Starting phenix.real_space_refine on Thu Mar 5 19:16:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zox_11329/03_2026/6zox_11329.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zox_11329/03_2026/6zox_11329.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6zox_11329/03_2026/6zox_11329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zox_11329/03_2026/6zox_11329.map" model { file = "/net/cci-nas-00/data/ceres_data/6zox_11329/03_2026/6zox_11329.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zox_11329/03_2026/6zox_11329.cif" } 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 117 5.16 5 C 15702 2.51 5 N 4020 2.21 5 O 4857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 138 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24696 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7938 Classifications: {'peptide': 1017} Link IDs: {'PTRANS': 47, 'TRANS': 969} Chain breaks: 7 Chain: "B" Number of atoms: 7938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7938 Classifications: {'peptide': 1017} Link IDs: {'PTRANS': 47, 'TRANS': 969} Chain breaks: 7 Chain: "C" Number of atoms: 7938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7938 Classifications: {'peptide': 1017} Link IDs: {'PTRANS': 47, 'TRANS': 969} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.94, per 1000 atoms: 0.24 Number of scatterers: 24696 At special positions: 0 Unit cell: (129.442, 138.991, 161.272, 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 117 16.00 O 4857 8.00 N 4020 7.00 C 15702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.06 Simple disulfide: pdb=" SG CYS A 413 " - pdb=" SG CYS C 987 " distance=2.01 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 987 " - pdb=" SG CYS B 413 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.06 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 987 " - pdb=" SG CYS C 413 " distance=2.05 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.06 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 603 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A 709 " " NAG A1316 " - " ASN A1074 " " NAG A1321 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 603 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B 709 " " NAG B1316 " - " ASN B1074 " " NAG B1321 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 603 " " NAG C1309 " - " ASN C 616 " " NAG C1310 " - " ASN C 657 " " NAG C1311 " - " ASN C 709 " " NAG C1316 " - " ASN C1074 " " NAG C1321 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C 234 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C1098 " " NAG R 1 " - " ASN C1134 " Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 930.6 milliseconds 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 48 sheets defined 23.7% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 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: 3.895A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.281A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.327A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) 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 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: 3.744A 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: 3.555A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.638A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.382A pdb=" N VAL A 991 " --> pdb=" O CYS A 987 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (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: 3.896A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.281A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.327A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.744A 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: 3.556A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.638A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) 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 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: 4.382A pdb=" N VAL B 991 " --> pdb=" O CYS B 987 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (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: 3.896A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.281A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.327A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) 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 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: 3.744A 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: 3.554A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.638A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) 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 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: 4.383A pdb=" N VAL C 991 " --> pdb=" O CYS C 987 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.394A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.872A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.331A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.824A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.570A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.334A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 6.711A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.488A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.124A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.431A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.483A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.483A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.388A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.277A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.394A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.873A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.331A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.823A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.569A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.335A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 