Starting phenix.real_space_refine on Fri Mar 6 09:28:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ws9_32751/03_2026/7ws9_32751.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ws9_32751/03_2026/7ws9_32751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ws9_32751/03_2026/7ws9_32751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ws9_32751/03_2026/7ws9_32751.map" model { file = "/net/cci-nas-00/data/ceres_data/7ws9_32751/03_2026/7ws9_32751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ws9_32751/03_2026/7ws9_32751.cif" } resolution = 2.9 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= -0.001 sd= 0.052 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 140 5.16 5 C 18989 2.51 5 N 4887 2.21 5 O 5694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 29710 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Chain: "B" Number of atoms: 8096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8096 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 8096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8096 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} 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: "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: "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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" 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: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 6.71, per 1000 atoms: 0.23 Number of scatterers: 29710 At special positions: 0 Unit cell: (134.784, 143.936, 243.776, 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 140 16.00 O 5694 8.00 N 4887 7.00 C 18989 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 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 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 282 " " NAG A1303 " - " ASN A 709 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 709 " " NAG C1301 " - " ASN C 709 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 90 " " NAG D 703 " - " ASN D 103 " " NAG D 704 " - " ASN D 322 " " NAG D 705 " - " ASN D 432 " " NAG D 706 " - " ASN D 546 " " NAG E 1 " - " ASN B 801 " " NAG F 1 " - " ASN B1074 " " NAG G 1 " - " ASN B1098 " " NAG H 1 " - " ASN B1134 " " NAG I 1 " - " ASN C 717 " " NAG J 1 " - " ASN C 801 " " NAG K 1 " - " ASN C1074 " " NAG L 1 " - " ASN C1098 " " NAG M 1 " - " ASN C1134 " " NAG N 1 " - " ASN A 717 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN A 801 " " NAG Q 1 " - " ASN A1098 " " NAG R 1 " - " ASN A1134 " Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 1.3 seconds 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6946 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 49 sheets defined 32.2% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 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 364 through 370 removed outlier: 3.768A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.605A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.054A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.590A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (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 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.057A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.648A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.321A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.462A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (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 Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.977A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.623A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.520A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.038A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.005A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (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: 4.123A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.529A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.638A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.699A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.772A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.531A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (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 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.515A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.030A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.544A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (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: 4.282A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.519A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.503A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.725A pdb=" N LYS D 94 " --> pdb=" O ASN D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 149 through 154 removed outlier: 3.544A pdb=" N ALA D 153 " --> pdb=" O ASN D 149 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN D 154 " --> pdb=" O GLU D 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 149 through 154' Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.625A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.566A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 221 through 252 removed outlier: 4.380A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.645A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.884A pdb=" N MET D 297 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 Processing helix chain 'D' and resid 325 through 331 removed outlier: 3.768A pdb=" N GLU D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.522A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 413 removed outlier: 4.408A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 432 through 447 removed outlier: 3.969A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE D 438 " --> pdb=" O THR D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.348A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 499 through 503 Processing helix chain 'D' and resid 505 through 509 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.181A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D 528 " --> pdb=" O