726 restraints weight = 209513.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.047983 restraints weight = 106476.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.048732 restraints weight = 69348.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 74)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.049127 restraints weight = 53564.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.049446 restraints weight = 45445.800| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 31533 Z= 0.189 Angle : 0.615 16.353 42969 Z= 0.306 Chirality : 0.043 0.324 4962 Planarity : 0.004 0.055 5464 Dihedral : 5.111 26.622 4175 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.80 % Favored : 94.17 % Rotamer: Outliers : 0.93 % Allowed : 9.34 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.03 % 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: -1.47 (0.13), residues: 3827 helix: 0.84 (0.20), residues: 686 sheet: -1.31 (0.16), residues: 912 loop : -1.43 (0.13), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 18 TYR 0.019 0.001 TYR B 269 PHE 0.019 0.002 PHE A 135 TRP 0.056 0.002 TRP K 35 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 (31446) covalent geometry : angle 0.60172 / 0.30 (42754) SS BOND : bond 0.00339 / 0.23 ( 43) SS BOND : angle 1.56716 / 1.02 ( 86) hydrogen bonds : bond 0.03679 / 2.41 ( 1029) hydrogen bonds : angle 5.69529 / 3.99 ( 2757) Misc. bond : bond 0.00086 / 0.05 ( 1) link_BETA1-4 : bond 0.00523 / 0.37 ( 14) link_BETA1-4 : angle 2.06600 / 1.41 ( 42) link_NAG-ASN : bond 0.00499 / 0.30 ( 29) link_NAG-ASN : angle 2.07528 / 1.32 ( 87) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6440.78 seconds wall clock time: 111 minutes 42.20 seconds (6702.20 seconds total)