6.711A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.488A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.124A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.404A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.483A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.636A 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: 6.483A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.342A 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: 4.388A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.279A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.394A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.872A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN C 271 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.331A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.823A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.569A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.334A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 6.711A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.488A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (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: 6.124A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.621A 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: 6.482A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.636A 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: 6.482A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.342A 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: 4.388A 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: 4.278A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1000 hydrogen bonds defined for protein. 2784 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.52 Time building geometry restraints manager: 2.89 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: 7578 1.34 - 1.48: 7154 1.48 - 1.62: 10348 1.62 - 1.75: 12 1.75 - 1.89: 135 Bond restraints: 25227 Sorted by residual: bond pdb=" CZ ARG C 346 " pdb=" NH2 ARG C 346 " ideal model delta sigma weight residual 1.330 1.267 0.063 1.30e-02 5.92e+03 2.31e+01 bond pdb=" CZ ARG B 346 " pdb=" NH2 ARG B 346 " ideal model delta sigma weight residual 1.330 1.268 0.062 1.30e-02 5.92e+03 2.26e+01 bond pdb=" CZ ARG A 346 " pdb=" NH2 ARG A 346 " ideal model delta sigma weight residual 1.330 1.268 0.062 1.30e-02 5.92e+03 2.26e+01 bond pdb=" CB PRO B 57 " pdb=" CG PRO B 57 " ideal model delta sigma weight residual 1.492 1.297 0.195 5.00e-02 4.00e+02 1.52e+01 bond pdb=" CB PRO C 57 " pdb=" CG PRO C 57 " ideal model delta sigma weight residual 1.492 1.297 0.195 5.00e-02 4.00e+02 1.52e+01 ... (remaining 25222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.10: 33287 4.10 - 8.21: 940 8.21 - 12.31: 51 12.31 - 16.42: 15 16.42 - 20.52: 6 Bond angle restraints: 34299 Sorted by residual: angle pdb=" CA CYS B 525 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " ideal model delta sigma weight residual 114.40 134.92 -20.52 2.30e+00 1.89e-01 7.96e+01 angle pdb=" CA CYS C 525 " pdb=" CB CYS C 525 " pdb=" SG CYS C 525 " ideal model delta sigma weight residual 114.40 134.92 -20.52 2.30e+00 1.89e-01 7.96e+01 angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 134.87 -20.47 2.30e+00 1.89e-01 7.92e+01 angle pdb=" CA ARG A 102 " pdb=" CB ARG A 102 " pdb=" CG ARG A 102 " ideal model delta sigma weight residual 114.10 129.89 -15.79 2.00e+00 2.50e-01 6.23e+01 angle pdb=" CA ARG C 102 " pdb=" CB ARG C 102 " pdb=" CG ARG C 102 " ideal model delta sigma weight residual 114.10 129.89 -15.79 2.00e+00 2.50e-01 6.23e+01 ... (remaining 34294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 14801 17.71 - 35.42: 718 35.42 - 53.13: 236 53.13 - 70.84: 64 70.84 - 88.55: 27 Dihedral angle restraints: 15846 sinusoidal: 6975 harmonic: 8871 Sorted by residual: dihedral pdb=" CA LEU B 517 " pdb=" C LEU B 517 " pdb=" N LEU B 518 " pdb=" CA LEU B 518 " ideal model delta harmonic sigma weight residual -180.00 -131.21 -48.79 0 5.00e+00 4.00e-02 9.52e+01 dihedral pdb=" CA LEU A 517 " pdb=" C LEU A 517 " pdb=" N LEU A 518 " pdb=" CA LEU A 518 " ideal model delta harmonic sigma weight residual -180.00 -131.22 -48.78 0 5.00e+00 4.00e-02 9.52e+01 dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual -180.00 -131.23 -48.77 0 5.00e+00 4.00e-02 9.51e+01 ... (remaining 15843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 3644 0.138 - 0.276: 378 0.276 - 0.414: 43 0.414 - 0.552: 12 0.552 - 0.690: 3 Chirality restraints: 4080 Sorted by residual: chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" C1 NAG C1308 " pdb=" ND2 ASN C 603 " pdb=" C2 NAG C1308 " pdb=" O5 NAG C1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" C1 NAG A1308 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1308 " pdb=" O5 NAG A1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.18e+01 ... (remaining 4077 not shown) Planarity restraints: 4404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 490 " 0.070 2.00e-02 2.50e+03 6.34e-02 7.03e+01 pdb=" CG PHE A 490 " -0.142 2.00e-02 2.50e+03 pdb=" CD1 PHE A 490 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE A 490 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 490 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A 490 " 0.029 2.00e-02 2.50e+03 pdb=" CZ PHE A 490 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 490 " 0.070 2.00e-02 2.50e+03 6.33e-02 7.01e+01 pdb=" CG PHE B 490 " -0.142 2.00e-02 2.50e+03 pdb=" CD1 PHE B 490 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 PHE B 490 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 490 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE B 490 " 0.029 2.00e-02 2.50e+03 pdb=" CZ PHE B 490 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 490 " 0.070 2.00e-02 2.50e+03 6.33e-02 7.01e+01 pdb=" CG PHE C 490 " -0.142 2.00e-02 2.50e+03 pdb=" CD1 PHE C 490 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE C 490 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 490 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE C 490 " 0.030 2.00e-02 2.50e+03 pdb=" CZ PHE C 490 " 0.015 2.00e-02 2.50e+03 ... (remaining 4401 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 