Starting phenix.real_space_refine on Thu Mar 5 23:24:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xlu_22251/03_2026/6xlu_22251.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xlu_22251/03_2026/6xlu_22251.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xlu_22251/03_2026/6xlu_22251.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xlu_22251/03_2026/6xlu_22251.map" model { file = "/net/cci-nas-00/data/ceres_data/6xlu_22251/03_2026/6xlu_22251.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xlu_22251/03_2026/6xlu_22251.cif" } resolution = 2.4 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= 0.003 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 111 5.16 5 C 16374 2.51 5 N 4198 2.21 5 O 5307 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25990 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1057, 8262 Classifications: {'peptide': 1057} Link IDs: {'PTRANS': 51, 'TRANS': 1005} Chain breaks: 7 Conformer: "B" Number of residues, atoms: 1057, 8262 Classifications: {'peptide': 1057} Link IDs: {'PTRANS': 51, 'TRANS': 1005} Chain breaks: 7 bond proxies already assigned to first conformer: 8431 Chain: "B" Number of atoms: 8302 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1061, 8288 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 52, 'TRANS': 1008} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 1061, 8288 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 52, 'TRANS': 1008} Chain breaks: 6 bond proxies already assigned to first conformer: 8460 Chain: "C" Number of atoms: 8294 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1060, 8280 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 7 Conformer: "B" Number of residues, atoms: 1060, 8280 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 7 bond proxies already assigned to first conformer: 8451 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "C" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Time building chain proxies: 11.00, per 1000 atoms: 0.42 Number of scatterers: 25990 At special positions: 0 Unit cell: (133.45, 135.15, 176.8, 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 111 16.00 O 5307 8.00 N 4198 7.00 C 16374 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.06 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.05 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.04 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 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.05 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.07 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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=0, 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C 234 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C1098 " " NAG R 1 " - " ASN C1134 " Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 1.8 seconds 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5974 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 48 sheets defined 26.6% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.679A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.559A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.565A pdb=" N VAL A 635 " --> pdb=" O PRO A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.806A 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: 3.620A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 835 through 839 Processing helix chain 'A' and resid 848 through 855 removed outlier: 3.528A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.135A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.041A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.525A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.623A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.483A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.647A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.701A 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: 3.602A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 834 through 839 removed outlier: 3.781A pdb=" N GLY B 838 " --> pdb=" O ILE B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.621A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.133A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.973A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.527A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1129 removed outlier: 3.725A pdb=" N VAL B1128 " --> pdb=" O ASN B1125 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL B1129 " --> pdb=" O CYS B1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1125 through 1129' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.645A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.496A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.838A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.641A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (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: 3.829A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 834 through 838 Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.559A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.116A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.058A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.577A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1125 through 1129 removed outlier: 3.784A pdb=" N VAL C1128 " --> pdb=" O ASN C1125 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL C1129 " --> pdb=" O CYS