Starting phenix.real_space_refine on Mon Jul 6 10:09:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wrh_32726/07_2026/7wrh_32726.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrh_32726/07_2026/7wrh_32726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wrh_32726/07_2026/7wrh_32726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrh_32726/07_2026/7wrh_32726.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wrh_32726/07_2026/7wrh_32726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrh_32726/07_2026/7wrh_32726.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wrh_32726/07_2026/7wrh_32726.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wrh_32726/07_2026/7wrh_32726.cif" } resolution = 2.66 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= 0.087 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4695 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 143 5.16 5 C 19629 2.51 5 N 5043 2.21 5 O 5955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30771 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8327 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 59, 'TRANS': 1001} Chain breaks: 7 Chain: "B" Number of atoms: 8327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8327 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 59, 'TRANS': 1001} Chain breaks: 7 Chain: "C" Number of atoms: 8327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8327 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 59, 'TRANS': 1001} Chain breaks: 7 Chain: "D" Number of atoms: 4851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4851 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 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 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 chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.96, per 1000 atoms: 0.23 Number of scatterers: 30771 At special positions: 0 Unit cell: (144.1, 150.7, 248.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 143 16.00 O 5955 8.00 N 5043 7.00 C 19629 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 616 " " NAG B1301 " - " ASN B 17 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 122 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 234 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 331 " " NAG B1308 " - " ASN B 343 " " NAG B1309 " - " ASN B 616 " " NAG C1301 " - " ASN C 17 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 234 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 616 " " NAG E 1 " - " ASN A 122 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 282 " " NAG H 1 " - " ASN A 331 " " NAG I 1 " - " ASN A 709 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 709 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1074 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 282 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C1074 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " Time building additional restraints: 3.03 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" NE2 HIS D 378 " pdb="ZN ZN D 701 " - pdb=" NE2 HIS D 374 " 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7116 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 47 sheets defined 30.1% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.522A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.524A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (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 758 through 783 removed outlier: 3.728A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.664A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.018A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.518A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 993 " --> pdb=" O ALA A 989 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.932A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 637 through 640 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 removed outlier: 3.505A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 753 " --> pdb=" O CYS B 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 746 through 753' Processing helix chain 'B' and resid 754 through 757 removed outlier: 4.150A pdb=" N GLY B 757 " --> pdb=" O LEU B 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 754 through 757' Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.788A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.544A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.511A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.941A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.887A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.536A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.254A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.911A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.660A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.651A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.807A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 637 through 640 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.696A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.569A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.196A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.519A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.967A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'D' and resid 20 through 53 removed outlier: 4.262A pdb=" N ASP D 38 " --> pdb=" O GLN D 34 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 80 removed outlier: 4.064A pdb=" N SER D 63 " --> pdb=" O ALA D 59 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA D 65 " --> pdb=" O LYS D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 100 Processing helix chain 'D' and resid 103 through 108 removed outlier: 4.111A pdb=" N ALA D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 145 through 154 removed outlier: 4.182A pdb=" N ASP D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 172 removed outlier: 3.718A pdb=" N VAL D 172 " --> pdb=" O TRP D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 193 removed outlier: 4.128A pdb=" N LEU D 179 " --> pdb=" O GLN D 175 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 232 removed outlier: 3.594A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N THR D 229 " --> pdb=" O ASP D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 250 removed outlier: 4.096A pdb=" N ASP D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 297 removed outlier: 4.087A pdb=" N MET D 297 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 316 Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 365 through 384 Processing helix chain 'D' and resid 399 through 413 removed outlier: 4.293A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 420 Processing helix chain 'D' and resid 431 through 447 removed outlier: 4.217A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE D 446 " --> pdb=" O GLN D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 472 through 474 No H-bonds generated for 'chain 'D' and resid 472 through 474' Processing helix chain 'D' and resid 475 through 484 removed outlier: 4.090A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET D 480 " --> pdb=" O LYS D 476 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS D 481 " --> pdb=" O TRP D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 removed outlier: 3.821A pdb=" N ASN D 508 " --> pdb=" O PHE D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 531 removed outlier: 3.998A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN D 526 " --> pdb=" O GLN D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.941A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 558 removed outlier: 3.605A pdb=" N LEU D 555 " --> pdb=" O GLY D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 583 through 588 Processing helix chain 'D' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 7.942A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.252A 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: 4.107A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.898A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.347A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 326 removed outlier: 5.396A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.868A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.146A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.787A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.817A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.817A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.508A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 31 removed outlier: 8.182A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.200A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.400A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.937A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.617A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 133 through 142 removed outlier: 9.151A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 