340 2.59 - 3.17: 20934 3.17 - 3.75: 37277 3.75 - 4.32: 53379 4.32 - 4.90: 88973 Nonbonded interactions: 200903 Sorted by model distance: nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.015 3.040 nonbonded pdb=" OD1 ASP B 442 " pdb=" OH TYR B 451 " model vdw 2.016 3.040 nonbonded pdb=" OD1 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.016 3.040 nonbonded pdb=" OG SER C 98 " pdb=" O GLU C 180 " model vdw 2.096 3.040 nonbonded pdb=" OG SER B 98 " pdb=" O GLU B 180 " model vdw 2.096 3.040 ... (remaining 200898 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' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.120 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.280 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 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 : 0.011 0.195 25332 Z= 0.498 Angle : 1.688 30.555 34572 Z= 0.954 Chirality : 0.093 0.690 4080 Planarity : 0.010 0.112 4356 Dihedral : 12.343 88.548 10008 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.60 % Favored : 96.20 % Rotamer: Outliers : 0.90 % Allowed : 0.83 % Favored : 98.27 % Cbeta Deviations : 0.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.14), residues: 3003 helix: 0.49 (0.19), residues: 609 sheet: 0.90 (0.18), residues: 729 loop : -0.20 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.003 ARG C 346 TYR 0.056 0.005 TYR B 495 PHE 0.142 0.007 PHE A 490 TRP 0.060 0.007 TRP A 64 HIS 0.013 0.004 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.01124 (25227) covalent geometry : angle 1.60744 (34299) SS BOND : bond 0.01350 ( 42) SS BOND : angle 4.56273 ( 84) hydrogen bonds : bond 0.16743 ( 961) hydrogen bonds : angle 8.31523 ( 2784) link_BETA1-4 : bond 0.00770 ( 15) link_BETA1-4 : angle 2.23367 ( 45) link_NAG-ASN : bond 0.01390 ( 48) link_NAG-ASN : angle 7.43136 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 292 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 ASP cc_start: 0.7669 (t0) cc_final: 0.7345 (t0) REVERT: B 104 TRP cc_start: 0.7835 (m-90) cc_final: 0.7495 (m-90) REVERT: B 164 ASN cc_start: 0.7352 (t0) cc_final: 0.7136 (t0) REVERT: B 190 ARG cc_start: 0.7314 (ttp-170) cc_final: 0.7041 (ttp-170) REVERT: B 192 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7955 (m-80) REVERT: C 164 ASN cc_start: 0.7410 (t0) cc_final: 0.7131 (t0) REVERT: C 365 TYR cc_start: 0.8518 (m-80) cc_final: 0.8187 (m-80) outliers start: 24 outliers final: 4 residues processed: 304 average time/residue: 0.6705 time to fit residues: 234.8648 Evaluate side-chains 188 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 183 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 603 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.0370 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 317 ASN A 414 GLN A 613 GLN A 901 GLN A 926 GLN A 957 GLN A 969 ASN A1071 GLN B 317 ASN B 414 GLN B 901 GLN B 926 GLN B 957 GLN B1071 GLN C 196 ASN C 317 ASN C 414 GLN C 901 GLN C 926 GLN C 957 GLN C1071 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.150893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.103024 restraints weight = 41030.275| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.87 r_work: 0.3091 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25332 Z= 0.187 Angle : 0.784 19.450 34572 Z= 0.385 Chirality : 0.052 0.403 4080 Planarity : 0.005 0.058 4356 Dihedral : 7.691 59.896 4586 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.73 % Allowed : 6.09 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.45 (0.14), residues: 3003 helix: 1.21 (0.20), residues: 648 sheet: 0.89 (0.18), residues: 717 loop : -0.31 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 102 TYR 0.020 0.002 TYR C 453 PHE 0.031 0.002 PHE A 140 TRP 0.021 0.002 TRP C 886 HIS 0.006 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00421 (25227) covalent geometry : angle 0.70958 (34299) SS BOND : bond 0.00574 ( 42) SS BOND : angle 2.03610 ( 84) hydrogen bonds : bond 0.04659 ( 961) hydrogen bonds : angle 6.15242 ( 2784) link_BETA1-4 : bond 0.00396 ( 15) link_BETA1-4 : angle 1.02989 ( 45) link_NAG-ASN : bond 0.00635 ( 48) link_NAG-ASN : angle 4.97080 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 225 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8360 (tm-30) cc_final: 0.7706 (tm-30) REVERT: A 164 ASN cc_start: 0.7478 (t0) cc_final: 0.7183 (t0) REVERT: A 346 ARG cc_start: 0.7970 (tpm170) cc_final: 0.7697 (mmp-170) REVERT: A 360 ASN cc_start: 0.8688 (t0) cc_final: 0.8369 (t0) REVERT: A 492 LEU cc_start: 0.9300 (mt) cc_final: 0.9065 (mm) REVERT: B 52 GLN cc_start: 0.8264 (tm-30) cc_final: 0.7690 (tm-30) REVERT: B 88 ASP cc_start: 0.8663 (m-30) cc_final: 0.8423 (m-30) REVERT: B 164 ASN cc_start: 0.7199 (t0) cc_final: 0.6827 (t0) REVERT: B 360 ASN cc_start: 0.8698 (t0) cc_final: 0.8366 (t0) REVERT: B 456 PHE cc_start: 0.7989 (m-80) cc_final: 0.7642 (m-10) REVERT: B 740 MET cc_start: 0.8991 (ttm) cc_final: 0.8784 (ttm) REVERT: C 132 GLU cc_start: 0.7739 (tt0) cc_final: 0.7492 (mm-30) REVERT: C 164 ASN cc_start: 0.7279 (t0) cc_final: 0.6925 (t0) REVERT: C 346 ARG cc_start: 0.7874 (tpm-80) cc_final: 0.7609 (tpm-80) REVERT: C 360 ASN cc_start: 0.8766 (t0) cc_final: 0.8434 (t0) REVERT: C 365 TYR cc_start: 0.8679 (m-80) cc_final: 0.8357 (m-80) REVERT: C 564 GLN cc_start: 0.7964 (tp40) cc_final: 0.7036 (tp-100) REVERT: C 731 MET cc_start: 0.9287 (ptt) cc_final: 0.9003 (ptm) outliers start: 46 outliers final: 16 residues processed: 257 average time/residue: 0.5938 time to fit residues: 179.0397 Evaluate side-chains 199 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 166 optimal weight: 4.9990 chunk 265 optimal weight: 1.9990 chunk 276 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 280 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 297 optimal weight: 2.9990 chunk 218 optimal weight: 8.9990 chunk 290 optimal weight: 0.6980 chunk 143 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 314 GLN A 317 ASN A 957 GLN A1036 GLN B 245 HIS B 317 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1054 GLN C 