C1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1125 through 1129' Processing helix chain 'C' and resid 1141 through 1145 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.362A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.631A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.615A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 157 through 164 removed outlier: 7.092A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.378A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.573A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.573A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.581A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.509A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.612A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.638A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.572A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.425A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.504A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.587A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.667A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.771A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 10.360A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE B 140 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.649A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.220A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.591A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.591A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.655A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.497A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.509A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.620A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.553A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.493A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.538A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.595A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.599A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.203A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.576A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.576A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.609A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.188A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.651A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.542A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.492A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 992 hydrogen bonds defined for protein. 2708 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: 5.91 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 8089 1.34 - 1.48: 7349 1.48 - 1.62: 10739 1.62 - 1.76: 14 1.76 - 1.91: 121 Bond restraints: 26312 Sorted by residual: bond pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " ideal model delta sigma weight residual 1.808 1.690 0.118 3.30e-02 9.18e+02 1.27e+01 bond pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " ideal model delta sigma weight residual 1.808 1.692 0.116 3.30e-02 9.18e+02 1.24e+01 bond pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " ideal model delta sigma weight residual 1.808 1.692 0.116 3.30e-02 9.18e+02 1.23e+01 bond pdb=" C PRO B 986 " pdb=" N PRO B 987 " ideal model delta sigma weight residual 1.335 1.378 -0.043 1.36e-02 5.41e+03 9.80e+00 bond pdb=" C1 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.19e+00 ... (remaining 26307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.73: 35427 3.73 - 7.45: 349 7.45 - 11.18: 38 11.18 - 14.91: 5 14.91 - 18.63: 1 Bond angle restraints: 35820 Sorted by residual: angle pdb=" CA CYS C 525 " pdb=" CB CYS C 525 " pdb=" SG CYS C 525 " ideal model delta sigma weight residual 114.40 133.03 -18.63 2.30e+00 1.89e-01 6.56e+01 angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 133.71 -12.17 1.91e+00 2.74e-01 4.06e+01 angle pdb=" C SER A 31 " pdb=" N PHE A 32 " pdb=" CA PHE A 32 " ideal model delta sigma weight residual 121.54 133.62 -12.08 1.91e+00 2.74e-01 4.00e+01 angle pdb=" CA BTYR A 904 " pdb=" CB BTYR A 904 " pdb=" CG BTYR A 904 " ideal model delta sigma weight residual 113.90 125.27 -11.37 1.80e+00 3.09e-01 3.99e+01 angle pdb=" CA BTYR C 904 " pdb=" CB BTYR C 904 " pdb=" CG BTYR C 904 " ideal model delta sigma weight residual 113.90 124.93 -11.03 1.80e+00 3.09e-01 3.76e+01 ... (remaining 35815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 14877 17.90 - 35.80: 1315 35.80 - 53.71: 224 53.71 - 71.61: 42 71.61 - 89.51: 36 Dihedral angle restraints: 16494 sinusoidal: 7209 harmonic: 9285 Sorted by residual: dihedral pdb=" CA ILE B 794 " pdb=" C ILE B 794 " pdb=" N LYS B 795 " pdb=" CA LYS B 795 " ideal model delta harmonic sigma weight residual 180.00 142.97 37.03 0 5.00e+00 4.00e-02 5.49e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 37.23 55.77 1 1.00e+01 1.00e-02 4.20e+01 dihedral pdb=" CA GLN C 836 " pdb=" C GLN C 836 " pdb=" N TYR C 837 " pdb=" CA TYR C 837 " ideal model delta harmonic sigma weight residual 180.00 147.64 32.36 0 5.00e+00 4.00e-02 4.19e+01 ... (remaining 16491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.243: 4242 0.243 - 0.486: 8 0.486 - 0.729: 1 0.729 - 0.971: 0 0.971 - 1.214: 3 Chirality restraints: 4254 Sorted by residual: chirality pdb=" CG LEU C 916 " pdb=" CB LEU C 916 " pdb=" CD1 LEU C 916 " pdb=" CD2 LEU C 916 " both_signs ideal model delta sigma weight residual False -2.59 -1.38 -1.21 2.00e-01 2.50e+01 3.69e+01 chirality pdb=" CG LEU B 916 " pdb=" CB LEU B 916 " pdb=" CD1 LEU B 916 " pdb=" CD2 LEU B 916 " both_signs ideal model delta sigma weight residual False -2.59 -1.42 -1.17 2.00e-01 2.50e+01 3.43e+01 chirality pdb=" CG LEU A 916 " pdb=" CB LEU A 916 " pdb=" CD1 LEU A 916 " pdb=" CD2 LEU A 916 " both_signs ideal model delta sigma weight residual False -2.59 -1.45 -1.14 2.00e-01 2.50e+01 3.23e+01 ... (remaining 4251 not shown) Planarity restraints: 4605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 886 " 0.030 2.00e-02 2.50e+03 2.59e-02 1.68e+01 pdb=" CG TRP B 886 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP B 886 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP B 886 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B 886 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 886 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 886 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 886 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 886 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 886 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " -0.029 2.00e-02 2.50e+03 2.51e-02 1.58e+01 pdb=" CG TRP C 886 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 886 " 0.030 2.00e-02 2.50e+03 2.47e-02 1.52e+01 pdb=" CG TRP A 886 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP A 886 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP A 886 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 886 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 886 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 886 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 886 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 886 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 886 " 0.020 2.00e-02 2.50e+03 ... (remaining 4602 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4392 2.77 - 3.30: 21671 3.30 - 3.84: 42544 3.84 - 4.37: 50830 4.37 - 4.90: 85348 Nonbonded interactions: 204785 Sorted by model distance: nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.240 3.040 nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 2.252 3.040 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 2.257 3.040 nonbonded pdb=" O HOH B1403 " pdb=" O HOH B1451 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR A1138 " pdb=" OE2 GLU A1144 " model vdw 2.266 3.040 ... (remaining 204780 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 27 through 172 or resid 186 through 250 or resid 265 throu \ gh 903 or resid 905 through 954 or resid 956 through 1310)) selection = (chain 'B' and (resid 27 through 250 or resid 265 through 828 or resid 834 throu \ gh 903 or resid 905 through 954 or resid 956 through 1310)) selection = (chain 'C' and (resid 27 through 250 or resid 265 through 828 or resid 834 throu \ gh 903 or resid 905 through 954 or resid 956 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.490 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: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 30.790 Find NCS groups from input model: 0.800 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:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 : 0.010 0.118 26416 Z= 0.427 Angle : 1.179 19.001 36090 Z= 0.634 Chirality : 0.077 1.214 4254 Planarity : 0.008 0.069 4558 Dihedral : 14.128 89.511 10394 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.03 % Favored : 93.84 % Rotamer: Outliers : 0.36 % Allowed : 3.45 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.50 (0.13), residues: 3138 helix: -1.12 (0.17), residues: 708 sheet: -0.48 (0.18), residues: 668 loop : -2.47 (0.12), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 847 TYR 0.031 0.004 TYR A1067 PHE 0.034 0.004 PHE B 32 TRP 0.064 0.005 TRP C 886 HIS 0.014 0.003 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00977 (26312) covalent geometry : angle 1.11713 (35820) SS BOND : bond 0.01023 ( 42) SS BOND : angle 3.49120 ( 84) hydrogen bonds : bond 0.20781 ( 976) hydrogen bonds : angle 7.74774 ( 2708) link_BETA1-4 : bond 0.01080 ( 15) link_BETA1-4 : angle 4.40818 ( 45) link_NAG-ASN : bond 0.01023 ( 47) link_NAG-ASN : angle 5.05543 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 250 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.6850 (tpt170) cc_final: 0.6305 (ttp-170) REVERT: A 394 ASN cc_start: 0.8030 (m-40) cc_final: 0.7824 (m110) REVERT: A 516 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7098 (mm-30) REVERT: A 900 MET cc_start: 0.8777 (mtp) cc_final: 0.8295 (mtp) REVERT: A 1029 MET cc_start: 0.9049 (tpp) cc_final: 0.8684 (tpp) REVERT: C 394 ASN cc_start: 0.8042 (m110) cc_final: 0.7828 (m110) REVERT: C 872 GLN cc_start: 0.8132 (tt0) cc_final: 0.7922 (tp-100) outliers start: 5 outliers final: 1 residues processed: 254 average time/residue: 0.6512 time to fit residues: 191.5605 Evaluate side-chains 191 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.0770 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.5980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 66 HIS A 81 ASN A 414 GLN A 607 GLN A 675 GLN A 901 GLN B 81 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 644 GLN B 675 GLN B 901 GLN B1002 GLN B1142 GLN C 30 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN C 675 GLN C1002 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.208091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.143780 restraints weight = 