GLN D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 561 removed outlier: 3.519A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU D 560 " --> pdb=" O ASN D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 removed outlier: 3.769A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.691A pdb=" N LEU D 585 " --> pdb=" O VAL D 581 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.787A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.006A 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: 3.635A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 11.561A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.179A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.434A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.387A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.228A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 313 Processing sheet with id=AA5, first strand: chain 'A' and resid 317 through 319 Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.998A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.570A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.863A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.504A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 553 through 554 removed outlier: 3.574A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.897A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.944A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.801A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.801A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.905A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.902A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.579A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.003A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.146A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 9.394A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.337A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.558A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.620A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.116A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.984A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.594A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.678A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.678A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.405A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.969A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.156A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.687A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 133 through 142 removed outlier: 8.086A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.060A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 9.988A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU C 156 " --> pdb=" O ASP C 142 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 316 removed outlier: 5.216A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.991A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.578A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.518A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 448 through 454 removed outlier: 6.367A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) 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 654 through 655 removed outlier: 5.918A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.680A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.680A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.095A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF3, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.708A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'D' and resid 347 through 352 removed outlier: 3.761A pdb=" N THR D 347 " --> pdb=" O LEU D 359 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 1280 hydrogen bonds defined for protein. 3585 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: 6.83 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5099 1.32 - 1.45: 8403 1.45 - 1.58: 16727 1.58 - 1.70: 1 1.70 - 1.83: 188 Bond restraints: 30418 Sorted by residual: bond pdb=" N VAL A 595 " pdb=" CA VAL A 595 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.14e-02 7.69e+03 1.08e+01 bond pdb=" CA SER C 591 " pdb=" CB SER C 591 " ideal model delta sigma weight residual 1.530 1.480 0.051 1.62e-02 3.81e+03 9.85e+00 bond pdb=" N VAL B 367 " pdb=" CA VAL B 367 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.06e-02 8.90e+03 9.17e+00 bond pdb=" C PRO C 589 " pdb=" O PRO C 589 " ideal model delta sigma weight residual 1.233 1.198 0.035 1.21e-02 6.83e+03 8.27e+00 bond pdb=" CG1 ILE C 742 " pdb=" CD1 ILE C 742 " ideal model delta sigma weight residual 1.513 1.402 0.111 3.90e-02 6.57e+02 8.11e+00 ... (remaining 30413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 40203 1.58 - 3.16: 1008 3.16 - 4.74: 131 4.74 - 6.32: 23 6.32 - 7.90: 7 Bond angle restraints: 41372 Sorted by residual: angle pdb=" CA PRO D 146 " pdb=" N PRO D 146 " pdb=" CD PRO D 146 " ideal model delta sigma weight residual 112.00 105.46 6.54 1.40e+00 5.10e-01 2.18e+01 angle pdb=" N PHE B 338 " pdb=" CA PHE B 338 " pdb=" C PHE B 338 " ideal model delta sigma weight residual 113.50 108.36 5.14 1.23e+00 6.61e-01 1.75e+01 angle pdb=" CA GLY C 594 " pdb=" C GLY C 594 " pdb=" O GLY C 594 " ideal model delta sigma weight residual 120.94 117.72 3.22 7.80e-01 1.64e+00 1.70e+01 angle pdb=" N LEU B 368 " pdb=" CA LEU B 368 " pdb=" C LEU B 368 " ideal model delta sigma weight residual 113.55 108.82 4.73 1.26e+00 6.30e-01 1.41e+01 angle pdb=" N CYS C 432 " pdb=" CA CYS C 432 " pdb=" C CYS C 432 " ideal model delta sigma weight residual 108.60 113.96 -5.36 1.46e+00 4.69e-01 1.35e+01 ... (remaining 41367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.51: 17210 19.51 - 39.02: 1181 39.02 - 58.54: 196 58.54 - 78.05: 52 78.05 - 97.56: 22 Dihedral angle restraints: 18661 sinusoidal: 7886 harmonic: 10775 Sorted by residual: dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 36.76 56.24 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" CA CYS C 617 " pdb=" C CYS C 617 " pdb=" N THR C 618 " pdb=" CA THR C 618 " ideal model delta