11.377A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.688A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.373A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.414A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.573A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.131A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.603A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.603A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 31 removed outlier: 8.334A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.892A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.872A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 140 through 141 removed outlier: 3.646A pdb=" N PHE C 140 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.341A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.075A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.504A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.767A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.127A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.665A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.665A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.693A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF1, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.992A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'D' and resid 347 through 350 1288 hydrogen bonds defined for protein. 3546 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.64 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 4956 1.31 - 1.45: 9138 1.45 - 1.59: 17217 1.59 - 1.73: 0 1.73 - 1.87: 191 Bond restraints: 31502 Sorted by residual: bond pdb=" C ASN C 717 " pdb=" O ASN C 717 " ideal model delta sigma weight residual 1.234 1.171 0.063 1.20e-02 6.94e+03 2.80e+01 bond pdb=" C PRO C 715 " pdb=" O PRO C 715 " ideal model delta sigma weight residual 1.233 1.171 0.062 1.23e-02 6.61e+03 2.58e+01 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.498 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C THR C 716 " pdb=" O THR C 716 " ideal model delta sigma weight residual 1.236 1.177 0.059 1.34e-02 5.57e+03 1.94e+01 bond pdb=" CA SER C 967 " pdb=" CB SER C 967 " ideal model delta sigma weight residual 1.532 1.469 0.062 1.74e-02 3.30e+03 1.29e+01 ... (remaining 31497 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 42366 2.64 - 5.28: 453 5.28 - 7.91: 35 7.91 - 10.55: 2 10.55 - 13.19: 1 Bond angle restraints: 42857 Sorted by residual: angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 127.59 -13.19 2.30e+00 1.89e-01 3.29e+01 angle pdb=" N CYS C 525 " pdb=" CA CYS C 525 " pdb=" C CYS C 525 " ideal model delta sigma weight residual 107.88 115.00 -7.12 1.41e+00 5.03e-01 2.55e+01 angle pdb=" N LEU C 560 " pdb=" CA LEU C 560 " pdb=" C LEU C 560 " ideal model delta sigma weight residual 110.36 103.66 6.70 1.34e+00 5.57e-01 2.50e+01 angle pdb=" O LYS C 964 " pdb=" C LYS C 964 " pdb=" N GLN C 965 " ideal model delta sigma weight residual 122.41 114.44 7.97 1.60e+00 3.91e-01 2.48e+01 angle pdb=" N VAL A 622 " pdb=" CA VAL A 622 " pdb=" C VAL A 622 " ideal model delta sigma weight residual 111.62 107.81 3.81 7.90e-01 1.60e+00 2.33e+01 ... (remaining 42852 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 16511 17.92 - 35.84: 1426 35.84 - 53.76: 208 53.76 - 71.68: 65 71.68 - 89.60: 30 Dihedral angle restraints: 18240 sinusoidal: 7201 harmonic: 11039 Sorted by residual: dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual -86.00 -147.61 61.61 1 1.00e+01 1.00e-02 5.04e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 32.84 60.16 1 1.00e+01 1.00e-02 4.82e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -28.18 -57.82 1 1.00e+01 1.00e-02 4.49e+01 ... (remaining 18237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 4789 0.109 - 0.217: 185 0.217 - 0.326: 5 0.326 - 0.434: 1 0.434 - 0.543: 4 Chirality restraints: 4984 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.77e+01 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.37e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.58e+00 ... (remaining 4981 not shown) Planarity restraints: 5493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 506 " -0.080 5.00e-02 4.00e+02 1.19e-01 2.25e+01 pdb=" N PRO C 507 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO C 507 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO C 507 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A1142 " -0.071 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO A1143 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO A1143 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A1143 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 525 " -0.021 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C CYS A 525 " 0.070 2.00e-02 2.50e+03 pdb=" O CYS A 525 " -0.026 