Starting phenix.real_space_refine on Tue Apr 7 04:41:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zp0_11332/04_2026/6zp0_11332.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zp0_11332/04_2026/6zp0_11332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zp0_11332/04_2026/6zp0_11332.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zp0_11332/04_2026/6zp0_11332.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zp0_11332/04_2026/6zp0_11332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zp0_11332/04_2026/6zp0_11332.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 15867 2.51 5 N 4071 2.21 5 O 4908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 191 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24957 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8039 Classifications: {'peptide': 1030} Link IDs: {'PTRANS': 48, 'TRANS': 981} Chain breaks: 6 Chain: "B" Number of atoms: 8039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8039 Classifications: {'peptide': 1030} Link IDs: {'PTRANS': 48, 'TRANS': 981} Chain breaks: 6 Chain: "C" Number of atoms: 8039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8039 Classifications: {'peptide': 1030} Link IDs: {'PTRANS': 48, 'TRANS': 981} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 5.56, per 1000 atoms: 0.22 Number of scatterers: 24957 At special positions: 0 Unit cell: (129.442, 142.174, 174.004, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 4908 8.00 N 4071 7.00 C 15867 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.01 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=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 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=2.06 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=2.00 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.06 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 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=2.01 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=2.05 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 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=2.06 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=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.06 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.01 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=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.06 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1315 " - " ASN A1074 " " NAG A1320 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1315 " - " ASN B1074 " " NAG B1320 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1315 " - " ASN C1074 " " NAG C1320 " - " ASN C 165 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN A1134 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 1.1 seconds 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5784 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 48 sheets defined 25.1% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 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 349 through 353 removed outlier: 3.806A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.469A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.312A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.688A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.601A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.503A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (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 removed outlier: 3.952A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.075A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.555A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (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 349 through 353 removed outlier: 3.805A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.469A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.312A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 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 removed outlier: 3.688A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.602A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.502A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (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: 3.953A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.075A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.555A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (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 349 through 353 removed outlier: 3.806A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.470A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.312A 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 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.689A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.601A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.502A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (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: 