harmonic sigma weight residual 180.00 152.31 27.69 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA CYS A 617 " pdb=" C CYS A 617 " pdb=" N THR A 618 " pdb=" CA THR A 618 " ideal model delta harmonic sigma weight residual 180.00 156.10 23.90 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 18658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4156 0.070 - 0.140: 571 0.140 - 0.211: 12 0.211 - 0.281: 2 0.281 - 0.351: 1 Chirality restraints: 4742 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" C1 NAG D 702 " pdb=" ND2 ASN D 90 " pdb=" C2 NAG D 702 " pdb=" O5 NAG D 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA VAL A 320 " pdb=" N VAL A 320 " pdb=" C VAL A 320 " pdb=" CB VAL A 320 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 4739 not shown) Planarity restraints: 5322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 461 " 0.023 2.00e-02 2.50e+03 2.39e-02 1.43e+01 pdb=" CG TRP D 461 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP D 461 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP D 461 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 461 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 461 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 461 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 461 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 461 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 461 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 318 " 0.017 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C PHE A 318 " -0.061 2.00e-02 2.50e+03 pdb=" O PHE A 318 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG A 319 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 90 " 0.002 2.00e-02 2.50e+03 2.91e-02 1.06e+01 pdb=" CG ASN D 90 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN D 90 " -0.035 2.00e-02 2.50e+03 pdb=" ND2 ASN D 90 " 0.032 2.00e-02 2.50e+03 pdb=" C1 NAG D 702 " -0.031 2.00e-02 2.50e+03 ... (remaining 5319 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 444 2.66 - 3.22: 27296 3.22 - 3.78: 45741 3.78 - 4.34: 63478 4.34 - 4.90: 104141 Nonbonded interactions: 241100 Sorted by model distance: nonbonded pdb=" OG1 THR C 732 " pdb=" ND2 ASN C 955 " model vdw 2.095 3.120 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.151 3.040 nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.161 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.168 3.040 nonbonded pdb=" OE1 GLU B 516 " pdb=" OH TYR C 200 " model vdw 2.174 3.040 ... (remaining 241095 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 518 or (resid 519 through 520 and (name N or na \ me CA or name C or name O or name CB )) or resid 521 through 1301)) selection = (chain 'B' and resid 14 through 1301) selection = chain 'C' } ncs_group { reference = 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.470 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: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 27.880 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 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:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 30500 Z= 0.199 Angle : 0.597 8.076 41576 Z= 0.330 Chirality : 0.045 0.351 4742 Planarity : 0.004 0.064 5296 Dihedral : 13.615 97.559 11589 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.31 % Favored : 97.52 % Rotamer: Outliers : 0.03 % Allowed : 0.68 % Favored : 99.29 % 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: 0.33 (0.14), residues: 3635 helix: 1.64 (0.17), residues: 1019 sheet: 0.34 (0.20), residues: 603 loop : -0.55 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 355 TYR 0.014 0.001 TYR B 453 PHE 0.031 0.001 PHE C 429 TRP 0.064 0.001 TRP D 461 HIS 0.004 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00378 (30418) covalent geometry : angle 0.58829 (41372) SS BOND : bond 0.00290 ( 42) SS BOND : angle 1.15106 ( 84) hydrogen bonds : bond 0.20903 ( 1244) hydrogen bonds : angle 8.15881 ( 3585) link_BETA1-4 : bond 0.00355 ( 14) link_BETA1-4 : angle 0.85458 ( 42) link_NAG-ASN : bond 0.00268 ( 26) link_NAG-ASN : angle 2.12997 ( 78) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 MET cc_start: 0.7370 (mtp) cc_final: 0.7162 (mtp) REVERT: D 323 MET cc_start: -0.1217 (mtt) cc_final: -0.2688 (pmm) REVERT: D 360 MET cc_start: -0.1345 (mmp) cc_final: -0.1602 (mmp) REVERT: D 383 MET cc_start: 0.6603 (mpp) cc_final: 0.6379 (mpt) REVERT: D 523 PHE cc_start: 0.5535 (m-80) cc_final: 0.4593 (m-80) REVERT: D 579 MET cc_start: -0.0476 (mmt) cc_final: -0.2701 (ppp) outliers start: 1 outliers final: 1 residues processed: 222 average time/residue: 0.5611 time to fit residues: 151.6877 Evaluate side-chains 151 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 274 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.0970 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.2980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 907 ASN C 417 ASN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN D 175 GLN D 580 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.166774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.098309 restraints weight = 55119.352| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 3.96 r_work: 0.3074 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30500 Z= 0.142 Angle : 0.562 8.357 41576 Z= 0.289 Chirality : 0.045 0.292 4742 Planarity : 0.004 0.051 5296 Dihedral : 6.342 61.774 4800 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.83 % Allowed : 6.04 % Favored : 93.13 % 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: 0.60 (0.14), residues: 3635 helix: 1.86 (0.16), residues: 1010 sheet: 0.79 (0.19), residues: 658 loop : -0.51 (0.13), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 319 TYR 0.023 0.001 TYR C1067 PHE 0.020 0.001 PHE C 168 TRP 0.039 0.001 TRP D 461 HIS 0.014 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00321 (30418) covalent geometry : angle 0.55433 (41372) SS BOND : bond 0.00319 ( 42) SS BOND : angle 1.13745 ( 84) hydrogen bonds : bond 0.05109 ( 1244) hydrogen bonds : angle 6.03851 ( 3585) link_BETA1-4 : bond 0.00460 ( 14) link_BETA1-4 : angle 0.94389 ( 42) link_NAG-ASN : bond 0.00301 ( 26) link_NAG-ASN : angle 1.83206 ( 78) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7012 (t0) cc_final: 0.6772 (t0) REVERT: A 170 TYR cc_start: 0.7148 (t80) cc_final: 0.6751 (t80) REVERT: A 237 ARG cc_start: 0.6814 (ptm-80) cc_final: 0.6432 (ttt90) REVERT: A 239 GLN cc_start: 0.6344 (OUTLIER) cc_final: 0.6129 (tp40) REVERT: A 823 PHE cc_start: 0.8620 (t80) cc_final: 0.7870 (m-80) REVERT: C 491 PRO cc_start: 0.7806 (Cg_endo) cc_final: 0.7560 (Cg_exo) REVERT: C 740 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8733 (tpp) REVERT: D 139 GLN cc_start: 0.0837 (pm20) cc_final: 0.0124 (mt0) REVERT: D 225 ASP cc_start: 0.1683 (m-30) cc_final: 0.0969 (m-30) REVERT: D 243 TYR cc_start: 0.4928 (t80) cc_final: 0.4423 (m-80) REVERT: D 323 MET cc_start: -0.0258 (mtt) cc_final: -0.2485 (pmm) REVERT: D 579 MET cc_start: 0.0091 (mmt) cc_final: -0.2620 (ppp) outliers start: 27 outliers final: 11 residues processed: 193 average time/residue: 0.6020 time to fit residues: 140.3847 Evaluate side-chains 160 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 274 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 89 optimal weight: 0.7980 chunk 314 optimal weight: 30.0000 chunk 92 optimal weight: 1.9990 chunk 311 optimal weight: 30.0000 chunk 122 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 335 optimal weight: 0.0970 chunk 157 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 180 optimal weight: 0.4980 chunk 272 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN D 580 ASN D 586 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.166718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.098232 restraints weight = 55045.433| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 3.96 r_work: 0.3063 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30500 Z= 0.126 Angle : 0.528 8.522 41576 Z= 0.269 Chirality : 0.044 0.362 4742 Planarity : 0.004 0.077 5296 Dihedral : 5.466 54.114 4800 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.36 % Allowed : 8.26 % Favored : 90.39 % 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: 0.70 (0.14), residues: 3635 helix: 2.01 (0.16), residues: 1002 sheet: 0.89 (0.19), residues: 686 loop : -0.51 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 319 TYR 0.020 0.001 TYR C 473 PHE 0.018 0.001 PHE A 106 TRP 0.024 0.001 TRP D 461 HIS 0.010 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00285 (30418) covalent geometry : angle 0.51890 (41372) SS BOND : bond 0.00296 ( 42) SS BOND : angle 1.41287 ( 84) hydrogen bonds : bond 0.04544 ( 1244) hydrogen bonds : angle 5.56703 ( 3585) link_BETA1-4 : bond 0.00294 ( 14) link_BETA1-4 : angle 1.00751 ( 42) link_NAG-ASN : bond 0.00237 ( 26) link_NAG-ASN : angle 1.74067 ( 78) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7065 (t0) cc_final: 0.6782 (t0) REVERT: A 133 PHE cc_start: 0.5463 (m-80) cc_final: 0.4747 (m-80) REVERT: A 170 TYR cc_start: 0.7057 (t80) cc_final: 0.6703 (t80) REVERT: A 823 PHE cc_start: 0.8605 (t80) cc_final: 0.7905 (m-80) REVERT: B 200 TYR cc_start: 0.7669 (m-80) cc_final: 0.7428 (m-80) REVERT: B 776 LYS cc_start: 0.8764 (ttmm) cc_final: 0.8560 (tttp) REVERT: C 170 TYR cc_start: 0.8196 (t80) cc_final: 0.7978 (t80) REVERT: C 309 GLU cc_start: 0.8406 (mp0) cc_final: 0.7793 (pm20) REVERT: C 491 PRO cc_start: 0.7948 (Cg_endo) cc_final: 0.7714 (Cg_exo) REVERT: C 740 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8748 (tpp) REVERT: C 990 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7295 (tm-30) REVERT: D 139 GLN cc_start: 0.0698 (pm20) cc_final: 0.0107 (tt0) REVERT: D 225 ASP cc_start: 0.1509 (m-30) cc_final: 0.0942 (m-30) REVERT: D 243 TYR cc_start: 0.5170 (t80) cc_final: 0.4660 (m-80) REVERT: D 297 MET cc_start: -0.1720 (OUTLIER) cc_final: -0.2003 (mmt) REVERT: D 323 MET cc_start: 0.0428 (mtt) cc_final: -0.2403 (pmm) REVERT: D 360 MET cc_start: -0.1445 (mmp) cc_final: -0.1715 (mmp) REVERT: D 366 MET cc_start: 0.2966 (tpt) cc_final: 0.2711 (tpt) REVERT: D 383 MET cc_start: 0.6553 (mmm) cc_final: 0.6323 (mmm) REVERT: D 579 MET cc_start: 0.0426 (mmt) cc_final: -0.2497 (ppp) outliers start: 44 outliers final: 14 residues processed: 197 average time/residue: 0.6428 time to fit residues: 152.3275 Evaluate side-chains 166 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 274 PHE Chi-restraints excluded: chain D residue 297 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 62 optimal weight: 1.9990 chunk 248 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 103 optimal weight: 20.0000 chunk 274 optimal weight: 1.9990 chunk 35 optimal weight: 20.0000 chunk 142 optimal weight: 0.0060 chunk 195 optimal weight: 3.9990 chunk 230 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 304 optimal weight: 1.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 388 ASN ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN C 282 ASN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 935 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.165990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.099406 restraints weight = 54745.268| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 4.44 r_work: 0.3006 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 30500 Z= 0.164 Angle : 0.548 12.195 41576 Z= 0.278 Chirality : 0.045 0.282 4742 Planarity : 0.004 0.048 5296 Dihedral : 5.071 54.292 4800 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.63 % Allowed : 9.80 % Favored : 88.57 % 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: 0.69 (0.14), residues: 3635 helix: 2.01 (0.16), residues: 1002 sheet: 0.69 (0.19), residues: 710 loop : -0.47 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 905 TYR 0.021 0.001 TYR C1067 PHE 0.018 0.001 PHE C 106 TRP 0.015 0.001 TRP D 461 HIS 0.009 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00389 (30418) covalent geometry : angle 0.53842 (41372) SS BOND : bond 0.00378 ( 42) SS BOND : angle 1.51506 ( 84) hydrogen bonds : bond 0.04702 ( 1244) hydrogen bonds : angle 5.41128 ( 3585) link_BETA1-4 : bond 0.00244 ( 14) link_BETA1-4 : angle 1.04193 ( 42) link_NAG-ASN : bond 0.00262 ( 26) link_NAG-ASN : angle 1.80437 ( 78) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 163 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7203 (t0) cc_final: 0.6942 (t0) REVERT: A 170 TYR cc_start: 0.7101 (t80) cc_final: 0.6881 (t80) REVERT: A 237 ARG cc_start: 0.6804 (ptm-80) cc_final: 0.6034 (mtm110) REVERT: A 823 PHE cc_start: 0.8637 (t80) cc_final: 0.7952 (m-80) REVERT: B 200 TYR cc_start: 0.7953 (m-80) cc_final: 0.7672 (m-80) REVERT: B 371 LEU cc_start: 0.1251 (OUTLIER) cc_final: 0.0912 (tm) REVERT: B 983 ARG cc_start: 0.8071 (ttp80) cc_final: 0.7823 (ttp80) REVERT: C 170 TYR cc_start: 0.8227 (t80) cc_final: 0.8005 (t80) REVERT: C 309 GLU cc_start: 0.8441 (mp0) cc_final: 0.7879 (pm20) REVERT: D 139 GLN cc_start: 0.0697 (pm20) cc_final: 0.0145 (tt0) REVERT: D 225 ASP cc_start: 0.1727 (m-30) cc_final: 0.1099 (m-30) REVERT: D 243 TYR cc_start: 0.5070 (t80) cc_final: 0.4614 (m-80) REVERT: D 297 MET cc_start: -0.1820 (OUTLIER) cc_final: -0.2124 (mmt) REVERT: D 323 MET cc_start: 0.0394 (mtt) cc_final: -0.2498 (pmm) REVERT: D 360 MET cc_start: -0.1406 (mmp) cc_final: -0.1642 (mmp) REVERT: D 383 MET cc_start: 0.6464 (mmm) cc_final: 0.6254 (mmm) REVERT: D 535 HIS cc_start: 0.2288 (OUTLIER) cc_final: 0.1733 (t-90) REVERT: D 579 MET cc_start: 0.0223 (mmt) cc_final: -0.2408 (ppp) outliers start: 53 outliers final: 20 residues processed: 202 average time/residue: 0.6025 time to fit residues: 146.9852 Evaluate side-chains 165 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 274 PHE Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 535 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 132 optimal weight: 0.0980 chunk 208 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 257 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 chunk 264 optimal weight: 0.6980 chunk 130 optimal weight: 0.0060 chunk 82 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 344 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN A1002 GLN C 314 GLN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 935 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.166328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.095141 restraints weight = 55167.017| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.96 r_work: 0.3079 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 30500 Z= 0.100 Angle : 0.508 10.697 41576 Z= 0.254 Chirality : 0.043 0.309 4742 Planarity : 0.003 0.047 5296 Dihedral : 4.682 55.108 4800 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.33 % Allowed : 11.28 % Favored : 87.40 % 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: 0.85 (0.14), residues: 3635 helix: 2.20 (0.17), residues: 992 sheet: 0.82 (0.19), residues: 711 loop : -0.39 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 319 TYR 0.021 0.001 TYR C 473 PHE 0.011 0.001 PHE B1121 TRP 0.012 0.001 TRP D 461 HIS 0.008 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00217 (30418) covalent geometry : angle 0.50063 (41372) SS BOND : bond 0.00343 ( 42) SS BOND : angle 1.27736 ( 84) hydrogen bonds : bond 0.03954 ( 1244) hydrogen bonds : angle 5.17149 ( 3585) link_BETA1-4 : bond 0.00404 ( 14) link_BETA1-4 : angle 0.94575 ( 42) link_NAG-ASN : bond 0.00199 ( 26) link_NAG-ASN : angle 1.56043 ( 78) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 161 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7276 (t0) cc_final: 0.7070 (t0) REVERT: A 170 TYR cc_start: 0.7224 (t80) cc_final: 0.6980 (t80) REVERT: A 227 VAL cc_start: 0.8010 (OUTLIER) cc_final: 0.7786 (p) REVERT: A 237 ARG cc_start: 0.6899 (ptm-80) cc_final: 0.6326 (mtm110) REVERT: A 239 GLN cc_start: 0.6566 (mm-40) cc_final: 0.6331 (mm-40) REVERT: A 823 PHE cc_start: 0.8679 (t80) cc_final: 0.7939 (m-80) REVERT: A 858 LEU cc_start: 0.4073 (pt) cc_final: 0.3774 (mm) REVERT: B 53 ASP cc_start: 0.8585 (t70) cc_final: 0.8336 (t70) REVERT: B 140 PHE cc_start: 0.7240 (p90) cc_final: 0.7027 (p90) REVERT: B 200 TYR cc_start: 0.7884 (m-80) cc_final: 0.7591 (m-80) REVERT: B 371 LEU cc_start: 0.0866 (OUTLIER) cc_final: 0.0605 (tm) REVERT: B 995 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8125 (ttp80) REVERT: B 1040 VAL cc_start: 0.9292 (OUTLIER) cc_final: 0.9024 (m) REVERT: C 309 GLU cc_start: 0.8549 (mp0) cc_final: 0.7941 (pm20) REVERT: C 755 GLN cc_start: 0.9005 (mt0) cc_final: 0.8659 (mp10) REVERT: C 990 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7316 (tm-30) REVERT: D 225 ASP cc_start: 0.0857 (m-30) cc_final: 0.0616 (m-30) REVERT: D 243 TYR cc_start: 0.4737 (t80) cc_final: 0.4489 (m-80) REVERT: D 323 MET cc_start: 0.1399 (mtt) cc_final: -0.2159 (pmm) REVERT: D 360 MET cc_start: -0.1561 (mmp) cc_final: -0.1830 (mmp) REVERT: D 462 MET cc_start: 0.4932 (ttt) cc_final: 0.4641 (mmp) REVERT: D 535 HIS cc_start: 0.3545 (OUTLIER) cc_final: 0.3206 (t-90) REVERT: D 579 MET cc_start: 0.1969 (mmt) cc_final: -0.1793 (ppp) outliers start: 43 outliers final: 14 residues processed: 193 average time/residue: 0.6125 time to fit residues: 143.0296 Evaluate side-chains 168 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 535 HIS Chi-restraints excluded: chain D residue 597 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 301 optimal weight: 1.9990 chunk 243 optimal weight: 0.8980 chunk 218 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 181 optimal weight: 0.0980 chunk 3 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 291 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN A1002 GLN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.165616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.093911 restraints weight = 54516.090| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.00 r_work: 0.3072 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30500 Z= 0.145 Angle : 0.532 12.270 41576 Z= 0.265 Chirality : 0.044 0.314 4742 Planarity : 0.004 0.047 5296 Dihedral : 4.572 53.476 4798 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.51 % Allowed : 11.90 % Favored : 86.59 % 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: 0.83 (0.14), residues: 3635 helix: 2.18 (0.17), residues: 997 sheet: 0.74 (0.19), residues: 722 loop : -0.39 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 983 TYR 0.028 0.001 TYR C 473 PHE 0.019 0.001 PHE C 106 TRP 0.010 0.001 TRP D 461 HIS 0.008 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00344 (30418) covalent geometry : angle 0.52446 (41372) SS BOND : bond 0.00325 ( 42) SS BOND : angle 1.36108 ( 84) hydrogen bonds : bond 0.04260 ( 1244) hydrogen bonds : angle 5.15311 ( 3585) link_BETA1-4 : bond 0.00252 ( 14) link_BETA1-4 : angle 0.98381 ( 42) link_NAG-ASN : bond 0.00242 ( 26) link_NAG-ASN : angle 1.62010 ( 78) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 155 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7298 (t0) cc_final: 0.7086 (t0) REVERT: A 227 VAL cc_start: 0.8000 (OUTLIER) cc_final: 0.7696 (p) REVERT: A 237 ARG cc_start: 0.7029 (ptm-80) cc_final: 0.6408 (mtm110) REVERT: A 239 GLN cc_start: 0.6587 (mm-40) cc_final: 0.6383 (mm-40) REVERT: A 304 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.8797 (mppt) REVERT: A 794 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8496 (pp) REVERT: A 823 PHE cc_start: 0.8681 (t80) cc_final: 0.7951 (m-80) REVERT: A 858 LEU cc_start: 0.4042 (pt) cc_final: 0.3711 (mm) REVERT: B 53 ASP cc_start: 0.8557 (t70) cc_final: 0.8349 (t70) REVERT: B 200 TYR cc_start: 0.7979 (m-80) cc_final: 0.7702 (m-80) REVERT: B 371 LEU cc_start: 0.1211 (OUTLIER) cc_final: 0.0882 (tm) REVERT: B 995 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8139 (ttp80) REVERT: C 309 GLU cc_start: 0.8554 (mp0) cc_final: 0.7956 (pm20) REVERT: C 326 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7908 (pt) REVERT: C 987 PRO cc_start: 0.8534 (Cg_exo) cc_final: 0.8303 (Cg_endo) REVERT: D 225 ASP cc_start: 0.1702 (m-30) cc_final: 0.1158 (m-30) REVERT: D 323 MET cc_start: 0.0338 (mtt) cc_final: -0.2484 (pmm) REVERT: D 360 MET cc_start: -0.1446 (mmp) cc_final: -0.1673 (mmp) REVERT: D 462 MET cc_start: 0.4731 (ttt) cc_final: 0.4178 (mmt) REVERT: D 535 HIS cc_start: 0.2377 (OUTLIER) cc_final: 0.1736 (t-90) REVERT: D 579 MET cc_start: 0.0274 (mmt) cc_final: -0.2374 (ppp) outliers start: 49 outliers final: 20 residues processed: 194 average time/residue: 0.6216 time to fit residues: 146.0589 Evaluate side-chains 172 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 274 PHE Chi-restraints excluded: chain D residue 535 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 319 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 291 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 103 optimal weight: 20.0000 chunk 193 optimal weight: 1.9990 chunk 346 optimal weight: 8.9990 chunk 212 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1002 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.163736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.095867 restraints weight = 54618.329| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 4.05 r_work: 0.2994 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 30500 Z= 0.198 Angle : 0.575 12.560 41576 Z= 0.289 Chirality : 0.046 0.291 4742 Planarity : 0.004 0.047 5296 Dihedral : 4.713 52.649 4798 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.85 % Allowed : 11.99 % Favored : 86.16 % 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: 0.70 (0.14), residues: 3635 helix: 2.07 (0.17), residues: 1009 sheet: 0.60 (0.19), residues: 725 loop : -0.46 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 983 TYR 0.021 0.001 TYR B1067 PHE 0.013 0.001 PHE A 220 TRP 0.016 0.001 TRP B 886 HIS 0.009 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00477 (30418) covalent geometry : angle 0.56574 (41372) SS BOND : bond 0.00370 ( 42) SS BOND : angle 1.56443 ( 84) hydrogen bonds : bond 0.04957 ( 1244) hydrogen bonds : angle 5.25593 ( 3585) link_BETA1-4 : bond 0.00181 ( 14) link_BETA1-4 : angle 1.03930 ( 42) link_NAG-ASN : bond 0.00318 ( 26) link_NAG-ASN : angle 1.81784 ( 78) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 153 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7320 (t0) cc_final: 0.7074 (t0) REVERT: A 237 ARG cc_start: 0.7080 (ptm-80) cc_final: 0.6487 (mtm110) REVERT: A 239 GLN cc_start: 0.6607 (mm-40) cc_final: 0.6406 (mm-40) REVERT: A 794 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8518 (pp) REVERT: B 53 ASP cc_start: 0.8575 (t70) cc_final: 0.8334 (t70) REVERT: B 200 TYR cc_start: 0.8211 (m-80) cc_final: 0.7916 (m-80) REVERT: B 468 ILE cc_start: 0.3616 (OUTLIER) cc_final: 0.3333 (mt) REVERT: B 995 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8182 (ttp80) REVERT: C 309 GLU cc_start: 0.8602 (mp0) cc_final: 0.8018 (pm20) REVERT: C 326 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7845 (pt) REVERT: C 990 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7533 (tm-30) REVERT: D 225 ASP cc_start: 0.1705 (m-30) cc_final: 0.1152 (m-30) REVERT: D 243 TYR cc_start: 0.5130 (t80) cc_final: 0.4653 (m-80) REVERT: D 297 MET cc_start: -0.1897 (OUTLIER) cc_final: -0.2256 (mmt) REVERT: D 323 MET cc_start: 0.0502 (mtt) cc_final: -0.2444 (pmm) REVERT: D 360 MET cc_start: -0.1337 (mmp) cc_final: -0.1590 (mmp) REVERT: D 535 HIS cc_start: 0.2383 (OUTLIER) cc_final: 0.1667 (t-90) REVERT: D 579 MET cc_start: 0.0332 (mmt) cc_final: -0.2325 (ppp) outliers start: 60 outliers final: 23 residues processed: 198 average time/residue: 0.6094 time to fit residues: 145.8752 Evaluate side-chains 177 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 535 HIS Chi-restraints excluded: chain D residue 555 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 103 optimal weight: 10.0000 chunk 189 optimal weight: 3.9990 chunk 305 optimal weight: 0.0670 chunk 62 optimal weight: 0.9980 chunk 246 optimal weight: 0.7980 chunk 234 optimal weight: 4.9990 chunk 178 optimal weight: 0.7980 chunk 144 optimal weight: 10.0000 chunk 335 optimal weight: 5.9990 chunk 280 optimal weight: 0.3980 chunk 117 optimal weight: 9.