2.00e-02 2.50e+03 pdb=" N GLY A 526 " -0.024 2.00e-02 2.50e+03 ... (remaining 5490 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 372 2.66 - 3.22: 27236 3.22 - 3.78: 44662 3.78 - 4.34: 62819 4.34 - 4.90: 103962 Nonbonded interactions: 239051 Sorted by model distance: nonbonded pdb=" OE2 GLU D 402 " pdb="ZN ZN D 701 " model vdw 2.100 2.230 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.198 3.040 nonbonded pdb=" OG SER C 884 " pdb=" OG1 THR C 887 " model vdw 2.208 3.040 nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.228 3.040 nonbonded pdb=" OD1 ASN C 188 " pdb=" NE2 HIS C 207 " model vdw 2.229 3.120 ... (remaining 239046 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 15 through 1306) selection = (chain 'C' and resid 15 through 1306) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.130 Set scattering table: 0.130 Process input model: 34.440 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.110 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:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 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 : 0.005 0.202 31612 Z= 0.228 Angle : 0.710 13.191 43140 Z= 0.378 Chirality : 0.051 0.543 4984 Planarity : 0.005 0.119 5448 Dihedral : 13.884 89.599 11001 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.71 % Favored : 94.15 % Rotamer: Outliers : 0.12 % Allowed : 0.39 % Favored : 99.49 % 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: -0.49 (0.13), residues: 3728 helix: 1.03 (0.17), residues: 966 sheet: 1.00 (0.20), residues: 637 loop : -1.47 (0.12), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 328 TYR 0.027 0.001 TYR C 674 PHE 0.023 0.001 PHE C 906 TRP 0.020 0.001 TRP C 633 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.22 (31502) covalent geometry : angle 0.68019 / 0.37 (42857) SS BOND : bond 0.00498 / 0.32 ( 41) SS BOND : angle 1.72809 / 1.16 ( 82) hydrogen bonds : bond 0.14788 / 9.63 ( 1252) hydrogen bonds : angle 6.47609 / 4.42 ( 3546) metal coordination : bond 0.20176 / 10.12 ( 2) link_BETA1-4 : bond 0.00835 / 0.57 ( 22) link_BETA1-4 : angle 2.49247 / 1.48 ( 66) link_NAG-ASN : bond 0.00622 / 0.46 ( 45) link_NAG-ASN : angle 3.05212 / 2.37 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 277 time to evaluate : 1.423 Fit side-chains revert: symmetry clash REVERT: C 921 LYS cc_start: 0.7788 (mmpt) cc_final: 0.7583 (mppt) REVERT: D 323 MET cc_start: 0.1690 (mmp) cc_final: 0.1074 (mmp) REVERT: D 383 MET cc_start: 0.4960 (ppp) cc_final: 0.3972 (ppp) outliers start: 4 outliers final: 1 residues processed: 279 average time/residue: 0.6397 time to fit residues: 213.7203 Evaluate side-chains 207 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 716 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 3.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN B 81 ASN B 125 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 901 GLN B 954 HIS C 460 ASN C 675 GLN C 690 GLN C 804 GLN D 239 HIS D 397 ASN D 493 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.210857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.170772 restraints weight = 36585.271| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 1.95 r_work: 0.3382 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31612 Z= 0.187 Angle : 0.680 12.453 43140 Z= 0.344 Chirality : 0.050 0.523 4984 Planarity : 0.005 0.077 5448 Dihedral : 4.671 28.712 4061 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.12 % Favored : 94.80 % Rotamer: Outliers : 1.45 % Allowed : 6.09 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.13), residues: 3728 helix: 1.27 (0.17), residues: 1001 sheet: 1.02 (0.20), residues: 653 loop : -1.56 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 403 TYR 0.024 0.002 TYR A 265 PHE 0.019 0.002 PHE B 168 TRP 0.022 0.001 TRP C 633 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (31502) covalent geometry : angle 0.65486 / 0.34 (42857) SS BOND : bond 0.00492 / 0.32 ( 41) SS BOND : angle 1.87737 / 1.31 ( 82) hydrogen bonds : bond 0.06990 / 4.62 ( 1252) hydrogen bonds : angle 5.39424 / 3.68 ( 3546) metal coordination : bond 0.01425 / 0.72 ( 2) link_BETA1-4 : bond 0.00840 / 0.59 ( 22) link_BETA1-4 : angle 2.05076 / 1.20 ( 66) link_NAG-ASN : bond 0.00618 / 0.46 ( 45) link_NAG-ASN : angle 2.71223 / 2.12 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7697 (tm-30) REVERT: A 226 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7029 (pt) REVERT: B 661 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8487 (tt0) REVERT: B 1010 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.7966 (mp10) REVERT: C 921 LYS