3.953A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (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 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.075A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.555A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.118A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.769A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.302A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.124A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 134 through 140 removed outlier: 8.275A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.015A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.712A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.336A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.676A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.201A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.642A 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: 6.569A pdb=" N ALA A 701 " --> pdb=" O ILE C 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: 3.524A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.642A 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: 3.524A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.550A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.674A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.118A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.769A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.302A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.123A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 134 through 140 removed outlier: 8.276A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.014A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.712A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.677A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.201A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.523A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.523A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.550A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.674A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.117A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.301A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.124A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 134 through 140 removed outlier: 8.277A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.015A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.712A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.677A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.201A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.524A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.524A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.550A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.674A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 987 hydrogen bonds defined for protein. 2727 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.95 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 7618 1.34 - 1.48: 7107 1.48 - 1.62: 10628 1.62 - 1.75: 12 1.75 - 1.89: 129 Bond restraints: 25494 Sorted by residual: bond pdb=" CB LYS A 378 " pdb=" CG LYS A 378 " ideal model delta sigma weight residual 1.520 1.417 0.103 3.00e-02 1.11e+03 1.18e+01 bond pdb=" CB LYS C 378 " pdb=" CG LYS C 378 " ideal model delta sigma weight residual 1.520 1.417 0.103 3.00e-02 1.11e+03 1.18e+01 bond pdb=" CB LYS B 378 " pdb=" CG LYS B 378 " ideal model delta sigma weight residual 1.520 1.418 0.102 3.00e-02 1.11e+03 1.17e+01 bond pdb=" CE LYS B 378 " pdb=" NZ LYS B 378 " ideal model delta sigma weight residual 1.489 1.387 0.102 3.00e-02 1.11e+03 1.16e+01 bond pdb=" CE LYS C 378 " pdb=" NZ LYS C 378 " ideal model delta sigma weight residual 1.489 1.387 0.102 3.00e-02 1.11e+03 1.15e+01 ... (remaining 25489 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.84: 34542 6.84 - 13.67: 105 13.67 - 20.51: 21 20.51 - 27.34: 0 27.34 - 34.18: 3 Bond angle restraints: 34671 Sorted by residual: angle pdb=" CB MET A 177 " pdb=" CG MET A 177 " pdb=" SD MET A 177 " ideal model delta sigma weight residual 112.70 146.88 -34.18 3.00e+00 1.11e-01 1.30e+02 angle pdb=" CB MET C 177 " pdb=" CG MET C 177 " pdb=" SD MET C 177 " ideal model delta sigma weight residual 112.70 146.87 -34.17 3.00e+00 1.11e-01 1.30e+02 angle pdb=" CB MET B 177 " pdb=" CG MET B 177 " pdb=" SD MET B 177 " ideal model delta sigma weight residual 112.70 146.87 -34.17 3.00e+00 1.11e-01 1.30e+02 angle pdb=" CD ARG B 466 " pdb=" NE ARG B 466 " pdb=" CZ ARG B 466 " ideal model delta sigma weight residual 124.40 138.16 -13.76 1.40e+00 5.10e-01 9.66e+01 angle pdb=" CD ARG C 466 " pdb=" NE ARG C 466 " pdb=" CZ ARG C 466 " ideal model delta sigma weight residual 124.40 138.16 -13.76 1.40e+00 5.10e-01 