245 HIS C 317 ASN C 957 GLN C1036 GLN C1054 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.149420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.099067 restraints weight = 41167.387| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.15 r_work: 0.3038 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25332 Z= 0.199 Angle : 0.709 17.386 34572 Z= 0.350 Chirality : 0.050 0.380 4080 Planarity : 0.004 0.039 4356 Dihedral : 7.111 59.198 4582 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.07 % Allowed : 8.61 % Favored : 89.33 % 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 (0.15), residues: 3003 helix: 1.28 (0.20), residues: 666 sheet: 0.64 (0.18), residues: 735 loop : -0.49 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 408 TYR 0.015 0.002 TYR B1067 PHE 0.025 0.002 PHE C 140 TRP 0.014 0.001 TRP A 886 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00456 (25227) covalent geometry : angle 0.64358 (34299) SS BOND : bond 0.00535 ( 42) SS BOND : angle 1.96189 ( 84) hydrogen bonds : bond 0.04335 ( 961) hydrogen bonds : angle 5.78769 ( 2784) link_BETA1-4 : bond 0.00273 ( 15) link_BETA1-4 : angle 0.95190 ( 45) link_NAG-ASN : bond 0.00666 ( 48) link_NAG-ASN : angle 4.42659 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 207 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8365 (tm-30) cc_final: 0.7629 (tm-30) REVERT: A 132 GLU cc_start: 0.7874 (tt0) cc_final: 0.7657 (mm-30) REVERT: A 346 ARG cc_start: 0.7963 (tpm170) cc_final: 0.7644 (mmp-170) REVERT: A 360 ASN cc_start: 0.8918 (t0) cc_final: 0.8492 (t0) REVERT: A 1092 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7718 (mm-30) REVERT: B 52 GLN cc_start: 0.8292 (tm-30) cc_final: 0.7683 (tm-30) REVERT: B 88 ASP cc_start: 0.8665 (m-30) cc_final: 0.8379 (m-30) REVERT: B 132 GLU cc_start: 0.7776 (tt0) cc_final: 0.7534 (mm-30) REVERT: B 164 ASN cc_start: 0.7027 (t0) cc_final: 0.6623 (t0) REVERT: B 324 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7713 (pm20) REVERT: B 360 ASN cc_start: 0.8894 (t0) cc_final: 0.8457 (t0) REVERT: B 427 ASP cc_start: 0.8558 (m-30) cc_final: 0.8044 (m-30) REVERT: B 456 PHE cc_start: 0.8048 (m-80) cc_final: 0.7791 (m-10) REVERT: B 1029 MET cc_start: 0.9081 (tpp) cc_final: 0.8866 (tpp) REVERT: C 346 ARG cc_start: 0.7926 (tpm-80) cc_final: 0.7636 (tpm-80) REVERT: C 360 ASN cc_start: 0.8986 (t0) cc_final: 0.8544 (t0) REVERT: C 546 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7237 (pp) REVERT: C 564 GLN cc_start: 0.8134 (tp40) cc_final: 0.7085 (tp-100) REVERT: C 731 MET cc_start: 0.9363 (ptt) cc_final: 0.9045 (ptm) outliers start: 55 outliers final: 32 residues processed: 244 average time/residue: 0.5378 time to fit residues: 155.1968 Evaluate side-chains 213 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 124 optimal weight: 0.9990 chunk 108 optimal weight: 0.0000 chunk 281 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 120 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 194 optimal weight: 0.5980 chunk 144 optimal weight: 9.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 317 ASN A1135 ASN B 317 ASN B 394 ASN B 784 GLN B 957 GLN C 317 ASN C1135 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.151351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.100581 restraints weight = 40879.121| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.84 r_work: 0.3122 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25332 Z= 0.118 Angle : 0.636 16.016 34572 Z= 0.310 Chirality : 0.048 0.366 4080 Planarity : 0.004 0.043 4356 Dihedral : 6.595 58.409 4582 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.14 % Allowed : 10.37 % Favored : 87.49 % 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: 0.27 (0.15), residues: 3003 helix: 1.42 (0.21), residues: 672 sheet: 0.62 (0.18), residues: 714 loop : -0.54 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 357 TYR 0.010 0.001 TYR C1067 PHE 0.022 0.001 PHE A 140 TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00258 (25227) covalent geometry : angle 0.57423 (34299) SS BOND : bond 0.00476 ( 42) SS BOND : angle 1.62283 ( 84) hydrogen bonds : bond 0.03720 ( 961) hydrogen bonds : angle 5.47125 ( 2784) link_BETA1-4 : bond 0.00348 ( 15) link_BETA1-4 : angle 0.95620 ( 45) link_NAG-ASN : bond 0.00671 ( 48) link_NAG-ASN : angle 4.09246 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 190 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8354 (tm-30) cc_final: 0.7747 (tm-30) REVERT: A 104 TRP cc_start: 0.8326 (m-90) cc_final: 0.8005 (m-90) REVERT: A 132 GLU cc_start: 0.7920 (tt0) cc_final: 0.7641 (mm-30) REVERT: A 346 ARG cc_start: 0.8034 (tpm170) cc_final: 0.7701 (mmp-170) REVERT: A 360 ASN cc_start: 0.9008 (t0) cc_final: 0.8528 (t0) REVERT: A 556 ASN cc_start: 0.8691 (p0) cc_final: 0.8419 (m-40) REVERT: A 1092 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7754 (mm-30) REVERT: B 52 GLN cc_start: 0.8382 (tm-30) cc_final: 0.7839 (tm-30) REVERT: B 88 ASP cc_start: 0.8665 (m-30) cc_final: 0.8399 (m-30) REVERT: B 132 GLU cc_start: 0.7791 (tt0) cc_final: 0.7485 (mm-30) REVERT: B 164 ASN cc_start: 0.7060 (t0) cc_final: 0.6766 (t0) REVERT: B 192 PHE cc_start: 0.8100 (m-80) cc_final: 0.7749 (m-80) REVERT: B 277 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8751 (mm) REVERT: B 346 ARG cc_start: 0.7886 (tpm-80) cc_final: 0.7510 (tpm-80) REVERT: B 360 ASN cc_start: 0.8986 (t0) cc_final: 0.8545 (t0) REVERT: B 427 ASP cc_start: 0.8598 (m-30) cc_final: 0.8170 (m-30) REVERT: B 574 ASP cc_start: 0.8373 (t0) cc_final: 0.7892 (t0) REVERT: B 731 MET cc_start: 0.9498 (OUTLIER) cc_final: 0.8779 (ptm) REVERT: B 780 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8038 (mp0) REVERT: C 346 ARG cc_start: 0.7921 (tpm-80) cc_final: 0.7626 (tpm-80) REVERT: C 360 ASN cc_start: 0.9106 (t0) cc_final: 0.8680 (t0) REVERT: C 546 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7421 (pp) REVERT: C 564 GLN cc_start: 0.8188 (tp40) cc_final: 0.7149 (tp-100) REVERT: C 646 ARG cc_start: 0.8425 (tmt170) cc_final: 0.8082 (tpt-90) REVERT: C 731 MET cc_start: 