41430.868| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 4.23 r_work: 0.3129 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26416 Z= 0.140 Angle : 0.706 13.653 36090 Z= 0.366 Chirality : 0.048 0.401 4254 Planarity : 0.005 0.056 4558 Dihedral : 7.272 59.278 4722 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.64 % Favored : 96.30 % Rotamer: Outliers : 1.01 % Allowed : 7.12 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.14), residues: 3138 helix: 0.53 (0.19), residues: 715 sheet: 0.31 (0.19), residues: 647 loop : -2.06 (0.12), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 567 TYR 0.021 0.001 TYR A1067 PHE 0.026 0.001 PHE B 32 TRP 0.031 0.002 TRP C 886 HIS 0.008 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00281 (26312) covalent geometry : angle 0.65881 (35820) SS BOND : bond 0.00525 ( 42) SS BOND : angle 2.26757 ( 84) hydrogen bonds : bond 0.07167 ( 976) hydrogen bonds : angle 5.99172 ( 2708) link_BETA1-4 : bond 0.00398 ( 15) link_BETA1-4 : angle 2.22573 ( 45) link_NAG-ASN : bond 0.00552 ( 47) link_NAG-ASN : angle 3.57837 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8153 (m) cc_final: 0.7893 (p) REVERT: A 319 ARG cc_start: 0.5970 (tpt170) cc_final: 0.5556 (tpt90) REVERT: A 394 ASN cc_start: 0.7597 (m-40) cc_final: 0.7319 (m110) REVERT: A 516 GLU cc_start: 0.7502 (mt-10) cc_final: 0.6748 (mm-30) REVERT: A 988 GLU cc_start: 0.7552 (pm20) cc_final: 0.7193 (pp20) REVERT: A 990 GLU cc_start: 0.8018 (tt0) cc_final: 0.7620 (mt-10) REVERT: A 1005 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8783 (tm-30) REVERT: B 790 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7975 (ptpp) REVERT: B 1017 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8230 (mt-10) REVERT: C 53 ASP cc_start: 0.6592 (OUTLIER) cc_final: 0.6299 (t0) REVERT: C 319 ARG cc_start: 0.5621 (tpt90) cc_final: 0.5359 (tpt170) REVERT: C 394 ASN cc_start: 0.7525 (m110) cc_final: 0.7217 (m110) REVERT: C 790 LYS cc_start: 0.8132 (tptp) cc_final: 0.7831 (mtpp) REVERT: C 872 GLN cc_start: 0.8866 (tt0) cc_final: 0.8495 (tp-100) REVERT: C 988 GLU cc_start: 0.7464 (pm20) cc_final: 0.7257 (pp20) REVERT: C 1005 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8711 (tm-30) REVERT: C 1138 TYR cc_start: 0.7832 (t80) cc_final: 0.7631 (t80) outliers start: 22 outliers final: 5 residues processed: 222 average time/residue: 0.7139 time to fit residues: 183.0447 Evaluate side-chains 199 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 190 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 96 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 293 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 265 optimal weight: 7.9990 chunk 134 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 292 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 675 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.208564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.158793 restraints weight = 42236.412| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.26 r_work: 0.3147 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26416 Z= 0.133 Angle : 0.655 13.159 36090 Z= 0.338 Chirality : 0.047 0.386 4254 Planarity : 0.004 0.049 4558 Dihedral : 6.670 58.186 4721 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.54 % Favored : 96.42 % Rotamer: Outliers : 1.22 % Allowed : 8.20 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.14), residues: 3138 helix: 1.05 (0.20), residues: 717 sheet: 0.59 (0.20), residues: 638 loop : -1.85 (0.12), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 567 TYR 0.024 0.001 TYR A1138 PHE 0.024 0.001 PHE B 32 TRP 0.021 0.002 TRP C 886 HIS 0.007 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00278 (26312) covalent geometry : angle 0.61313 (35820) SS BOND : bond 0.00482 ( 42) SS BOND : angle 1.90728 ( 84) hydrogen bonds : bond 0.06736 ( 976) hydrogen bonds : angle 5.68263 ( 2708) link_BETA1-4 : bond 0.00447 ( 15) link_BETA1-4 : angle 2.01844 ( 45) link_NAG-ASN : bond 0.00518 ( 47) link_NAG-ASN : angle 3.29241 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8327 (m) cc_final: 0.8070 (p) REVERT: A 394 ASN cc_start: 0.7857 (m-40) cc_final: 0.7515 (m110) REVERT: A 460 ASN cc_start: 0.8356 (m110) cc_final: 0.8137 (m-40) REVERT: A 516 GLU cc_start: 0.7544 (mt-10) cc_final: 0.6935 (mm-30) REVERT: A 868 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8133 (tm-30) REVERT: A 990 GLU cc_start: 0.7717 (tt0) cc_final: 0.7379 (mt-10) REVERT: B 460 ASN cc_start: 0.8369 (m-40) cc_final: 0.8116 (m110) REVERT: B 790 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7977 (ptpp) REVERT: C 319 ARG cc_start: 0.6177 (tpt90) cc_final: 0.5085 (ttt180) REVERT: C 357 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8256 (ttp80) REVERT: C 394 ASN cc_start: 0.7797 (m110) cc_final: 0.7437 (m110) REVERT: C 748 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: C 872 GLN cc_start: 0.8811 (tt0) cc_final: 0.8481 (tp-100) REVERT: C 1005 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8504 (tm-30) REVERT: C 1128 VAL cc_start: 0.8317 (m) cc_final: 0.7865 (p) outliers start: 28 outliers final: 8 residues processed: 218 average time/residue: 0.7023 time to fit residues: 175.7624 Evaluate side-chains 194 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 271 optimal weight: 7.9990 chunk 129 optimal weight: 0.0770 chunk 285 optimal weight: 5.9990 chunk 199 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 154 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 100 optimal weight: 0.6980 chunk 224 optimal weight: 10.0000 overall best weight: 0.