9.65e+01 ... (remaining 34666 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 14895 17.48 - 34.96: 726 34.96 - 52.43: 237 52.43 - 69.91: 84 69.91 - 87.39: 27 Dihedral angle restraints: 15969 sinusoidal: 6984 harmonic: 8985 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 171.95 -78.95 1 1.00e+01 1.00e-02 7.76e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 171.95 -78.95 1 1.00e+01 1.00e-02 7.76e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 171.92 -78.92 1 1.00e+01 1.00e-02 7.76e+01 ... (remaining 15966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 3633 0.109 - 0.218: 429 0.218 - 0.326: 30 0.326 - 0.435: 15 0.435 - 0.544: 9 Chirality restraints: 4116 Sorted by residual: chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.39e+00 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.29e+00 chirality pdb=" C1 NAG C1305 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1305 " pdb=" O5 NAG C1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.25e+00 ... (remaining 4113 not shown) Planarity restraints: 4464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 466 " 0.488 9.50e-02 1.11e+02 2.32e-01 1.04e+02 pdb=" NE ARG A 466 " -0.083 2.00e-02 2.50e+03 pdb=" CZ ARG A 466 " 0.144 2.00e-02 2.50e+03 pdb=" NH1 ARG A 466 " -0.047 2.00e-02 2.50e+03 pdb=" NH2 ARG A 466 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 466 " 0.487 9.50e-02 1.11e+02 2.32e-01 1.04e+02 pdb=" NE ARG C 466 " -0.083 2.00e-02 2.50e+03 pdb=" CZ ARG C 466 " 0.144 2.00e-02 2.50e+03 pdb=" NH1 ARG C 466 " -0.047 2.00e-02 2.50e+03 pdb=" NH2 ARG C 466 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 466 " 0.487 9.50e-02 1.11e+02 2.32e-01 1.04e+02 pdb=" NE ARG B 466 " -0.083 2.00e-02 2.50e+03 pdb=" CZ ARG B 466 " 0.144 2.00e-02 2.50e+03 pdb=" NH1 ARG B 466 " -0.047 2.00e-02 2.50e+03 pdb=" NH2 ARG B 466 " -0.036 2.00e-02 2.50e+03 ... (remaining 4461 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1043 2.70 - 3.25: 24106 3.25 - 3.80: 39536 3.80 - 4.35: 51286 4.35 - 4.90: 86529 Nonbonded interactions: 202500 Sorted by model distance: nonbonded pdb=" OG SER C 349 " pdb=" O LEU C 452 " model vdw 2.154 3.040 nonbonded pdb=" OG SER B 349 " pdb=" O LEU B 452 " model vdw 2.155 3.040 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.155 3.040 nonbonded pdb=" OG1 THR A 108 " pdb=" O ASN A 234 " model vdw 2.187 3.040 nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.188 3.040 ... (remaining 202495 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.830 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.116 25593 Z= 0.372 Angle : 1.429 34.178 34929 Z= 0.756 Chirality : 0.076 0.544 4116 Planarity : 0.009 0.232 4416 Dihedral : 12.627 87.391 10068 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.56 % Allowed : 0.56 % Favored : 98.89 % Cbeta Deviations : 0.31 % 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: 0.03 (0.14), residues: 3048 helix: 0.15 (0.18), residues: 669 sheet: 0.79 (0.17), residues: 726 loop : -0.31 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.150 0.004 ARG A 466 TYR 0.033 0.004 TYR A 612 PHE 0.054 0.004 PHE A 65 TRP 0.017 0.003 TRP C 886 HIS 0.008 0.002 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00863 (25494) covalent geometry : angle 1.39002 (34671) SS BOND : bond 0.01609 ( 39) SS BOND : angle 4.27287 ( 78) hydrogen bonds : bond 0.15037 ( 978) hydrogen bonds : angle 7.90275 ( 2727) link_BETA1-4 : bond 0.00574 ( 12) link_BETA1-4 : angle 1.45543 ( 36) link_NAG-ASN : bond 0.01244 ( 48) link_NAG-ASN : angle 4.42993 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 230 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 177 MET cc_start: -0.0802 (OUTLIER) cc_final: -0.1639 (mtm) REVERT: A 979 ASP cc_start: 0.7591 (t0) cc_final: 0.7314 (t0) REVERT: B 177 MET cc_start: -0.0866 (OUTLIER) cc_final: -0.1757 (mtm) REVERT: B 979 ASP cc_start: 0.7773 (t0) cc_final: 0.7330 (t0) REVERT: C 177 MET cc_start: -0.0962 (OUTLIER) cc_final: -0.1635 (mtm) REVERT: C 979 ASP cc_start: 0.7696 (t0) cc_final: 0.7334 (t0) outliers start: 15 outliers final: 0 residues processed: 235 average time/residue: 0.6532 time to fit residues: 176.4282 Evaluate side-chains 144 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 141 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain C residue 177 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 901 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 901 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.139915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.085544 restraints weight = 42045.731| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.82 r_work: 0.2927 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 25593 Z= 0.201 Angle : 0.726 12.899 34929 Z= 0.356 Chirality : 0.050 0.351 4116 Planarity : 0.004 0.069 4416 Dihedral : 7.328 58.559 4569 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.89 % Allowed : 5.86 % Favored : 93.24 % 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: 0.41 (0.14), residues: 3048 helix: 1.19 (0.21), residues: 684 sheet: 0.97 (0.17), residues: 699 loop : -0.40 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 646 TYR 0.023 0.002 TYR B 380 PHE 0.013 0.002 PHE B 888 TRP 0.024 0.002 TRP B 104 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00468 (25494) covalent geometry : angle 0.67271 (34671) SS BOND : bond 0.00653 ( 39) SS BOND : angle 2.30281 ( 78) hydrogen bonds : bond 0.04858 ( 978) hydrogen bonds : angle 5.94962 ( 2727) link_BETA1-4 : bond 0.00441 ( 12) link_BETA1-4 : angle 1.03955 ( 36) link_NAG-ASN : bond 0.00802 ( 48) link_NAG-ASN : angle 3.95943 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.747 Fit side-chains REVERT: A 52 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8301 (tm-30) REVERT: A 646 ARG cc_start: 0.8486 (ttp-110) cc_final: 0.8276 (ttp80) REVERT: A 979 ASP cc_start: 0.8160 (t0) cc_final: 0.7900 (t0) REVERT: B 52 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8272 (tm-30) REVERT: B 104 TRP cc_start: 0.7563 (m-90) cc_final: 0.7261 (m-90) REVERT: B 646 ARG cc_start: 0.8349 (ttp-110) cc_final: 0.7965 (ttp80) REVERT: B 979 ASP cc_start: 0.8301 (t0) cc_final: 0.7806 (t0) REVERT: C 54 LEU cc_start: 0.8785 (mt) cc_final: 0.8416 (mt) REVERT: C 646 ARG cc_start: 0.8407 (ttp-110) cc_final: 0.8133 (ttp80) REVERT: C 979 ASP cc_start: 0.8229 (t0) cc_final: 0.7844 (t0) outliers start: 24 outliers final: 8 residues processed: 191 average time/residue: 0.5804 time to fit residues: 129.4301 Evaluate side-chains 163 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 957 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 153 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 152 optimal weight: 10.0000 chunk 305 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 266 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 289 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 214 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 501 ASN A 901 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.137362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.082172 restraints weight = 42116.595| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.82 r_work: 0.2870 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 25593 Z= 0.222 Angle : 0.674 13.104 34929 Z= 0.325 Chirality : 0.049 0.372 4116 Planarity : 0.004 0.052 4416 Dihedral : 6.782 59.940 4560 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.89 % Allowed : 6.64 % Favored : 91.46 % 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: 0.26 (0.14), residues: 3048 helix: 1.33 (0.21), residues: 702 sheet: 0.69 (0.18), residues: 702 loop : -0.55 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 408 TYR 0.032 0.002 TYR A 873 PHE 0.013 0.001 PHE C 377 TRP 0.020 0.002 TRP C 104 HIS 0.004 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00523 (25494) covalent geometry : angle 0.61838 (34671) SS BOND : bond 0.00726 ( 39) SS BOND : angle 2.12185 ( 78) hydrogen bonds : bond 0.04734 ( 978) hydrogen bonds : angle 5.61140 ( 2727) link_BETA1-4 : bond 0.00139 ( 12) link_BETA1-4 : angle 1.03995 ( 36) link_NAG-ASN : bond 0.00792 ( 48) link_NAG-ASN : angle 3.94079 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 175 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8381 (tm-30) REVERT: A 383 SER cc_start: 0.8725 (OUTLIER) cc_final: 0.8499 (m) REVERT: A 408 ARG cc_start: 0.9013 (ttp80) cc_final: 0.8774 (tmm-80) REVERT: A 979 ASP cc_start: 0.8263 (t0) cc_final: 0.8024 (t0) REVERT: B 52 GLN cc_start: 0.8546 (tm-30) cc_final: 0.8314 (tm-30) REVERT: B 104 TRP cc_start: 0.7612 (m-90) cc_final: 0.7075 (m-90) REVERT: B 309 GLU cc_start: 0.8777 (mp0) cc_final: 0.8284 (mp0) REVERT: B 383 SER cc_start: 0.8741 (OUTLIER) cc_final: 0.8528 (m) REVERT: B 408 ARG cc_start: 0.8921 (ttp80) cc_final: 0.8676 (tmm-80) REVERT: B 979 ASP cc_start: 0.8355 (t0) cc_final: 0.7886 (OUTLIER) REVERT: C 309 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8373 (mp0) REVERT: C 408 ARG cc_start: 0.9077 (ttp80) cc_final: 0.8827 (tmm-80) REVERT: C 646 ARG cc_start: 0.8580 (ttp-110) cc_final: 0.8279 (ttp80) REVERT: C 979 ASP cc_start: 0.8277 (t0) cc_final: 0.7922 (t0) outliers start: 51 outliers final: 15 residues processed: 212 average time/residue: 0.5412 time to fit residues: 135.2328 Evaluate side-chains 172 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 263 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 207 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 154 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.136474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.081165 restraints weight = 41982.425| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.82 r_work: 0.2852 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25593 Z= 0.228 Angle : 0.656 13.091 34929 Z= 0.313 Chirality : 0.049 0.361 4116 Planarity : 0.004 0.036 4416 Dihedral : 6.386 58.195 4560 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.19 % Allowed : 7.83 % Favored : 89.98 % 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: 0.14 (0.15), residues: 3048 helix: 1.38 (0.21), residues: 702 sheet: 0.54 (0.18), residues: 666 loop : -0.64 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 346 TYR 0.030 0.002 TYR C 873 PHE 0.021 0.001 PHE C 456 TRP 0.023 0.002 TRP C 104 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00537 (25494) covalent geometry : angle 0.60145 (34671) SS BOND : bond 0.00688 ( 39) SS BOND : angle 2.09520 ( 78) hydrogen bonds : bond 0.04536 ( 978) hydrogen bonds : angle 5.47222 ( 2727) link_BETA1-4 : bond 0.00129 ( 12) link_BETA1-4 : angle 1.02867 ( 36) link_NAG-ASN : bond 0.00757 ( 48) link_NAG-ASN : angle 3.83756 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 173 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8384 (tm-30) REVERT: A 383 SER cc_start: 0.8752 (OUTLIER) cc_final: 0.8551 (m) REVERT: A 408 ARG cc_start: 0.9050 (ttp80) cc_final: 0.8764 (tmm-80) REVERT: A 979 ASP cc_start: 0.8419 (t0) cc_final: 0.8178 (t0) REVERT: B 52 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8236 (tm-30) REVERT: B 309 GLU cc_start: 0.8812 (mp0) cc_final: 0.8329 (mp0) REVERT: B 383 SER cc_start: 0.8765 (OUTLIER) cc_final: 0.8532 (m) REVERT: B 408 ARG cc_start: 0.9007 (ttp80) cc_final: 0.8742 (tmm-80) REVERT: B 979 ASP cc_start: 0.8362 (t0) cc_final: 0.7976 (t0) REVERT: C 309 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8300 (mp0) REVERT: C 408 ARG cc_start: 0.9128 (ttp80) cc_final: 0.8892 (tmm-80) REVERT: C 646 ARG cc_start: 0.8644 (ttp-110) cc_final: 0.8405 (ttp80) REVERT: C 979 ASP cc_start: 0.8288 (t0) cc_final: 0.7934 (t0) outliers start: 59 outliers final: 35 residues processed: 218 average time/residue: 0.5383 time to fit residues: 138.1452 Evaluate side-chains 193 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 112 optimal weight: 9.9990 chunk 41 optimal weight: 40.0000 chunk 15 optimal weight: 0.0980 chunk 232 optimal weight: 0.0770 chunk 39 optimal weight: 20.0000 chunk 259 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 308 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.2344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN C 196 ASN C 394 ASN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.138322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.082701 restraints weight = 42057.753| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.81 r_work: 0.2873 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 25593 Z= 0.192 Angle : 0.631 13.079 34929 Z= 0.301 Chirality : 0.048 0.357 4116 Planarity : 0.003 0.036 4416 Dihedral : 5.976 57.547 4560 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.82 % Allowed : 9.91 % Favored : 88.27 % 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: 0.16 (0.15), residues: 3048 helix: 1.49 (0.21), residues: 702 sheet: 0.48 (0.18), residues: 678 loop : -0.65 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 346 TYR 0.027 0.002 TYR A 380 PHE 0.020 0.001 PHE C 456 TRP 0.028 0.002 TRP C 104 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00451 (25494) covalent geometry : angle 0.57664 (34671) SS BOND : bond 0.00609 ( 39) SS BOND : angle 1.97999 ( 78) hydrogen bonds : bond 0.04290 ( 978) hydrogen bonds : angle 5.37377 ( 2727) link_BETA1-4 : bond 0.00185 ( 12) link_BETA1-4 : angle 1.01694 ( 36) link_NAG-ASN : bond 0.00745 ( 48) link_NAG-ASN : angle 3.74094 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 163 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8375 (tm-30) REVERT: A 408 ARG cc_start: 0.9060 (ttp80) cc_final: 0.8768 (tmm-80) REVERT: A 461 LEU cc_start: 0.9035 (mt) cc_final: 0.8835 (mp) REVERT: A 979 ASP cc_start: 0.8432 (t0) cc_final: 0.8186 (t0) REVERT: B 52 GLN cc_start: 0.8593 (tm-30) cc_final: 0.8282 (tm-30) REVERT: B 104 TRP cc_start: 0.7851 (m-90) cc_final: 0.7288 (m-90) REVERT: B 309 GLU cc_start: 0.8763 (mp0) cc_final: 0.8301 (mp0) REVERT: B 383 SER cc_start: 0.8712 (OUTLIER) cc_final: 0.8507 (m) REVERT: B 408 ARG cc_start: 0.8975 (ttp80) cc_final: 0.8712 (tmm-80) REVERT: B 979 ASP cc_start: 0.8341 (t0) cc_final: 0.7956 (t0) REVERT: C 309 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8283 (mp0) REVERT: C 408 ARG cc_start: 0.9107 (ttp80) cc_final: 0.8881 (tmm-80) REVERT: C 646 ARG cc_start: 0.8689 (ttp-110) cc_final: 0.8431 (ttp80) REVERT: C 979 ASP cc_start: 0.8279 (t0) cc_final: 0.7925 (t0) outliers start: 49 outliers final: 31 residues processed: 202 average time/residue: 0.5742 time to fit residues: 136.0153 Evaluate side-chains 184 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 123 optimal weight: 9.9990 chunk 163 optimal weight: 7.9990 chunk 202 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 