0.9453 (ptt) cc_final: 0.9220 (ptm) REVERT: C 1094 VAL cc_start: 0.7984 (OUTLIER) cc_final: 0.7683 (p) outliers start: 57 outliers final: 22 residues processed: 231 average time/residue: 0.5611 time to fit residues: 153.8605 Evaluate side-chains 194 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 190 optimal weight: 4.9990 chunk 267 optimal weight: 5.9990 chunk 189 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 211 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 296 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 957 GLN A1101 HIS ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1036 GLN C 317 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.147603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.099256 restraints weight = 40896.051| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.76 r_work: 0.3034 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25332 Z= 0.236 Angle : 0.684 15.268 34572 Z= 0.338 Chirality : 0.050 0.339 4080 Planarity : 0.004 0.049 4356 Dihedral : 6.450 58.536 4580 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.63 % Allowed : 10.22 % Favored : 87.15 % 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: 0.04 (0.15), residues: 3003 helix: 1.19 (0.21), residues: 669 sheet: 0.44 (0.18), residues: 750 loop : -0.67 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 357 TYR 0.016 0.002 TYR A1067 PHE 0.029 0.002 PHE B 456 TRP 0.012 0.001 TRP A 886 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00549 (25227) covalent geometry : angle 0.62737 (34299) SS BOND : bond 0.00454 ( 42) SS BOND : angle 1.92419 ( 84) hydrogen bonds : bond 0.04249 ( 961) hydrogen bonds : angle 5.52937 ( 2784) link_BETA1-4 : bond 0.00260 ( 15) link_BETA1-4 : angle 0.95827 ( 45) link_NAG-ASN : bond 0.00640 ( 48) link_NAG-ASN : angle 4.02549 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 193 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.5143 (OUTLIER) cc_final: 0.4680 (p) REVERT: A 52 GLN cc_start: 0.8405 (tm-30) cc_final: 0.7774 (tm-30) REVERT: A 104 TRP cc_start: 0.8562 (m-90) cc_final: 0.8297 (m-90) REVERT: A 346 ARG cc_start: 0.8014 (tpm170) cc_final: 0.7720 (tpm-80) REVERT: A 360 ASN cc_start: 0.8994 (t0) cc_final: 0.8495 (t0) REVERT: A 556 ASN cc_start: 0.8746 (p0) cc_final: 0.8475 (m-40) REVERT: A 564 GLN cc_start: 0.8147 (tp40) cc_final: 0.7162 (tp-100) REVERT: A 1092 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7309 (mm-30) REVERT: B 29 THR cc_start: 0.5139 (OUTLIER) cc_final: 0.4706 (p) REVERT: B 52 GLN cc_start: 0.8446 (tm-30) cc_final: 0.7903 (tm-30) REVERT: B 164 ASN cc_start: 0.7063 (t0) cc_final: 0.6714 (t0) REVERT: B 192 PHE cc_start: 0.8237 (m-80) cc_final: 0.7943 (m-80) REVERT: B 346 ARG cc_start: 0.7898 (tpm-80) cc_final: 0.7573 (tpm-80) REVERT: B 360 ASN cc_start: 0.8999 (t0) cc_final: 0.8598 (t0) REVERT: B 468 ILE cc_start: 0.9213 (mp) cc_final: 0.8951 (mm) REVERT: B 556 ASN cc_start: 0.8565 (p0) cc_final: 0.8291 (m-40) REVERT: B 731 MET cc_start: 0.9521 (OUTLIER) cc_final: 0.9189 (ptm) REVERT: C 29 THR cc_start: 0.5315 (OUTLIER) cc_final: 0.4894 (p) REVERT: C 52 GLN cc_start: 0.8453 (tm-30) cc_final: 0.7931 (tm-30) REVERT: C 346 ARG cc_start: 0.7893 (tpm-80) cc_final: 0.7600 (tpm-80) REVERT: C 360 ASN cc_start: 0.9136 (t0) cc_final: 0.8740 (t0) REVERT: C 556 ASN cc_start: 0.8677 (p0) cc_final: 0.8299 (m-40) REVERT: C 564 GLN cc_start: 0.8215 (tp40) cc_final: 0.7143 (tp-100) REVERT: C 731 MET cc_start: 0.9471 (ptt) cc_final: 0.9143 (ptm) outliers start: 70 outliers final: 31 residues processed: 248 average time/residue: 0.5322 time to fit residues: 156.3893 Evaluate side-chains 212 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 252 optimal weight: 8.9990 chunk 287 optimal weight: 0.0270 chunk 272 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 247 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 182 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN B 314 GLN B 317 ASN B 394 ASN B 613 GLN B 957 GLN C 314 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 957 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.149213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.099018 restraints weight = 40805.499| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.80 r_work: 0.3078 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25332 Z= 0.131 Angle : 0.627 14.887 34572 Z= 0.306 Chirality : 0.048 0.329 4080 Planarity : 0.004 0.050 4356 Dihedral : 6.187 58.825 4580 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.33 % Allowed : 11.05 % Favored : 86.62 % 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: 3003 helix: 1.33 (0.21), residues: 672 sheet: 0.47 (0.18), residues: 741 loop : -0.67 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 357 TYR 0.015 0.001 TYR B 489 PHE 0.030 0.001 PHE B 456 TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00297 (25227) covalent geometry : angle 0.56943 (34299) SS BOND : bond 0.00464 ( 42) SS BOND : angle 1.72900 ( 84) hydrogen bonds : bond 0.03678 ( 961) hydrogen bonds : angle 5.35392 ( 2784) link_BETA1-4 : bond 0.00319 ( 15) link_BETA1-4 : angle 0.93067 ( 45) link_NAG-ASN : bond 0.00670 ( 48) link_NAG-ASN : angle 3.87377 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 189 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.4836 (OUTLIER) cc_final: 0.4397 (p) REVERT: A 52 GLN cc_start: 0.8342 (tm-30) cc_final: 0.7677 (tm-30) REVERT: A 104 TRP cc_start: 0.8512 (m-90) cc_final: 0.8206 (m-90) REVERT: A 132 GLU cc_start: 0.8045 (tt0) cc_final: 0.7664 (mm-30) REVERT: A 346 ARG cc_start: 0.7989 (tpm170) cc_final: 0.7698 (tpm-80) REVERT: A 360 ASN cc_start: 0.9031 (t0) cc_final: 0.8560 (t0) REVERT: A 564 GLN cc_start: 0.8076 (tp40) cc_final: 0.7128 (tp-100) REVERT: A 1092 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7819 (pm20) REVERT: B 29 THR cc_start: 0.4838 (OUTLIER) cc_final: 0.4390 (p) REVERT: B 52 GLN cc_start: 0.8417 (tm-30) cc_final: 0.7892 (tm-30) REVERT: B 164 ASN cc_start: 0.7051 (t0) cc_final: 0.6271 (t0) REVERT: B 192 PHE cc_start: 0.8120 (m-80) cc_final: 