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 613 GLN A 675 GLN A1010 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN C 66 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 613 GLN C 675 GLN C1002 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.209615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.158767 restraints weight = 39189.593| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.22 r_work: 0.3179 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26416 Z= 0.122 Angle : 0.618 12.681 36090 Z= 0.319 Chirality : 0.047 0.382 4254 Planarity : 0.004 0.046 4558 Dihedral : 6.185 57.040 4721 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.35 % Favored : 96.62 % Rotamer: Outliers : 1.26 % Allowed : 9.39 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.14), residues: 3138 helix: 1.36 (0.20), residues: 717 sheet: 0.77 (0.20), residues: 631 loop : -1.69 (0.13), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 567 TYR 0.020 0.001 TYR A1067 PHE 0.021 0.001 PHE B 32 TRP 0.017 0.001 TRP B 886 HIS 0.007 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00251 (26312) covalent geometry : angle 0.57934 (35820) SS BOND : bond 0.00503 ( 42) SS BOND : angle 1.78329 ( 84) hydrogen bonds : bond 0.06174 ( 976) hydrogen bonds : angle 5.48550 ( 2708) link_BETA1-4 : bond 0.00423 ( 15) link_BETA1-4 : angle 1.83335 ( 45) link_NAG-ASN : bond 0.00484 ( 47) link_NAG-ASN : angle 3.07779 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8329 (m) cc_final: 0.8068 (p) REVERT: A 394 ASN cc_start: 0.7706 (m-40) cc_final: 0.7422 (m110) REVERT: A 516 GLU cc_start: 0.7511 (mt-10) cc_final: 0.6913 (mm-30) REVERT: A 748 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: A 868 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8032 (tm-30) REVERT: A 979 ASP cc_start: 0.8197 (m-30) cc_final: 0.7829 (t0) REVERT: A 1002 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8543 (tm-30) REVERT: A 1128 VAL cc_start: 0.8207 (m) cc_final: 0.7850 (p) REVERT: B 460 ASN cc_start: 0.8378 (m-40) cc_final: 0.8105 (m110) REVERT: B 1010 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8560 (tm-30) REVERT: B 1128 VAL cc_start: 0.8201 (m) cc_final: 0.7836 (p) REVERT: C 319 ARG cc_start: 0.6111 (tpt90) cc_final: 0.5052 (ttt180) REVERT: C 357 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8238 (ttt-90) REVERT: C 394 ASN cc_start: 0.7706 (m110) cc_final: 0.7281 (m110) REVERT: C 556 ASN cc_start: 0.7346 (m110) cc_final: 0.6975 (t0) REVERT: C 558 LYS cc_start: 0.7996 (mmtp) cc_final: 0.7766 (tppp) REVERT: C 748 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7545 (tm-30) REVERT: C 872 GLN cc_start: 0.8786 (tt0) cc_final: 0.8455 (tp-100) REVERT: C 1005 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8453 (tm-30) REVERT: C 1128 VAL cc_start: 0.8305 (m) cc_final: 0.7893 (p) outliers start: 29 outliers final: 10 residues processed: 212 average time/residue: 0.6858 time to fit residues: 166.8357 Evaluate side-chains 195 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 143 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 207 optimal weight: 0.7980 chunk 232 optimal weight: 9.9990 chunk 229 optimal weight: 8.9990 chunk 270 optimal weight: 0.6980 chunk 37 optimal weight: 9.9990 chunk 255 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 214 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 460 ASN C 613 GLN C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.205274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.155676 restraints weight = 38504.215| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.06 r_work: 0.3139 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 26416 Z= 0.255 Angle : 0.802 13.568 36090 Z= 0.418 Chirality : 0.056 0.534 4254 Planarity : 0.005 0.047 4558 Dihedral : 6.805 59.678 4721 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.95 % Favored : 95.02 % Rotamer: Outliers : 1.37 % Allowed : 9.71 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.14), residues: 3138 helix: 0.83 (0.19), residues: 722 sheet: 0.57 (0.20), residues: 657 loop : -1.80 (0.13), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1039 TYR 0.028 0.003 TYR A1067 PHE 0.028 0.002 PHE B 592 TRP 0.015 0.002 TRP C 886 HIS 0.010 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00597 (26312) covalent geometry : angle 0.76217 (35820) SS BOND : bond 0.00647 ( 42) SS BOND : angle 2.57494 ( 84) hydrogen bonds : bond 0.09102 ( 976) hydrogen bonds : angle 5.86514 ( 2708) link_BETA1-4 : bond 0.00619 ( 15) link_BETA1-4 : angle 2.26351 ( 45) link_NAG-ASN : bond 0.00594 ( 47) link_NAG-ASN : angle 3.41228 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.7950 (m-40) cc_final: 0.7679 (m110) REVERT: A 516 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7164 (mm-30) REVERT: A 990 GLU cc_start: 0.7975 (tt0) cc_final: 0.7685 (mt-10) REVERT: A 1002 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8697 (tm-30) REVERT: A 1029 MET cc_start: 0.9248 (tpp) cc_final: 0.8963 (tpp) REVERT: B 340 GLU cc_start: 0.7808 (pt0) cc_final: 0.7584 (pt0) REVERT: C 319 ARG cc_start: 0.6426 (tpt90) cc_final: 0.5462 (ttt180) REVERT: C 357 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8341 (ttp80) REVERT: C 394 ASN cc_start: 0.7988 (m110) cc_final: 0.7628 (m110) REVERT: C 748 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7818 (tm-30) REVERT: C 872 GLN cc_start: 0.8871 (tt0) cc_final: 0.8563 (tp-100) REVERT: C 1005 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8477 (tm-30) outliers start: 32 outliers final: 15 residues processed: 204 average time/residue: 0.7622 time to fit residues: 177.2355 Evaluate side-chains 200 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 27 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 212 optimal weight: 2.9990 chunk 120 optimal weight: 0.0970 chunk 60 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 460 ASN C 675 GLN C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.207212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.157259 restraints weight = 42841.604| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.32 r_work: 0.3125 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 26416 Z= 0.164 Angle : 0.692 13.000 36090 Z= 0.358 Chirality : 0.049 0.386 4254 Planarity : 0.004 0.084 4558 Dihedral : 6.452 58.989 4721 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.36 % Rotamer: Outliers : 1.58 % Allowed : 10.03 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.14), residues: 3138 helix: 1.11 (0.20), residues: 716 sheet: 0.70 (0.20), residues: 639 loop : -1.75 (0.13), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 319 TYR 0.024 0.002 TYR A1067 PHE 0.025 0.001 PHE C 592 TRP 0.014 0.002 TRP C 886 HIS 0.006 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00363 (26312) covalent geometry : angle 0.65275 (35820) SS BOND : bond 0.00515 ( 42) SS BOND : angle 2.11473 ( 84) hydrogen bonds : bond 0.07514 ( 976) hydrogen bonds : angle 5.66596 ( 2708) link_BETA1-4 : bond 0.00491 ( 15) link_BETA1-4 : angle 2.04847 ( 45) link_NAG-ASN : bond 0.00526 ( 47) link_NAG-ASN : angle 3.18983 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.7819 (m-40) cc_final: 0.7523 (m110) REVERT: A 516 GLU cc_start: 0.7575 (mt-10) cc_final: 0.6986 (mm-30) REVERT: A 990 GLU cc_start: 0.7875 (tt0) cc_final: 0.7548 (mt-10) REVERT: A 1002 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8648 (tm-30) REVERT: A 1128 VAL cc_start: 0.8215 (m) cc_final: 0.7826 (p) REVERT: A 1145 LEU cc_start: 0.4670 (OUTLIER) cc_final: 0.4126 (tp) REVERT: B 340 GLU cc_start: 0.7809 (pt0) cc_final: 0.7608 (pt0) REVERT: C 319 ARG cc_start: 0.6294 (tpt90) cc_final: 0.6031 (tpt170) REVERT: C 357 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8364 (ttp80) REVERT: C 394 ASN cc_start: 0.7856 (m110) cc_final: 0.7502 (m110) REVERT: C 748 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7615 (tm-30) REVERT: C 872 GLN cc_start: 0.8821 (tt0) cc_final: 0.8488 (tp-100) REVERT: C 1005 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8463 (tm-30) REVERT: C 1128 VAL cc_start: 0.8326 (m) cc_final: 0.7861 (p) outliers start: 38 outliers final: 16 residues processed: 211 average time/residue: 0.7494 time to fit residues: 181.2206 Evaluate side-chains 205 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 94 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 257 optimal weight: 8.9990 chunk 314 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 142 optimal weight: 9.9990 chunk 240 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 460 ASN C 613 GLN C 675 GLN C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.205172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.152187 restraints weight = 35958.293| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.26 r_work: 0.3083 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 26416 Z= 0.256 Angle : 0.810 13.583 36090 Z= 0.422 Chirality : 0.056 0.506 4254 Planarity : 0.005 0.068 4558 Dihedral : 6.821 58.595 4721 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.33 % Favored : 94.64 % Rotamer: Outliers : 1.55 % Allowed : 10.57 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.14), residues: 3138 helix: 0.78 (0.19), residues: 712 sheet: 0.47 (0.20), residues: 661 loop : -1.82 (0.13), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 319 TYR 0.027 0.003 TYR A1067 PHE 0.031 0.002 PHE C 592 TRP 0.013 0.002 TRP C 886 HIS 0.009 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00598 (26312) covalent geometry : angle 0.76944 (35820) SS BOND : bond 0.00648 ( 42) SS BOND : angle 2.51350 ( 84) hydrogen bonds : bond 0.09105 ( 976) hydrogen bonds : angle 5.86731 ( 2708) link_BETA1-4 : bond 0.00613 ( 15) link_BETA1-4 : angle 2.32458 ( 45) link_NAG-ASN : bond 0.00613 ( 47) link_NAG-ASN : angle 3.45477 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.7782 (m-40) cc_final: 0.7500 (m110) REVERT: A 516 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7014 (mm-30) REVERT: A 990 GLU cc_start: 0.8024 (tt0) cc_final: 0.7647 (mt-10) REVERT: A 1002 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8674 (tm-30) REVERT: A 1029 MET cc_start: 0.9287 (tpp) cc_final: 0.8961 (tpp) REVERT: A 1145 LEU cc_start: 0.4740 (OUTLIER) cc_final: 0.4184 (tp) REVERT: B 340 GLU cc_start: 0.7751 (pt0) cc_final: 0.7528 (pt0) REVERT: C 319 ARG cc_start: 0.6271 (tpt90) cc_final: 0.5248 (ttt180) REVERT: C 357 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8299 (ttp80) REVERT: C 394 ASN cc_start: 0.7815 (m110) cc_final: 0.7480 (m110) REVERT: C 748 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7860 (tm-30) REVERT: C 872 GLN cc_start: 0.8855 (tt0) cc_final: 0.8518 (tp-100) REVERT: C 1005 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8451 (tm-30) outliers start: 37 outliers