cc_start: 0.8799 (mmpt) cc_final: 0.8361 (mppt) REVERT: D 249 MET cc_start: 0.1571 (mmm) cc_final: -0.0149 (ptt) REVERT: D 383 MET cc_start: 0.4775 (ppp) cc_final: 0.3885 (ppp) REVERT: D 474 MET cc_start: -0.0969 (mmm) cc_final: -0.1621 (ttt) outliers start: 48 outliers final: 21 residues processed: 241 average time/residue: 0.6585 time to fit residues: 189.9421 Evaluate side-chains 225 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain D residue 347 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 232 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 178 optimal weight: 8.9990 chunk 195 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 315 optimal weight: 0.6980 chunk 329 optimal weight: 8.9990 chunk 44 optimal weight: 20.0000 chunk 181 optimal weight: 0.6980 chunk 233 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN B 81 ASN B 125 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN C 460 ASN D 397 ASN D 493 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.212160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.160686 restraints weight = 38090.682| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.53 r_work: 0.3239 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 31612 Z= 0.203 Angle : 0.693 9.737 43140 Z= 0.351 Chirality : 0.050 0.532 4984 Planarity : 0.005 0.060 5448 Dihedral : 4.756 29.670 4061 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.31 % Favored : 94.61 % Rotamer: Outliers : 2.08 % Allowed : 8.75 % Favored : 89.17 % 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: -0.39 (0.13), residues: 3728 helix: 1.34 (0.17), residues: 985 sheet: 1.05 (0.20), residues: 655 loop : -1.59 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 403 TYR 0.026 0.002 TYR A 265 PHE 0.020 0.002 PHE C 898 TRP 0.023 0.002 TRP C 633 HIS 0.008 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.20 (31502) covalent geometry : angle 0.66770 / 0.34 (42857) SS BOND : bond 0.00462 / 0.30 ( 41) SS BOND : angle 2.03529 / 1.44 ( 82) hydrogen bonds : bond 0.07038 / 4.63 ( 1252) hydrogen bonds : angle 5.29638 / 3.61 ( 3546) metal coordination : bond 0.00084 / 0.04 ( 2) link_BETA1-4 : bond 0.00861 / 0.59 ( 22) link_BETA1-4 : angle 2.10852 / 1.24 ( 66) link_NAG-ASN : bond 0.00492 / 0.35 ( 45) link_NAG-ASN : angle 2.71142 / 2.12 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 209 time to evaluate : 1.188 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7461 (tm-30) REVERT: A 100 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7498 (mp) REVERT: A 226 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.6989 (pt) REVERT: B 661 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8200 (tt0) REVERT: B 820 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8019 (m-30) REVERT: C 129 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.6504 (tttp) REVERT: C 634 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.6632 (mtt-85) REVERT: C 779 GLN cc_start: 0.8746 (tp40) cc_final: 0.8515 (tp40) REVERT: D 249 MET cc_start: 0.1667 (mmm) cc_final: 0.0290 (ptt) REVERT: D 360 MET cc_start: 0.2453 (ppp) cc_final: 0.2178 (tmt) REVERT: D 383 MET cc_start: 0.4719 (ppp) cc_final: 0.4224 (ppp) REVERT: D 474 MET cc_start: -0.0192 (mmm) cc_final: -0.0963 (ttt) outliers start: 69 outliers final: 31 residues processed: 250 average time/residue: 0.5467 time to fit residues: 166.4200 Evaluate side-chains 235 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 347 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 312 optimal weight: 0.8980 chunk 208 optimal weight: 1.9990 chunk 232 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 202 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 328 optimal weight: 30.0000 chunk 165 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 125 ASN B 207 HIS C 394 ASN ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN D 437 ASN D 493 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.211948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.174633 restraints weight = 36494.592| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 1.85 r_work: 0.3535 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31612 Z= 0.124 Angle : 0.600 10.383 43140 Z= 0.302 Chirality : 0.046 0.450 4984 Planarity : 0.004 0.054 5448 Dihedral : 4.424 27.691 4061 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.02 % Favored : 94.90 % Rotamer: Outliers : 1.90 % Allowed : 10.55 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.14), residues: 3728 helix: 1.65 (0.17), residues: 985 sheet: 1.16 (0.20), residues: 662 loop : -1.48 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 