0.7711 (m-80) REVERT: B 346 ARG cc_start: 0.7869 (tpm-80) cc_final: 0.7515 (tpm-80) REVERT: B 360 ASN cc_start: 0.8883 (t0) cc_final: 0.8505 (t0) REVERT: B 376 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8116 (p) REVERT: B 456 PHE cc_start: 0.8099 (m-80) cc_final: 0.7850 (m-80) REVERT: B 468 ILE cc_start: 0.9211 (mp) cc_final: 0.8955 (mm) REVERT: B 564 GLN cc_start: 0.8160 (tp40) cc_final: 0.7019 (tp-100) REVERT: B 646 ARG cc_start: 0.8349 (tpt170) cc_final: 0.8005 (tmt-80) REVERT: B 731 MET cc_start: 0.9523 (OUTLIER) cc_final: 0.8802 (ptm) REVERT: B 780 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8166 (mp0) REVERT: C 29 THR cc_start: 0.5334 (OUTLIER) cc_final: 0.4913 (p) REVERT: C 52 GLN cc_start: 0.8403 (tm-30) cc_final: 0.7844 (tm-30) REVERT: C 346 ARG cc_start: 0.7812 (tpm-80) cc_final: 0.7524 (tpm-80) REVERT: C 360 ASN cc_start: 0.9186 (t0) cc_final: 0.8809 (t0) REVERT: C 546 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7571 (pp) REVERT: C 564 GLN cc_start: 0.8181 (tp40) cc_final: 0.7092 (tp-100) REVERT: C 646 ARG cc_start: 0.8531 (tmt170) cc_final: 0.8089 (tpt-90) REVERT: C 731 MET cc_start: 0.9483 (ptt) cc_final: 0.9188 (ptm) REVERT: C 1094 VAL cc_start: 0.8085 (OUTLIER) cc_final: 0.7798 (p) outliers start: 62 outliers final: 30 residues processed: 235 average time/residue: 0.5105 time to fit residues: 143.1583 Evaluate side-chains 217 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 273 optimal weight: 0.0070 chunk 167 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 296 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 302 optimal weight: 0.8980 chunk 224 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN B 314 GLN B 317 ASN B 394 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1135 ASN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.150269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.100196 restraints weight = 40803.066| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.82 r_work: 0.3093 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25332 Z= 0.117 Angle : 0.605 14.516 34572 Z= 0.295 Chirality : 0.047 0.314 4080 Planarity : 0.004 0.050 4356 Dihedral : 5.941 59.786 4580 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.48 % Allowed : 11.24 % Favored : 86.28 % 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: 3003 helix: 1.63 (0.21), residues: 654 sheet: 0.57 (0.18), residues: 735 loop : -0.63 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 102 TYR 0.013 0.001 TYR C 369 PHE 0.028 0.001 PHE C 456 TRP 0.009 0.001 TRP C 436 HIS 0.002 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00262 (25227) covalent geometry : angle 0.54797 (34299) SS BOND : bond 0.00462 ( 42) SS BOND : angle 1.89059 ( 84) hydrogen bonds : bond 0.03457 ( 961) hydrogen bonds : angle 5.21682 ( 2784) link_BETA1-4 : bond 0.00347 ( 15) link_BETA1-4 : angle 0.91575 ( 45) link_NAG-ASN : bond 0.00670 ( 48) link_NAG-ASN : angle 3.75813 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 194 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.4910 (OUTLIER) cc_final: 0.4473 (p) REVERT: A 52 GLN cc_start: 0.8359 (tm-30) cc_final: 0.7695 (tp40) REVERT: A 53 ASP cc_start: 0.6714 (p0) cc_final: 0.6499 (p0) REVERT: A 104 TRP cc_start: 0.8524 (m-90) cc_final: 0.8153 (m-90) REVERT: A 132 GLU cc_start: 0.8034 (tt0) cc_final: 0.7602 (mm-30) REVERT: A 346 ARG cc_start: 0.8040 (tpm170) cc_final: 0.7750 (tpm-80) REVERT: A 360 ASN cc_start: 0.9111 (t0) cc_final: 0.8702 (t0) REVERT: A 564 GLN cc_start: 0.8000 (tp40) cc_final: 0.7154 (tp-100) REVERT: B 29 THR cc_start: 0.4732 (OUTLIER) cc_final: 0.4289 (p) REVERT: B 52 GLN cc_start: 0.8438 (tm-30) cc_final: 0.7890 (tm-30) REVERT: B 192 PHE cc_start: 0.8115 (m-80) cc_final: 0.7711 (m-80) REVERT: B 346 ARG cc_start: 0.7849 (tpm-80) cc_final: 0.7496 (tpm-80) REVERT: B 360 ASN cc_start: 0.8909 (t0) cc_final: 0.8545 (t0) REVERT: B 376 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8137 (p) REVERT: B 564 GLN cc_start: 0.8169 (tp40) cc_final: 0.7063 (tp-100) REVERT: B 731 MET cc_start: 0.9525 (OUTLIER) cc_final: 0.8801 (ptm) REVERT: B 780 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8227 (mp0) REVERT: C 29 THR cc_start: 0.5106 (OUTLIER) cc_final: 0.4717 (p) REVERT: C 52 GLN cc_start: 0.8420 (tm-30) cc_final: 0.7870 (tm-30) REVERT: C 346 ARG cc_start: 0.7794 (tpm-80) cc_final: 0.7507 (tpm-80) REVERT: C 360 ASN cc_start: 0.9097 (t0) cc_final: 0.8751 (t0) REVERT: C 546 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7606 (pp) REVERT: C 564 GLN cc_start: 0.8118 (tp40) cc_final: 0.7163 (tp-100) REVERT: C 646 ARG cc_start: 0.8547 (tmt170) cc_final: 0.8073 (tpt-90) REVERT: C 731 MET cc_start: 0.9482 (ptt) cc_final: 0.9169 (ptm) outliers start: 66 outliers final: 35 residues processed: 244 average time/residue: 0.5458 time to fit residues: 157.3332 Evaluate side-chains 217 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 176 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 24 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 215 optimal weight: 0.0370 chunk 206 optimal weight: 0.5980 chunk 220 optimal weight: 8.9990 chunk 286 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 284 optimal weight: 0.7980 overall best weight: 1.