final: 19 residues processed: 210 average time/residue: 0.7134 time to fit residues: 171.9615 Evaluate side-chains 207 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 232 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 167 optimal weight: 0.0970 chunk 23 optimal weight: 0.9980 chunk 316 optimal weight: 0.7980 chunk 182 optimal weight: 0.7980 chunk 176 optimal weight: 0.0570 chunk 208 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 192 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN A 762 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 460 ASN C 675 GLN C1002 GLN C1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.210150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.158535 restraints weight = 41189.772| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.33 r_work: 0.3175 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 26416 Z= 0.118 Angle : 0.611 12.372 36090 Z= 0.315 Chirality : 0.046 0.374 4254 Planarity : 0.004 0.083 4558 Dihedral : 5.977 58.099 4721 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.19 % Allowed : 10.90 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.14), residues: 3138 helix: 1.35 (0.20), residues: 717 sheet: 0.96 (0.21), residues: 617 loop : -1.64 (0.13), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 567 TYR 0.020 0.001 TYR B1138 PHE 0.019 0.001 PHE B 32 TRP 0.014 0.001 TRP B 886 HIS 0.007 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00241 (26312) covalent geometry : angle 0.57530 (35820) SS BOND : bond 0.00482 ( 42) SS BOND : angle 1.62639 ( 84) hydrogen bonds : bond 0.05876 ( 976) hydrogen bonds : angle 5.41341 ( 2708) link_BETA1-4 : bond 0.00398 ( 15) link_BETA1-4 : angle 1.87171 ( 45) link_NAG-ASN : bond 0.00478 ( 47) link_NAG-ASN : angle 2.98829 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8367 (m) cc_final: 0.8037 (p) REVERT: A 394 ASN cc_start: 0.7685 (m-40) cc_final: 0.7414 (m110) REVERT: A 516 GLU cc_start: 0.7477 (mt-10) cc_final: 0.6856 (mm-30) REVERT: A 990 GLU cc_start: 0.7646 (tt0) cc_final: 0.7314 (mt-10) REVERT: A 1002 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8623 (tm-30) REVERT: A 1128 VAL cc_start: 0.8203 (m) cc_final: 0.7853 (p) REVERT: A 1145 LEU cc_start: 0.4599 (OUTLIER) cc_final: 0.4056 (tp) REVERT: B 314 GLN cc_start: 0.7456 (mt0) cc_final: 0.7234 (pt0) REVERT: B 340 GLU cc_start: 0.7722 (pt0) cc_final: 0.7446 (pt0) REVERT: B 1128 VAL cc_start: 0.8183 (m) cc_final: 0.7817 (p) REVERT: C 319 ARG cc_start: 0.6107 (tpt90) cc_final: 0.5888 (tpt170) REVERT: C 357 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8180 (ttp80) REVERT: C 394 ASN cc_start: 0.7712 (m110) cc_final: 0.7310 (m110) REVERT: C 417 LYS cc_start: 0.7230 (ptpp) cc_final: 0.6636 (tppt) REVERT: C 556 ASN cc_start: 0.7243 (m110) cc_final: 0.6889 (m-40) REVERT: C 850 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.7150 (mm) REVERT: C 872 GLN cc_start: 0.8768 (tt0) cc_final: 0.8422 (tp-100) REVERT: C 1005 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8465 (tm-30) REVERT: C 1128 VAL cc_start: 0.8261 (m) cc_final: 0.7848 (p) outliers start: 27 outliers final: 11 residues processed: 207 average time/residue: 0.7526 time to fit residues: 178.2778 Evaluate side-chains 201 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 57 optimal weight: 0.9980 chunk 199 optimal weight: 1.9990 chunk 295 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 161 optimal weight: 6.9990 chunk 297 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN A 762 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 675 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN C 613 GLN C1002 GLN C1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.208737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.159372 restraints weight = 41984.928| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.29 r_work: 0.3145 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26416 Z= 0.139 Angle : 0.639 12.304 36090 Z= 0.331 Chirality : 0.048 0.374 4254 Planarity : 0.004 0.043 4558 Dihedral : 5.885 56.682 4721 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.86 % Favored : 96.10 % Rotamer: Outliers : 1.19 % Allowed : 11.18 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.14), residues: 3138 helix: 1.43 (0.20), residues: 716 sheet: 0.91 (0.21), residues: 625 loop : -1.59 (0.13), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 567 TYR 0.026 0.001 TYR A1138 PHE 0.025 0.001 PHE C 592 TRP 0.013 0.001 TRP B 886 HIS 0.006 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00297 (26312) covalent geometry : angle 0.60292 (35820) SS BOND : bond 0.00526 ( 42) SS BOND : angle 1.87926 ( 84) hydrogen bonds : bond 0.06814 ( 976) hydrogen bonds : angle 5.48487 ( 2708) link_BETA1-4 : bond 0.00464 ( 15) link_BETA1-4 : angle 1.85184 ( 45) link_NAG-ASN : bond 0.00491 ( 47) link_NAG-ASN : angle 2.99709 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.7784 (m-40) cc_final: 0.7488 (m110) REVERT: A 516 GLU cc_start: 0.7555 (mt-10) cc_final: 0.6972 (mm-30) REVERT: A 979 ASP cc_start: 0.8215 (m-30) cc_final: 0.7868 (t0) REVERT: A 990 GLU cc_start: 0.7777 (tt0) cc_final: 0.7462 (mt-10) REVERT: A 1128 VAL cc_start: 0.8250 (m) cc_final: 0.7910 (p) REVERT: A 1145 LEU cc_start: 0.4745 (OUTLIER) cc_final: 0.4239 (tp) REVERT: B 314 GLN cc_start: 0.7448 (mt0) cc_final: 0.7241 (pt0) REVERT: B 340 GLU cc_start: 0.7794 (pt0) cc_final: 0.7568 (pt0) REVERT: B 1128 VAL cc_start: 0.8215 (m) cc_final: 0.7847 (p) REVERT: C 319 ARG cc_start: 0.6258 (tpt90) cc_final: 0.5169 (ttt180) REVERT: C 357 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8325 (ttt-90) REVERT: C 394 ASN cc_start: 0.7847 (m110) cc_final: 0.7454 (m110) REVERT: C 556 ASN cc_start: 0.7360 (m110) cc_final: 0.7021 (m-40) REVERT: C 850 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7219 (mm) REVERT: C 872 GLN cc_start: 0.8836 (tt0) cc_final: 0.8509 (tp-100) REVERT: C 1005 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8505 (tm-30) REVERT: C 1128 VAL cc_start: 0.8300 (m) cc_final: 0.7891 (p) outliers start: 27 outliers final: 15 residues processed: 201 average time/residue: 0.6926 time to fit residues: 159.8414 Evaluate side-chains 199 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 53 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 177 optimal weight: 0.0040 chunk 39 optimal weight: 0.6980 chunk 220 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 285 optimal weight: 0.0670 chunk 111 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.1534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 675 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 460 ASN C 613 GLN C1002 GLN C1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.208695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.137912 restraints weight = 36212.413| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 3.61 r_work: 0.3125 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.169 26416 Z= 0.176 Angle : 0.772 59.194 36090 Z= 0.429 Chirality : 0.048 0.454 4254 Planarity : 0.004 0.043 4558 Dihedral : 5.892 56.684 4721 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.93 % Allowed : 11.40 % Favored : 87.67 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.14), residues: 3138 helix: 1.44 (0.20), residues: 716 sheet: 0.88 (0.21), residues: 635 loop : -1.60 (0.13), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 567 TYR 0.022 0.001 TYR A1067 PHE 0.023 0.001 PHE C 592 TRP 0.013 0.001 TRP B 886 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00362 (26312) covalent geometry : angle 0.74369 (35820) SS BOND : bond 0.00509 ( 42) SS BOND : angle 1.87333 ( 84) hydrogen bonds : bond 0.06851 ( 976) hydrogen bonds : angle 5.48431 ( 2708) link_BETA1-4 : bond 0.00515 ( 15) link_BETA1-4 : angle 1.85629 ( 45) link_NAG-ASN : bond 0.00491 ( 47) link_NAG-ASN : angle 2.99573 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.7516 (m-40) cc_final: 0.7219 (m110) REVERT: A 516 GLU cc_start: 0.7471 (mt-10) cc_final: 0.6711 (mm-30) REVERT: A 979 ASP cc_start: 0.8246 (m-30) cc_final: 0.7690 (t0) REVERT: A 990 GLU cc_start: 0.7852 (tt0) cc_final: 0.7464 (mt-10) REVERT: A 1128 VAL cc_start: 0.8168 (m) cc_final: 0.7805 (p) REVERT: A 1145 LEU cc_start: 0.4623 (OUTLIER) cc_final: 0.4094 (tp) REVERT: B 314 GLN cc_start: 0.7630 (mt0) cc_final: 0.7312 (pt0) REVERT: B 340 GLU cc_start: 0.7611 (pt0) cc_final: 0.7354 (pt0) REVERT: B 1010 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8441 (tm-30) REVERT: B 1128 VAL cc_start: 0.8118 (m) cc_final: 0.7729 (p) REVERT: C 319 ARG cc_start: 0.5730 (tpt90) cc_final: 0.4638 (ttt180) REVERT: C 357 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8272 (ttt-90) REVERT: C 394 ASN cc_start: 0.7568 (m110) cc_final: 0.7190 (m110) REVERT: C 556 ASN cc_start: 0.7113 (m110) cc_final: 0.6784 (m-40) REVERT: C 872 GLN cc_start: 0.8899 (tt0) cc_final: 0.8527 (tp-100) REVERT: C 1005 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8641 (tm-30) REVERT: C 1128 VAL cc_start: 0.8246 (m) cc_final: 0.7813 (p) outliers start: 20 outliers final: 14 residues processed: 191 average time/residue: 0.7528 time to fit residues: 164.7912 Evaluate side-chains 196 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 34 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 145 optimal weight: 0.0030 chunk 278 optimal weight: 0.7980 chunk 231 optimal weight: 3.9990 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN A 762 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 675 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 460 ASN C1002 GLN C1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.207913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.138824 restraints weight = 37609.222| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 3.80 r_work: 0.3136 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.169 26416 Z= 0.176 Angle : 0.772 59.194 36090 Z= 0.429 Chirality : 0.048 0.454 4254 Planarity : 0.004 0.043 4558 Dihedral : 5.892 56.684 4721 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.93 % Allowed : 11.43 % Favored : 87.63 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.14), residues: 3138 helix: 1.44 (0.20), residues: 716 sheet: 0.88 (0.21), residues: 635 loop : -1.60 (0.13), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 567 TYR 0.022 0.001 TYR A1067 PHE 0.023 0.001 PHE C 592 TRP 0.013 0.001 TRP B 886 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00362 (26312) covalent geometry : angle 0.74368 (35820) SS BOND : bond 0.00509 ( 42) SS BOND : angle 1.87333 ( 84) hydrogen bonds : bond 0.06851 ( 976) hydrogen bonds : angle 5.48431 ( 2708) link_BETA1-4 : bond 0.00515 ( 15) link_BETA1-4 : angle 1.85629 ( 45) link_NAG-ASN : bond 0.00491 ( 47) link_NAG-ASN : angle 2.99573 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12317.08 seconds wall clock time: 209 minutes 29.36 seconds (12569.36 seconds total)