403 TYR 0.024 0.001 TYR C 453 PHE 0.014 0.001 PHE C 981 TRP 0.023 0.001 TRP C 633 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (31502) covalent geometry : angle 0.57780 / 0.30 (42857) SS BOND : bond 0.00374 / 0.24 ( 41) SS BOND : angle 1.56316 / 1.08 ( 82) hydrogen bonds : bond 0.05402 / 3.56 ( 1252) hydrogen bonds : angle 5.01487 / 3.43 ( 3546) metal coordination : bond 0.00016 / 0.01 ( 2) link_BETA1-4 : bond 0.00792 / 0.55 ( 22) link_BETA1-4 : angle 2.01279 / 1.17 ( 66) link_NAG-ASN : bond 0.00401 / 0.27 ( 45) link_NAG-ASN : angle 2.39012 / 1.75 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 223 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7654 (tm-30) REVERT: A 100 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7554 (mp) REVERT: A 226 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7012 (pt) REVERT: A 365 TYR cc_start: 0.7442 (OUTLIER) cc_final: 0.6766 (m-80) REVERT: B 236 THR cc_start: 0.8393 (m) cc_final: 0.8113 (m) REVERT: B 239 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: B 820 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8294 (m-30) REVERT: C 41 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6445 (mmtp) REVERT: C 752 LEU cc_start: 0.7788 (tt) cc_final: 0.7531 (tp) REVERT: C 779 GLN cc_start: 0.8826 (tp40) cc_final: 0.8606 (tp40) REVERT: C 1002 GLN cc_start: 0.8702 (tp40) cc_final: 0.8456 (tp40) REVERT: D 249 MET cc_start: 0.1371 (mmm) cc_final: 0.0073 (ptt) REVERT: D 383 MET cc_start: 0.5210 (ppp) cc_final: 0.4267 (ppp) outliers start: 63 outliers final: 22 residues processed: 262 average time/residue: 0.6097 time to fit residues: 193.4725 Evaluate side-chains 237 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 347 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 66 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 342 optimal weight: 20.0000 chunk 216 optimal weight: 0.9990 chunk 270 optimal weight: 6.9990 chunk 302 optimal weight: 2.9990 chunk 20 optimal weight: 0.0770 chunk 81 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 352 optimal weight: 30.0000 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 GLN ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS D 397 ASN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.213078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.162328 restraints weight = 38544.462| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.56 r_work: 0.3278 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.916 31612 Z= 0.261 Angle : 0.683 9.940 43140 Z= 0.344 Chirality : 0.049 0.507 4984 Planarity : 0.005 0.054 5448 Dihedral : 4.639 28.867 4060 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.66 % Favored : 94.26 % Rotamer: Outliers : 2.32 % Allowed : 11.85 % Favored : 85.83 % 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: -0.30 (0.13), residues: 3728 helix: 1.51 (0.17), residues: 982 sheet: 1.05 (0.19), residues: 656 loop : -1.56 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 357 TYR 0.026 0.002 TYR C 453 PHE 0.019 0.002 PHE A 898 TRP 0.024 0.002 TRP B 633 HIS 0.008 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.20 (31502) covalent geometry : angle 0.65788 / 0.34 (42857) SS BOND : bond 0.00460 / 0.30 ( 41) SS BOND : angle 2.03201 / 1.42 ( 82) hydrogen bonds : bond 0.06844 / 4.51 ( 1252) hydrogen bonds : angle 5.17966 / 3.53 ( 3546) metal coordination : bond 0.64806 / 34.11 ( 2) link_BETA1-4 : bond 0.00788 / 0.54 ( 22) link_BETA1-4 : angle 2.07784 / 1.23 ( 66) link_NAG-ASN : bond 0.00466 / 0.33 ( 45) link_NAG-ASN : angle 2.61497 / 2.02 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 209 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7497 (tm-30) REVERT: A 100 ILE cc_start: 0.7679 (OUTLIER) cc_final: 0.7456 (mp) REVERT: A 153 MET cc_start: 0.2962 (tpt) cc_final: 0.1179 (ttp) REVERT: A 226 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.6952 (pt) REVERT: B 236 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7820 (m) REVERT: B 239 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7950 (tt0) REVERT: B 661 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8244 (tt0) REVERT: B 780 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7505 (pp20) REVERT: B 820 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8058 (m-30) REVERT: C 41 LYS cc_start: 0.7277 (OUTLIER) cc_final: 0.6286 (mmtp) REVERT: C 409 GLN cc_start: 0.8456 (mt0) cc_final: 0.8235 (mt0) REVERT: C 752 LEU cc_start: 0.8225 (tt) cc_final: 0.7951 (tp) REVERT: C 779 GLN cc_start: 0.8731 (tp40) cc_final: 0.8508 (tp40) REVERT: C 1002 GLN cc_start: 0.8591 (tp40) cc_final: 0.8259 (tp40) REVERT: D 62 MET cc_start: 0.3611 (mtt) cc_final: 0.3388 (mtt) REVERT: D 249 MET cc_start: 0.1552 (mmm) cc_final: 0.0223 (ptt) REVERT: D 270 MET cc_start: 0.2406 (mtp) cc_final: 0.0852 (tpt) REVERT: D 366 MET cc_start: 0.3424 (mtm) cc_final: 0.3156 (mtm) REVERT: D 383 MET cc_start: 0.4825 (ppp) cc_final: 0.4289 (ppp) REVERT: D 474 MET cc_start: -0.0775 (mmm) cc_final: -0.1736 (ttt) outliers start: 77 outliers final: 39 residues processed: 260 average time/residue: 0.5509 time to fit residues: 173.8509 Evaluate side-chains 243 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 195 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 347 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 78 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 chunk 191 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 368 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 224 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 284 optimal weight: 1.9990 chunk 339 optimal weight: 30.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 422 ASN C 81 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN D 374 HIS D 397 ASN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.213497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.162479 restraints weight = 38485.008| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 2.40 r_work: 0.3314 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.906 31612 Z= 0.236 Angle : 0.656 14.305 43140 Z= 0.328 Chirality : 0.049 0.788 4984 Planarity : 0.005 0.054 5448 Dihedral : 4.571 28.689 4060 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.28 % Favored : 94.64 % Rotamer: Outliers : 2.47 % Allowed : 12.24 % Favored : 85.28 % 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 (0.13), residues: 3728 helix: 1.55 (0.17), residues: 988 sheet: 1.05 (0.20), residues: 645 loop : -1.51 (0.13), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 158 TYR 0.026 0.001 TYR C 453 PHE 0.017 0.002 PHE C 898 TRP 0.024 0.001 TRP B 633 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.16 (31502) covalent geometry : angle 0.62849 / 0.32 (42857) SS BOND : bond 0.00415 / 0.26 ( 41) SS BOND : angle 1.90414 / 1.32 ( 82) hydrogen bonds : bond 0.06236 / 4.11 ( 1252) hydrogen bonds : angle 5.09376 / 3.47 ( 3546) metal coordination : bond 0.64100 / 33.74 ( 2) link_BETA1-4 : bond 0.00762 / 0.52 ( 22) link_BETA1-4 : angle 2.08805 / 1.25 ( 66) link_NAG-ASN : bond 0.00462 / 0.33 ( 45) link_NAG-ASN : angle 2.82450 / 2.19 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 205 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7497 (tm-30) REVERT: A 100 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7477 (mp) REVERT: A 226 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.6931 (pt) REVERT: A 365 TYR cc_start: 0.7943 (OUTLIER) cc_final: 0.7368 (m-80) REVERT: A 583 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7411 (pm20) REVERT: B 236 THR cc_start: 0.8344 (m) cc_final: 0.8042 (m) REVERT: B 239 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7906 (tt0) REVERT: B 554 GLU cc_start: 0.7159 (pp20) cc_final: 0.6918 (pm20) REVERT: B 661 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8197 (tt0) REVERT: B 820 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8006 (m-30) REVERT: C 41 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6306 (mmtp) REVERT: C 226 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7356 (pt) REVERT: C 779 GLN cc_start: 0.8672 (tp40) cc_final: 0.8454 (tp40) REVERT: C 1002 GLN cc_start: 0.8560 (tp40) cc_final: 0.8232 (tp40) REVERT: D 165 TRP cc_start: 0.0782 (t60) cc_final: 0.0554 (t60) REVERT: D 249 MET cc_start: 0.1575 (mmm) cc_final: 0.0381 (ptt) REVERT: D 270 MET cc_start: 0.2484 (mtp) cc_final: 0.0939 (tpt) REVERT: D 383 MET cc_start: 0.4819 (ppp) cc_final: 0.4295 (ppp) REVERT: D 474 MET cc_start: -0.0444 (mmm) cc_final: -0.1210 (ttt) outliers start: 82 outliers final: 43 residues processed: 267 average time/residue: 0.5142 time to fit residues: 167.8809 Evaluate side-chains 252 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 199 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 513 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 72 optimal weight: 0.0980 chunk 264 optimal weight: 0.5980 chunk 45 optimal weight: 20.0000 chunk 38 optimal weight: 0.0040 chunk 102 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 chunk 356 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 125 ASN C 394 ASN C 417 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN D 374 HIS D 397 