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 450 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 317 ASN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.149092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.097865 restraints weight = 40871.673| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.84 r_work: 0.3064 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25332 Z= 0.173 Angle : 0.625 14.360 34572 Z= 0.306 Chirality : 0.048 0.312 4080 Planarity : 0.004 0.052 4356 Dihedral : 5.923 58.069 4580 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.44 % Allowed : 11.88 % Favored : 85.68 % 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: 0.20 (0.15), residues: 3003 helix: 1.54 (0.21), residues: 654 sheet: 0.54 (0.18), residues: 741 loop : -0.65 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 357 TYR 0.017 0.001 TYR C 369 PHE 0.029 0.001 PHE C 456 TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00401 (25227) covalent geometry : angle 0.56999 (34299) SS BOND : bond 0.00443 ( 42) SS BOND : angle 1.91179 ( 84) hydrogen bonds : bond 0.03700 ( 961) hydrogen bonds : angle 5.23810 ( 2784) link_BETA1-4 : bond 0.00363 ( 15) link_BETA1-4 : angle 0.93908 ( 45) link_NAG-ASN : bond 0.00647 ( 48) link_NAG-ASN : angle 3.74392 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 180 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.4870 (OUTLIER) cc_final: 0.4443 (p) REVERT: A 52 GLN cc_start: 0.8362 (tm-30) cc_final: 0.7708 (tm-30) REVERT: A 104 TRP cc_start: 0.8522 (m-90) cc_final: 0.8196 (m-90) REVERT: A 132 GLU cc_start: 0.8010 (tt0) cc_final: 0.7612 (mm-30) REVERT: A 346 ARG cc_start: 0.8013 (tpm170) cc_final: 0.7721 (tpm-80) REVERT: A 360 ASN cc_start: 0.8958 (t0) cc_final: 0.8566 (t0) REVERT: A 564 GLN cc_start: 0.8019 (tp40) cc_final: 0.7142 (tp-100) REVERT: A 900 MET cc_start: 0.8876 (mmm) cc_final: 0.8384 (mtt) REVERT: B 29 THR cc_start: 0.4684 (OUTLIER) cc_final: 0.4238 (p) REVERT: B 52 GLN cc_start: 0.8419 (tm-30) cc_final: 0.7887 (tm-30) REVERT: B 192 PHE cc_start: 0.8156 (m-80) cc_final: 0.7877 (m-80) REVERT: B 346 ARG cc_start: 0.7877 (tpm-80) cc_final: 0.7514 (tpm-80) REVERT: B 360 ASN cc_start: 0.8915 (t0) cc_final: 0.8546 (t0) REVERT: B 376 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8120 (p) REVERT: B 547 THR cc_start: 0.8966 (m) cc_final: 0.8536 (p) REVERT: B 564 GLN cc_start: 0.8157 (tp40) cc_final: 0.7036 (tp-100) REVERT: B 731 MET cc_start: 0.9534 (OUTLIER) cc_final: 0.8848 (ptm) REVERT: C 29 THR cc_start: 0.5086 (OUTLIER) cc_final: 0.4694 (p) REVERT: C 52 GLN cc_start: 0.8434 (tm-30) cc_final: 0.7891 (tm-30) REVERT: C 335 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8164 (tt) REVERT: C 346 ARG cc_start: 0.7825 (tpm-80) cc_final: 0.7527 (tpm-80) REVERT: C 360 ASN cc_start: 0.9065 (t0) cc_final: 0.8733 (t0) REVERT: C 546 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7600 (pp) REVERT: C 564 GLN cc_start: 0.8101 (tp40) cc_final: 0.7129 (tp-100) REVERT: C 646 ARG cc_start: 0.8594 (tmt170) cc_final: 0.8005 (tpt-90) REVERT: C 731 MET cc_start: 0.9501 (ptt) cc_final: 0.9214 (ptm) REVERT: C 900 MET cc_start: 0.8997 (mmm) cc_final: 0.8632 (mtt) outliers start: 65 outliers final: 35 residues processed: 230 average time/residue: 0.5554 time to fit residues: 151.0678 Evaluate side-chains 218 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 254 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 93 optimal weight: 0.0040 chunk 253 optimal weight: 9.9990 chunk 288 optimal weight: 0.6980 chunk 188 optimal weight: 1.9990 chunk 218 optimal weight: 9.9990 chunk 242 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.150804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.100865 restraints weight = 40989.116| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.81 r_work: 0.3111 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25332 Z= 0.110 Angle : 0.606 14.136 34572 Z= 0.294 Chirality : 0.047 0.310 4080 Planarity : 0.004 0.053 4356 Dihedral : 5.687 57.461 4580 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.95 % Allowed : 12.44 % Favored : 85.61 % 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: 0.23 (0.15), residues: 3003 helix: 1.54 (0.21), residues: 672 sheet: 0.55 (0.18), residues: 756 loop : -0.65 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 102 TYR 0.017 0.001 TYR B 489 PHE 0.020 0.001 PHE C 65 TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00245 (25227) covalent geometry : angle 0.55427 (34299) SS BOND : bond 0.00468 ( 42) SS BOND : angle 1.69752 ( 84) hydrogen bonds : bond 0.03352 ( 961) hydrogen bonds : angle 5.13240 ( 2784) link_BETA1-4 : bond 0.00354 ( 15) link_BETA1-4 : angle 0.90395 ( 45) link_NAG-ASN : bond 0.00677 ( 48) link_NAG-ASN : angle 3.62693 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 189 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.4941 (OUTLIER) cc_final: 0.4519 (p) REVERT: A 52 GLN cc_start: 0.8338 (tm-30) cc_final: 0.7661 (tp40) REVERT: A 53 ASP cc_start: 0.6819 (p0) cc_final: 0.6586 (p0) REVERT: A 104 TRP cc_start: 0.8500 (m-90) cc_final: 0.8069 (m-90) REVERT: A 132 GLU cc_start: 0.8019 (tt0) cc_final: 0.7639 (mm-30) REVERT: A 346 ARG cc_start: 0.8029 (tpm170) cc_final: 0.7753 (tpm-80) REVERT: A 360 ASN cc_start: 0.9064 (t0) cc_final: 0.8677 (t0) REVERT: A 517 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6153 (tm) REVERT: A 564 GLN cc_start: 0.8007 (tp40) cc_final: 0.7117 (tp-100) REVERT: A 900 MET cc_start: 0.8680 (mmm) cc_final: 0.8246 (mtt) REVERT: B 29 THR cc_start: 0.4579 (OUTLIER) cc_final: 0.4138 (p) REVERT: B 52 GLN cc_start: 0.8383 (tm-30) cc_final: 0.7806 (tm-30) REVERT: B 104 TRP cc_start: 0.8109 (m-90) cc_final: 0.7582 (m-90) REVERT: B 192 PHE cc_start: 0.8123 (m-80) cc_final: 0.7707 (m-80) REVERT: B 346 ARG cc_start: 0.7840 (tpm-80) cc_final: 0.7445 (tpm-80) REVERT: B 360 ASN cc_start: 0.8941 (t0) cc_final: 0.8574 (t0) REVERT: B 376 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.8094 (p) REVERT: B 547 THR cc_start: 0.8916 (m) cc_final: 0.8537 (p) REVERT: B 564 GLN cc_start: 0.8087 (tp40) cc_final: 0.7003 (tp-100) REVERT: B 731 MET cc_start: 0.9531 (OUTLIER) cc_final: 0.8828 (ptm) REVERT: B 780 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8179 (mp0) REVERT: C 29 THR cc_start: 0.5153 (OUTLIER) cc_final: 0.4734 (p) REVERT: C 52 GLN cc_start: 0.8401 (tm-30) cc_final: 0.7874 (tm-30) REVERT: C 335 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8101 (tt) REVERT: C 346 ARG cc_start: 0.7794 (tpm-80) cc_final: 0.7482 (tpm-80) REVERT: C 360 ASN cc_start: 0.9051 (t0) cc_final: 0.8743 (t0) REVERT: C 546 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7567 (pp) REVERT: C 547 THR cc_start: 0.8828 (m) cc_final: 0.8520 (p) REVERT: C 564 GLN cc_start: 0.8018 (tp40) cc_final: 0.7112 (tp-100) REVERT: C 646 ARG cc_start: 0.8490 (tmt170) cc_final: 0.7881 (tpt-90) REVERT: C 731 MET cc_start: 0.9485 (ptt) cc_final: 0.9201 (ptm) REVERT: C 900 MET cc_start: 0.8924 (mmm) cc_final: 0.8512 (mtt) outliers start: 52 outliers final: 34 residues processed: 226 average time/residue: 0.5857 time to fit residues: 155.6546 Evaluate side-chains 220 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 130 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 111 optimal weight: 20.0000 chunk 171 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 234 optimal weight: 2.9990 chunk 282 optimal weight: 5.9990 chunk 176 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 219 optimal weight: 10.