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN A1002 GLN B1142 GLN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 935 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.165530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.094056 restraints weight = 55153.011| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.95 r_work: 0.3067 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 30500 Z= 0.108 Angle : 0.527 13.682 41576 Z= 0.262 Chirality : 0.043 0.371 4742 Planarity : 0.004 0.047 5296 Dihedral : 4.501 55.497 4798 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.11 % Allowed : 13.07 % Favored : 85.82 % 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: 0.84 (0.14), residues: 3635 helix: 2.20 (0.17), residues: 1010 sheet: 0.73 (0.19), residues: 718 loop : -0.40 (0.14), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 983 TYR 0.024 0.001 TYR C 473 PHE 0.021 0.001 PHE C 106 TRP 0.010 0.001 TRP D 461 HIS 0.007 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00242 (30418) covalent geometry : angle 0.52076 (41372) SS BOND : bond 0.00313 ( 42) SS BOND : angle 1.10121 ( 84) hydrogen bonds : bond 0.03981 ( 1244) hydrogen bonds : angle 5.04562 ( 3585) link_BETA1-4 : bond 0.00351 ( 14) link_BETA1-4 : angle 0.92708 ( 42) link_NAG-ASN : bond 0.00192 ( 26) link_NAG-ASN : angle 1.51259 ( 78) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7294 (t0) cc_final: 0.7073 (t0) REVERT: A 237 ARG cc_start: 0.6987 (ptm-80) cc_final: 0.6450 (mtm110) REVERT: A 239 GLN cc_start: 0.6595 (mm-40) cc_final: 0.6384 (mm-40) REVERT: A 811 LYS cc_start: 0.7761 (tptp) cc_final: 0.7234 (tppt) REVERT: A 823 PHE cc_start: 0.8677 (t80) cc_final: 0.7936 (m-80) REVERT: A 858 LEU cc_start: 0.4179 (pt) cc_final: 0.3885 (mm) REVERT: B 53 ASP cc_start: 0.8575 (t70) cc_final: 0.8341 (t70) REVERT: B 200 TYR cc_start: 0.8114 (m-80) cc_final: 0.7848 (m-80) REVERT: B 347 PHE cc_start: 0.5278 (OUTLIER) cc_final: 0.5041 (m-10) REVERT: B 468 ILE cc_start: 0.3626 (OUTLIER) cc_final: 0.3390 (mt) REVERT: B 740 MET cc_start: 0.8661 (ttm) cc_final: 0.8164 (mtp) REVERT: B 981 PHE cc_start: 0.7929 (m-80) cc_final: 0.7665 (m-80) REVERT: B 995 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8152 (ttp80) REVERT: B 1040 VAL cc_start: 0.9321 (OUTLIER) cc_final: 0.9036 (m) REVERT: C 309 GLU cc_start: 0.8566 (mp0) cc_final: 0.7976 (pm20) REVERT: C 326 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7861 (pt) REVERT: C 441 LEU cc_start: 0.8747 (mp) cc_final: 0.8466 (pt) REVERT: C 492 LEU cc_start: 0.8437 (mt) cc_final: 0.8228 (mm) REVERT: C 755 GLN cc_start: 0.9114 (mt0) cc_final: 0.8733 (mp10) REVERT: C 987 PRO cc_start: 0.8517 (Cg_exo) cc_final: 0.8272 (Cg_endo) REVERT: D 225 ASP cc_start: 0.0870 (m-30) cc_final: 0.0660 (m-30) REVERT: D 243 TYR cc_start: 0.4844 (t80) cc_final: 0.4602 (m-80) REVERT: D 297 MET cc_start: -0.1767 (OUTLIER) cc_final: -0.2015 (mmt) REVERT: D 323 MET cc_start: 0.1633 (mtt) cc_final: -0.2064 (pmm) REVERT: D 360 MET cc_start: -0.1393 (mmp) cc_final: -0.1649 (mmp) REVERT: D 462 MET cc_start: 0.5234 (ptm) cc_final: 0.4851 (mmt) REVERT: D 535 HIS cc_start: 0.3744 (OUTLIER) cc_final: 0.3398 (t-90) REVERT: D 579 MET cc_start: 0.2223 (mmt) cc_final: -0.1422 (ppp) outliers start: 36 outliers final: 17 residues processed: 186 average time/residue: 0.6396 time to fit residues: 142.3616 Evaluate side-chains 171 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 535 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 267 optimal weight: 6.9990 chunk 302 optimal weight: 0.0370 chunk 296 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 284 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 290 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN A1002 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN C 314 GLN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 935 GLN D 96 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.164435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.093143 restraints weight = 54706.026| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.93 r_work: 0.3093 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 30500 Z= 0.192 Angle : 0.578 14.724 41576 Z= 0.289 Chirality : 0.045 0.253 4742 Planarity : 0.004 0.049 5296 Dihedral : 4.603 52.528 4798 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.20 % Allowed : 13.28 % Favored : 85.52 % 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: 0.71 (0.14), residues: 3635 helix: 2.12 (0.17), residues: 1016 sheet: 0.58 (0.19), residues: 726 loop : -0.47 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 983 TYR 0.023 0.001 TYR C 473 PHE 0.020 0.001 PHE A 106 TRP 0.012 0.001 TRP B 886 HIS 0.007 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00462 (30418) covalent geometry : angle 0.56966 (41372) SS BOND : bond 0.00374 ( 42) SS BOND : angle 1.43550 ( 84) hydrogen bonds : bond 0.04793 ( 1244) hydrogen bonds : angle 5.15061 ( 3585) link_BETA1-4 : bond 0.00230 ( 14) link_BETA1-4 : angle 1.06412 ( 42) link_NAG-ASN : bond 0.00329 ( 26) link_NAG-ASN : angle 1.74481 ( 78) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7392 (t0) cc_final: 0.7177 (t0) REVERT: A 189 LEU cc_start: 0.7802 (tt) cc_final: 0.7584 (mp) REVERT: A 237 ARG cc_start: 0.7329 (ptm-80) cc_final: 0.6661 (mtm110) REVERT: A 239 GLN cc_start: 0.6649 (mm-40) cc_final: 0.6352 (mm-40) REVERT: A 318 PHE cc_start: 0.7858 (p90) cc_final: 0.6157 (t80) REVERT: A 794 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8654 (pp) REVERT: B 53 ASP cc_start: 0.8592 (t70) cc_final: 0.8088 (t70) REVERT: B 200 TYR cc_start: 0.8379 (m-80) cc_final: 0.8058 (m-80) REVERT: B 347 PHE cc_start: 0.5108 (OUTLIER) cc_final: 0.4868 (m-10) REVERT: B 468 ILE cc_start: 0.3523 (OUTLIER) cc_final: 0.3216 (mt) REVERT: B 740 MET cc_start: 0.8839 (ttm) cc_final: 0.8172 (mtp) REVERT: B 981 PHE cc_start: 0.8031 (m-80) cc_final: 0.7772 (m-80) REVERT: B 983 ARG cc_start: 0.8220 (ttp80) cc_final: 0.7830 (ttp-170) REVERT: B 995 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8243 (ttp80) REVERT: C 309 GLU cc_start: 0.8602 (mp0) cc_final: 0.8101 (pm20) REVERT: C 326 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8077 (pt) REVERT: C 492 LEU cc_start: 0.8505 (mt) cc_final: 0.8266 (mm) REVERT: C 755 GLN cc_start: 0.9156 (mt0) cc_final: 0.8810 (mp10) REVERT: C 987 PRO cc_start: 0.8578 (Cg_exo) cc_final: 0.8289 (Cg_endo) REVERT: C 990 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7614 (tm-30) REVERT: D 225 ASP cc_start: 0.1698 (m-30) cc_final: 0.1203 (m-30) REVERT: D 243 TYR cc_start: 0.5309 (t80) cc_final: 0.4886 (m-80) REVERT: D 323 MET cc_start: 0.0383 (mtt) cc_final: -0.2432 (pmm) REVERT: D 360 MET cc_start: -0.1341 (mmp) cc_final: -0.1579 (mmp) REVERT: D 462 MET cc_start: 0.4851 (ptm) cc_final: 0.3960 (mmp) REVERT: D 523 PHE cc_start: 0.5432 (m-80) cc_final: 0.5018 (m-80) REVERT: D 535 HIS cc_start: 0.2569 (OUTLIER) cc_final: 0.1814 (t-90) REVERT: D 579 MET cc_start: 0.0242 (mmt) cc_final: -0.2320 (ppp) outliers start: 39 outliers final: 24 residues processed: 187 average time/residue: 0.6049 time to fit residues: 135.8872 Evaluate side-chains 181 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain D residue 535 HIS Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 175 optimal weight: 0.6980 chunk 272 optimal weight: 4.9990 chunk 303 optimal weight: 0.8980 chunk 226 optimal weight: 9.9990 chunk 269 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 352 optimal weight: 50.0000 chunk 340 optimal weight: 20.0000 chunk 2 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN B1142 GLN C 314 GLN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 935 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.164825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.095821 restraints weight = 54685.263| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.76 r_work: 0.3034 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30500 Z= 0.140 Angle : 0.547 14.593 41576 Z= 0.272 Chirality : 0.044 0.239 4742 Planarity : 0.004 0.049 5296 Dihedral : 4.515 54.162 4798 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.14 % Allowed : 13.44 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.14), residues: 3635 helix: 2.19 (0.17), residues: 1011 sheet: 0.61 (0.19), residues: 726 loop : -0.46 (0.14), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 983 TYR 0.027 0.001 TYR A 170 PHE 0.021 0.001 PHE B 168 TRP 0.010 0.001 TRP B 886 HIS 0.007 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00332 (30418) covalent geometry : angle 0.54033 (41372) SS BOND : bond 0.00340 ( 42) SS BOND : angle 1.30840 ( 84) hydrogen bonds : bond 0.04273 ( 1244) hydrogen bonds : angle 5.05234 ( 3585) link_BETA1-4 : bond 0.00298 ( 14) link_BETA1-4 : angle 0.95021 ( 42) link_NAG-ASN : bond 0.00221 ( 26) link_NAG-ASN : angle 1.56747 ( 78) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7329 (t0) cc_final: 0.7091 (t0) REVERT: A 189 LEU cc_start: 0.7727 (tt) cc_final: 0.7481 (mp) REVERT: A 237 ARG cc_start: 0.7082 (ptm-80) cc_final: 0.6795 (ttt90) REVERT: A 318 PHE cc_start: 0.7599 (p90) cc_final: 0.6199 (t80) REVERT: A 811 LYS cc_start: 0.7793 (tptp) cc_final: 0.7255 (tppt) REVERT: A 858 LEU cc_start: 0.4258 (pt) cc_final: 0.3865 (mm) REVERT: B 53 ASP cc_start: 0.8576 (t70) cc_final: 0.8344 (t70) REVERT: B 200 TYR cc_start: 0.8227 (m-80) cc_final: 0.7911 (m-80) REVERT: B 347 PHE cc_start: 0.5282 (OUTLIER) cc_final: 0.5044 (m-10) REVERT: B 468 ILE cc_start: 0.3549 (OUTLIER) cc_final: 0.3290 (mt) REVERT: B 740 MET cc_start: 0.8664 (ttm) cc_final: 0.8217 (mtp) REVERT: B 979 ASP cc_start: 0.8429 (t0) cc_final: 0.8200 (t0) REVERT: B 981 PHE cc_start: 0.7935 (m-80) cc_final: 0.7681 (m-80) REVERT: B 983 ARG cc_start: 0.8179 (ttp80) cc_final: 0.7760 (ttp-170) REVERT: B 995 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8204 (ttp80) REVERT: C 309 GLU cc_start: 0.8569 (mp0) cc_final: 0.7982 (pm20) REVERT: C 326 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7784 (pt) REVERT: C 441 LEU cc_start: 0.8731 (mp) cc_final: 0.8454 (pt) REVERT: C 492 LEU cc_start: 0.8380 (mt) cc_final: 0.8137 (mm) REVERT: C 755 GLN cc_start: 0.9128 (mt0) cc_final: 0.8740 (mp10) REVERT: C 987 PRO cc_start: 0.8553 (Cg_exo) cc_final: 0.8250 (Cg_endo) REVERT: C 990 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7460 (tm-30) REVERT: C 1145 LEU cc_start: 0.8347 (mp) cc_final: 0.7976 (tt) REVERT: D 225 ASP cc_start: 0.1649 (m-30) cc_final: 0.1168 (m-30) REVERT: D 297 MET cc_start: -0.1833 (OUTLIER) cc_final: -0.2107 (mmt) REVERT: D 323 MET cc_start: 0.0383 (mtt) cc_final: -0.2384 (pmm) REVERT: D 360 MET cc_start: -0.1356 (mmp) cc_final: -0.1678 (mmt) REVERT: D 462 MET cc_start: 0.5004 (ptm) cc_final: 0.4312 (mmp) REVERT: D 523 PHE cc_start: 0.5393 (m-80) cc_final: 0.4940 (m-80) REVERT: D 535 HIS cc_start: 0.2729 (OUTLIER) cc_final: 0.1987 (t-90) REVERT: D 579 MET cc_start: 0.0308 (mmt) cc_final: -0.2293 (ppp) outliers start: 37 outliers final: 21 residues processed: 183 average time/residue: 0.6272 time to fit residues: 137.9037 Evaluate side-chains 179 residues out of total 3247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 535 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 219 optimal weight: 10.0000 chunk 205 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 216 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 228 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 253 optimal weight: 5.9990 chunk 286 optimal weight: 0.9980 chunk 349 optimal weight: 4.9990 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 532 ASN A1002 GLN B1142 GLN C 314 GLN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.165279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.096633 restraints weight = 54775.642| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.67 r_work: 0.3044 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30500 Z= 0.122 Angle : 0.538 14.478 41576 Z= 0.267 Chirality : 0.043 0.233 4742 Planarity : 0.004 0.049 5296 Dihedral : 4.375 53.729 4798 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.05 % Allowed : 13.65 % Favored : 85.30 % 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: 0.82 (0.14), residues: 3635 helix: 2.24 (0.17), residues: 1012 sheet: 0.67 (0.19), residues: 720 loop : -0.43 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 983 TYR 0.021 0.001 TYR C 473 PHE 0.022 0.001 PHE B 168 TRP 0.028 0.001 TRP A 353 HIS 0.007 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00284 (30418) covalent geometry : angle 0.53113 (41372) SS BOND : bond 0.00333 ( 42) SS BOND : angle 1.21948 ( 84) hydrogen bonds : bond 0.04043 ( 1244) hydrogen bonds : angle 4.95464 ( 3585) link_BETA1-4 : bond 0.00311 ( 14) link_BETA1-4 : angle 0.95749 ( 42) link_NAG-ASN : bond 0.00198 ( 26) link_NAG-ASN : angle 1.51969 ( 78) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14932.04 seconds wall clock time: 253 minutes 56.27 seconds (15236.27 seconds total)