chunk 41 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 133 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 164 optimal weight: 0.9980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 907 ASN C 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.138350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.086213 restraints weight = 42044.912| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.08 r_work: 0.2855 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 25593 Z= 0.242 Angle : 0.647 13.135 34929 Z= 0.310 Chirality : 0.049 0.352 4116 Planarity : 0.003 0.035 4416 Dihedral : 5.753 58.156 4560 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.15 % Allowed : 10.39 % Favored : 87.45 % 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: 0.10 (0.15), residues: 3048 helix: 1.44 (0.21), residues: 702 sheet: 0.41 (0.18), residues: 678 loop : -0.67 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 346 TYR 0.030 0.002 TYR B 380 PHE 0.013 0.001 PHE B 898 TRP 0.027 0.002 TRP C 104 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00572 (25494) covalent geometry : angle 0.59544 (34671) SS BOND : bond 0.00707 ( 39) SS BOND : angle 1.98057 ( 78) hydrogen bonds : bond 0.04503 ( 978) hydrogen bonds : angle 5.39684 ( 2727) link_BETA1-4 : bond 0.00118 ( 12) link_BETA1-4 : angle 1.05409 ( 36) link_NAG-ASN : bond 0.00726 ( 48) link_NAG-ASN : angle 3.70687 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 159 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8391 (tm-30) REVERT: A 408 ARG cc_start: 0.9086 (ttp80) cc_final: 0.8789 (tmm-80) REVERT: A 979 ASP cc_start: 0.8530 (t0) cc_final: 0.8313 (t0) REVERT: B 52 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8352 (tm-30) REVERT: B 104 TRP cc_start: 0.7913 (m-90) cc_final: 0.7315 (m-90) REVERT: B 309 GLU cc_start: 0.8810 (mp0) cc_final: 0.8372 (mp0) REVERT: B 408 ARG cc_start: 0.8976 (ttp80) cc_final: 0.8729 (tmm-80) REVERT: B 979 ASP cc_start: 0.8453 (t0) cc_final: 0.8076 (t0) REVERT: C 309 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8338 (mp0) REVERT: C 408 ARG cc_start: 0.9117 (ttp80) cc_final: 0.8886 (tmm-80) REVERT: C 646 ARG cc_start: 0.8705 (ttp-110) cc_final: 0.8425 (ttp80) REVERT: C 979 ASP cc_start: 0.8408 (t0) cc_final: 0.8057 (t0) outliers start: 58 outliers final: 40 residues processed: 208 average time/residue: 0.5607 time to fit residues: 137.7654 Evaluate side-chains 191 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 104 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 276 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 186 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 163 optimal weight: 5.9990 chunk 279 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 314 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.139107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.087676 restraints weight = 41910.314| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.67 r_work: 0.2902 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25593 Z= 0.176 Angle : 0.621 13.071 34929 Z= 0.296 Chirality : 0.047 0.350 4116 Planarity : 0.003 0.035 4416 Dihedral : 5.519 57.374 4560 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.82 % Allowed : 11.51 % Favored : 86.67 % 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: 0.14 (0.15), residues: 3048 helix: 1.48 (0.21), residues: 705 sheet: 0.44 (0.18), residues: 672 loop : -0.65 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 346 TYR 0.015 0.001 TYR A1067 PHE 0.013 0.001 PHE A 400 TRP 0.031 0.001 TRP C 104 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00412 (25494) covalent geometry : angle 0.56960 (34671) SS BOND : bond 0.00562 ( 39) SS BOND : angle 1.97940 ( 78) hydrogen bonds : bond 0.04182 ( 978) hydrogen bonds : angle 5.30640 ( 2727) link_BETA1-4 : bond 0.00172 ( 12) link_BETA1-4 : angle 1.00590 ( 36) link_NAG-ASN : bond 0.00728 ( 48) link_NAG-ASN : angle 3.63182 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 161 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8376 (tm-30) REVERT: A 408 ARG cc_start: 0.9088 (ttp80) cc_final: 0.8788 (tmm-80) REVERT: A 979 ASP cc_start: 0.8499 (t0) cc_final: 0.8268 (t0) REVERT: B 52 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8320 (tm-30) REVERT: B 104 TRP cc_start: 0.7886 (m-90) cc_final: 0.7325 (m-90) REVERT: B 309 GLU cc_start: 0.8778 (mp0) cc_final: 0.8363 (mp0) REVERT: B 408 ARG cc_start: 0.8970 (ttp80) cc_final: 0.8717 (tmm-80) REVERT: B 979 ASP cc_start: 0.8397 (t0) cc_final: 0.8019 (t0) REVERT: C 177 MET cc_start: 0.2881 (tpp) cc_final: 0.2306 (tmt) REVERT: C 309 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8353 (mp0) REVERT: C 408 ARG cc_start: 0.9092 (ttp80) cc_final: 0.8875 (tmm-80) REVERT: C 646 ARG cc_start: 0.8613 (ttp-110) cc_final: 0.8374 (ttp80) REVERT: C 979 ASP cc_start: 0.8392 (t0) cc_final: 0.8042 (t0) outliers