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.149180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.097761 restraints weight = 41099.309| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.85 r_work: 0.3062 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25332 Z= 0.178 Angle : 0.639 13.989 34572 Z= 0.313 Chirality : 0.048 0.307 4080 Planarity : 0.004 0.053 4356 Dihedral : 5.708 57.953 4580 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.88 % Allowed : 13.30 % Favored : 84.82 % 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: 0.16 (0.15), residues: 3003 helix: 1.42 (0.21), residues: 672 sheet: 0.57 (0.18), residues: 741 loop : -0.68 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 237 TYR 0.018 0.001 TYR C 369 PHE 0.036 0.002 PHE B 456 TRP 0.039 0.002 TRP C 104 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00414 (25227) covalent geometry : angle 0.58725 (34299) SS BOND : bond 0.00425 ( 42) SS BOND : angle 1.95623 ( 84) hydrogen bonds : bond 0.03729 ( 961) hydrogen bonds : angle 5.18675 ( 2784) link_BETA1-4 : bond 0.00350 ( 15) link_BETA1-4 : angle 0.92828 ( 45) link_NAG-ASN : bond 0.00648 ( 48) link_NAG-ASN : angle 3.64321 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 179 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.4921 (OUTLIER) cc_final: 0.4502 (p) REVERT: A 52 GLN cc_start: 0.8359 (tm-30) cc_final: 0.7653 (tp40) REVERT: A 53 ASP cc_start: 0.6908 (p0) cc_final: 0.6643 (p0) REVERT: A 104 TRP cc_start: 0.8495 (m-90) cc_final: 0.8180 (m-90) REVERT: A 132 GLU cc_start: 0.7985 (tt0) cc_final: 0.7623 (mm-30) REVERT: A 346 ARG cc_start: 0.8033 (tpm170) cc_final: 0.7754 (tpm-80) REVERT: A 360 ASN cc_start: 0.9073 (t0) cc_final: 0.8718 (t0) REVERT: A 517 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6239 (tm) REVERT: A 564 GLN cc_start: 0.8041 (tp40) cc_final: 0.7113 (tp-100) REVERT: A 900 MET cc_start: 0.8847 (mmm) cc_final: 0.8422 (mtt) REVERT: A 1092 GLU cc_start: 0.8219 (pm20) cc_final: 0.7947 (pp20) REVERT: B 29 THR cc_start: 0.4634 (OUTLIER) cc_final: 0.4210 (p) REVERT: B 52 GLN cc_start: 0.8404 (tm-30) cc_final: 0.7842 (tm-30) REVERT: B 104 TRP cc_start: 0.8262 (m-90) cc_final: 0.7882 (m-90) REVERT: B 192 PHE cc_start: 0.8203 (m-80) cc_final: 0.7788 (m-80) REVERT: B 346 ARG cc_start: 0.7887 (tpm-80) cc_final: 0.7486 (tpm-80) REVERT: B 360 ASN cc_start: 0.8944 (t0) cc_final: 0.8589 (t0) REVERT: B 376 THR cc_start: 0.8455 (OUTLIER) cc_final: 0.8083 (p) REVERT: B 547 THR cc_start: 0.8946 (m) cc_final: 0.8561 (p) REVERT: B 556 ASN cc_start: 0.8547 (p0) cc_final: 0.8309 (m-40) REVERT: B 564 GLN cc_start: 0.8096 (tp40) cc_final: 0.7065 (tp-100) REVERT: B 731 MET cc_start: 0.9534 (OUTLIER) cc_final: 0.8860 (ptm) REVERT: B 780 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8145 (mp0) REVERT: C 29 THR cc_start: 0.5191 (OUTLIER) cc_final: 0.4766 (p) REVERT: C 52 GLN cc_start: 0.8439 (tm-30) cc_final: 0.7918 (tm-30) REVERT: C 335 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8071 (tt) REVERT: C 346 ARG cc_start: 0.7804 (tpm-80) cc_final: 0.7494 (tpm-80) REVERT: C 360 ASN cc_start: 0.9064 (t0) cc_final: 0.8754 (t0) REVERT: C 546 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7637 (pp) REVERT: C 564 GLN cc_start: 0.8046 (tp40) cc_final: 0.7107 (tp-100) REVERT: C 646 ARG cc_start: 0.8511 (tmt170) cc_final: 0.7910 (tpt-90) REVERT: C 731 MET cc_start: 0.9502 (ptt) cc_final: 0.9225 (ptm) REVERT: C 900 MET cc_start: 0.8982 (mmm) cc_final: 0.8625 (mtt) outliers start: 50 outliers final: 35 residues processed: 215 average time/residue: 0.5286 time to fit residues: 134.4354 Evaluate side-chains 216 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 173 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 92 optimal weight: 0.0770 chunk 164 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 246 optimal weight: 0.7980 chunk 288 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 242 optimal weight: 7.9990 chunk 284 optimal weight: 0.6980 chunk 210 optimal weight: 6.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 317 ASN B 394 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 957 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.150716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.100792 restraints weight = 40792.421| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.79 r_work: 0.3122 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25332 Z= 0.112 Angle : 0.607 13.896 34572 Z= 0.293 Chirality : 0.047 0.310 4080 Planarity : 0.004 0.054 4356 Dihedral : 5.521 57.338 4580 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.84 % Allowed : 13.42 % Favored : 84.74 % 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: 3003 helix: 1.53 (0.21), residues: 672 sheet: 0.59 (0.18), residues: 756 loop : -0.64 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 237 TYR 0.019 0.001 TYR B 489 PHE 0.022 0.001 PHE C 65 TRP 0.034 0.001 TRP C 104 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00250 (25227) covalent geometry : angle 0.55692 (34299) SS BOND : bond 0.00415 ( 42) SS BOND : angle 1.64672 ( 84) hydrogen bonds : bond 0.03354 ( 961) hydrogen bonds : angle 5.09000 ( 2784) link_BETA1-4 : bond 0.00370 ( 15) link_BETA1-4 : angle 0.91525 ( 45) link_NAG-ASN : bond 0.00683 ( 48) link_NAG-ASN : angle 3.55150 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8690.27 seconds wall clock time: 148 minutes 48.35 seconds (8928.35 seconds total)