start: 49 outliers final: 38 residues processed: 200 average time/residue: 0.5735 time to fit residues: 134.4531 Evaluate side-chains 190 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 307 optimal weight: 0.1980 chunk 162 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 182 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 314 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.139117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.086084 restraints weight = 41971.052| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.04 r_work: 0.2903 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25593 Z= 0.151 Angle : 0.606 13.033 34929 Z= 0.289 Chirality : 0.047 0.347 4116 Planarity : 0.003 0.038 4416 Dihedral : 5.249 55.780 4560 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.74 % Allowed : 11.95 % Favored : 86.30 % 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: 0.21 (0.15), residues: 3048 helix: 1.56 (0.21), residues: 705 sheet: 0.51 (0.18), residues: 645 loop : -0.62 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.026 0.001 TYR A 380 PHE 0.012 0.001 PHE A 400 TRP 0.032 0.001 TRP C 104 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00351 (25494) covalent geometry : angle 0.55624 (34671) SS BOND : bond 0.00513 ( 39) SS BOND : angle 1.74868 ( 78) hydrogen bonds : bond 0.03962 ( 978) hydrogen bonds : angle 5.19278 ( 2727) link_BETA1-4 : bond 0.00257 ( 12) link_BETA1-4 : angle 1.00889 ( 36) link_NAG-ASN : bond 0.00729 ( 48) link_NAG-ASN : angle 3.55491 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8361 (tm-30) REVERT: A 408 ARG cc_start: 0.9101 (ttp80) cc_final: 0.8783 (tmm-80) REVERT: A 979 ASP cc_start: 0.8492 (t0) cc_final: 0.8249 (t0) REVERT: B 52 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8244 (tm-30) REVERT: B 104 TRP cc_start: 0.7736 (m-90) cc_final: 0.7269 (m-90) REVERT: B 309 GLU cc_start: 0.8785 (mp0) cc_final: 0.8322 (mp0) REVERT: B 408 ARG cc_start: 0.9012 (ttp80) cc_final: 0.8743 (tmm-80) REVERT: B 979 ASP cc_start: 0.8416 (t0) cc_final: 0.7994 (t0) REVERT: C 153 MET cc_start: 0.7376 (tpp) cc_final: 0.6962 (tpp) REVERT: C 309 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8304 (mp0) REVERT: C 408 ARG cc_start: 0.9098 (ttp80) cc_final: 0.8865 (tmm-80) REVERT: C 646 ARG cc_start: 0.8679 (ttp-110) cc_final: 0.8406 (ttp80) REVERT: C 979 ASP cc_start: 0.8385 (t0) cc_final: 0.8026 (t0) outliers start: 47 outliers final: 38 residues processed: 203 average time/residue: 0.5718 time to fit residues: 136.3239 Evaluate side-chains 188 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 33 optimal weight: 3.9990 chunk 258 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 173 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 261 optimal weight: 0.6980 chunk 152 optimal weight: 9.9990 chunk 252 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 314 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.139632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.084244 restraints weight = 42058.614| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.79 r_work: 0.2943 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25593 Z= 0.138 Angle : 0.603 13.058 34929 Z= 0.288 Chirality : 0.047 0.345 4116 Planarity : 0.003 0.034 4416 Dihedral : 5.140 55.795 4560 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.78 % Allowed : 12.51 % Favored : 85.71 % 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: 0.24 (0.15), residues: 3048 helix: 1.64 (0.21), residues: 702 sheet: 0.44 (0.19), residues: 642 loop : -0.57 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 346 TYR 0.055 0.001 TYR C 380 PHE 0.011 0.001 PHE A 400 TRP 0.035 0.001 TRP C 104 HIS 0.002 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00319 (25494) covalent geometry : angle 0.55550 (34671) SS BOND : bond 0.00478 ( 39) SS BOND : angle 1.63777 ( 78) hydrogen bonds : bond 0.03882 ( 978) hydrogen bonds : angle 5.15989 ( 2727) link_BETA1-4 : bond 0.00229 ( 12) link_BETA1-4 : angle 0.98888 ( 36) link_NAG-ASN : bond 0.00727 ( 48) link_NAG-ASN : angle 3.51323 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 154 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8330 (tm-30) REVERT: A 408 ARG cc_start: 0.9088 (ttp80) cc_final: 0.8769 (tmm-80) REVERT: A 979 ASP cc_start: 0.8434 (t0) cc_final: 0.8186 (t0) REVERT: B 52 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8219 (tm-30) REVERT: B 104 TRP cc_start: 0.7715 (m-90) cc_final: 0.7241 (m-90) REVERT: B 309 GLU cc_start: 0.8742 (mp0) cc_final: 0.8287 (mp0) REVERT: B 408 ARG cc_start: 0.9005 (ttp80) cc_final: 0.8775 (tmm-80) REVERT: B 979 ASP cc_start: 0.8382 (t0) cc_final: 0.7959 (t0) REVERT: C 153 MET cc_start: 0.7427 (tpp) cc_final: 0.6946 (tpp) REVERT: C 309 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8281 (mp0) REVERT: C 408 ARG cc_start: 0.9091 (ttp80) cc_final: 0.8861 (tmm-80) REVERT: C 465 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8045 (mp0) REVERT: C 646 ARG cc_start: 0.8645 (ttp-110) cc_final: 0.8350 (ttp80) REVERT: C 979 ASP cc_start: 0.8338 (t0) cc_final: 0.7980 (t0) outliers start: 48 outliers final: 41 residues processed: 196 average time/residue: 0.5470 time to fit residues: 127.2532 Evaluate side-chains 192 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 132 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 185 optimal weight: 6.9990 chunk 228 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 245 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 957 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.139405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.085049 restraints weight = 41941.677| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.98 r_work: 0.2917 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25593 Z= 0.154 Angle : 0.606 13.057 34929 Z= 0.290 Chirality : 0.047 0.344 4116 Planarity : 0.003 0.034 4416 Dihedral : 5.090 55.813 4560 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.67 % Allowed : 12.51 % 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: 0.25 (0.15), residues: 3048 helix: 1.65 (0.21), residues: 705 sheet: 0.45 (0.19), residues: 642 loop : -0.57 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.044 0.001 TYR C 380 PHE 0.011 0.001 PHE B 898 TRP 0.036 0.001 TRP C 104 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00360 (25494) covalent geometry : angle 0.55681 (34671) SS BOND : bond 0.00493 ( 39) SS BOND : angle 1.85445 ( 78) hydrogen bonds : bond 0.03938 ( 978) hydrogen bonds : angle 5.16303 ( 2727) link_BETA1-4 : bond 0.00217 ( 12) link_BETA1-4 : angle 1.01266 ( 36) link_NAG-ASN : bond 0.00719 ( 48) link_NAG-ASN : angle 3.49066 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8652 (tm-30) cc_final: 0.8337 (tm-30) REVERT: A 177 MET cc_start: 0.3441 (tpp) cc_final: 0.3033 (tmt) REVERT: A 408 ARG cc_start: 0.9095 (ttp80) cc_final: 0.8781 (tmm-80) REVERT: A 979 ASP cc_start: 0.8466 (t0) cc_final: 0.8214 (t0) REVERT: B 52 GLN cc_start: 0.8570 (tm-30) cc_final: 0.8221 (tm-30) REVERT: B 104 TRP cc_start: 0.7686 (m-90) cc_final: 0.7232 (m-90) REVERT: B 177 MET cc_start: 0.3417 (tpp) cc_final: 0.3206 (tmt) REVERT: B 309 GLU cc_start: 0.8747 (mp0) cc_final: 0.8277 (mp0) REVERT: B 408 ARG cc_start: 0.9034 (ttp80) cc_final: 0.8796 (tmm-80) REVERT: B 979 ASP cc_start: 0.8397 (t0) cc_final: 0.7978 (t0) REVERT: C 153 MET cc_start: 0.7346 (tpp) cc_final: 0.7066 (tpp) REVERT: C 309 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8299 (mp0) REVERT: C 408 ARG cc_start: 0.9082 (ttp80) cc_final: 0.8850 (tmm-80) REVERT: C 465 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8032 (mp0) REVERT: C 646 ARG cc_start: 0.8663 (ttp-110) cc_final: 0.8375 (ttp80) REVERT: C 979 ASP cc_start: 0.8357 (t0) cc_final: 0.7999 (t0) outliers start: 45 outliers final: 41 residues processed: 199 average time/residue: 0.5759 time to fit residues: 134.9512 Evaluate side-chains 190 residues out of total 2694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 263 optimal weight: 9.9990 chunk 271 optimal weight: 0.5980 chunk 209 optimal weight: 0.7980 chunk 300 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 297 optimal weight: 0.8980 chunk 301 optimal weight: 4.9990 chunk 307 optimal weight: 2.9990 chunk 7 optimal weight: 0.0470 chunk 155 optimal weight: 3.9990 chunk 123 optimal weight: 20.0000 overall best weight: 1.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN B 196 ASN B 957 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.140165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.087214 restraints weight = 41945.121| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.01 r_work: 0.2929 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 25593 Z= 0.130 Angle : 0.604 13.053 34929 Z= 0.289 Chirality : 0.047 0.343 4116 Planarity : 0.003 0.034 4416 Dihedral : 5.046 55.786 4560 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.74 % Allowed : 12.66 % Favored : 85.60 % 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: 0.29 (0.15), residues: 3048 helix: 1.78 (0.21), residues: 693 sheet: 0.49 (0.19), residues: 624 loop : -0.58 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 457 TYR 0.049 0.001 TYR A 380 PHE 0.010 0.001 PHE A 400 TRP 0.037 0.001 TRP C 104 HIS 0.002 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00303 (25494) covalent geometry : angle 0.55720 (34671) SS BOND : bond 0.00536 ( 39) SS BOND : angle 1.63354 ( 78) hydrogen bonds : bond 0.03789 ( 978) hydrogen bonds : angle 5.14431 ( 2727) link_BETA1-4 : bond 0.00242 ( 12) link_BETA1-4 : angle 0.99668 ( 36) link_NAG-ASN : bond 0.00727 ( 48) link_NAG-ASN : angle 3.46212 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9161.89 seconds wall clock time: 157 minutes 9.01 seconds (9429.01 seconds total)