ASN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.215095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.164561 restraints weight = 38724.515| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.38 r_work: 0.3365 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.925 31612 Z= 0.207 Angle : 0.588 10.945 43140 Z= 0.293 Chirality : 0.046 0.549 4984 Planarity : 0.004 0.054 5448 Dihedral : 4.269 26.785 4060 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.91 % Favored : 95.01 % Rotamer: Outliers : 1.96 % Allowed : 13.12 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.14), residues: 3728 helix: 1.82 (0.17), residues: 989 sheet: 1.13 (0.20), residues: 650 loop : -1.42 (0.13), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 357 TYR 0.026 0.001 TYR B 170 PHE 0.012 0.001 PHE B1121 TRP 0.021 0.001 TRP C 633 HIS 0.008 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (31502) covalent geometry : angle 0.56664 / 0.29 (42857) SS BOND : bond 0.00422 / 0.27 ( 41) SS BOND : angle 1.54316 / 1.04 ( 82) hydrogen bonds : bond 0.04822 / 3.17 ( 1252) hydrogen bonds : angle 4.86302 / 3.32 ( 3546) metal coordination : bond 0.65431 / 34.44 ( 2) link_BETA1-4 : bond 0.00760 / 0.53 ( 22) link_BETA1-4 : angle 1.96908 / 1.15 ( 66) link_NAG-ASN : bond 0.00475 / 0.37 ( 45) link_NAG-ASN : angle 2.31921 / 1.66 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 206 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7455 (tm-30) REVERT: A 365 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.7318 (m-80) REVERT: B 236 THR cc_start: 0.8061 (OUTLIER) cc_final: 0.7750 (m) REVERT: B 239 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: B 661 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8066 (tt0) REVERT: C 41 LYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6228 (mmtp) REVERT: C 752 LEU cc_start: 0.7853 (tt) cc_final: 0.7562 (tp) REVERT: C 779 GLN cc_start: 0.8524 (tp40) cc_final: 0.8317 (tp40) REVERT: C 1002 GLN cc_start: 0.8412 (tp40) cc_final: 0.8106 (tp40) REVERT: D 62 MET cc_start: 0.3170 (mtt) cc_final: 0.2923 (mtt) REVERT: D 165 TRP cc_start: 0.0712 (t60) cc_final: 0.0464 (t60) REVERT: D 249 MET cc_start: 0.1587 (mmm) cc_final: 0.0375 (ptt) REVERT: D 270 MET cc_start: 0.2530 (mtp) cc_final: 0.0780 (tpt) REVERT: D 297 MET cc_start: 0.0082 (mtp) cc_final: -0.0353 (mtt) REVERT: D 383 MET cc_start: 0.4782 (ppp) cc_final: 0.4257 (ppp) REVERT: D 474 MET cc_start: -0.0515 (mmm) cc_final: -0.1289 (ttt) REVERT: D 581 VAL cc_start: 0.0528 (OUTLIER) cc_final: 0.0204 (t) outliers start: 65 outliers final: 28 residues processed: 253 average time/residue: 0.5654 time to fit residues: 173.8530 Evaluate side-chains 232 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 581 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 99 optimal weight: 0.0370 chunk 28 optimal weight: 9.9990 chunk 326 optimal weight: 30.0000 chunk 75 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 342 optimal weight: 20.0000 chunk 331 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 236 optimal weight: 1.9990 chunk 124 optimal weight: 0.3980 chunk 287 optimal weight: 1.9990 overall best weight: 1.0864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 544 ASN B 81 ASN B 125 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS D 397 ASN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.214426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.162953 restraints weight = 38832.824| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.49 r_work: 0.3326 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.936 31612 Z= 0.223 Angle : 0.639 17.784 43140 Z= 0.314 Chirality : 0.047 0.511 4984 Planarity : 0.005 0.057 5448 Dihedral : 4.343 27.261 4060 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.26 % Favored : 94.66 % Rotamer: Outliers : 1.93 % Allowed : 13.72 % Favored : 84.35 % 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: -0.06 (0.14), residues: 3728 helix: 1.76 (0.17), residues: 993 sheet: 1.11 (0.19), residues: 659 loop : -1.42 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 518 TYR 0.022 0.001 TYR C1067 PHE 0.014 0.001 PHE C 898 TRP 0.020 0.001 TRP B 633 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (31502) covalent geometry : angle 0.60747 / 0.31 (42857) SS BOND : bond 0.00395 / 0.25 ( 41) SS BOND : angle 1.69821 / 1.16 ( 82) hydrogen bonds : bond 0.05511 / 3.62 ( 1252) hydrogen bonds : angle 4.92662 / 3.36 ( 3546) metal coordination : bond 0.66159 / 34.82 ( 2) link_BETA1-4 : bond 0.00727 / 0.50 ( 22) link_BETA1-4 : angle 2.02241 / 1.21 ( 66) link_NAG-ASN : bond 0.00403 / 0.29 ( 45) link_NAG-ASN : angle 3.12135 / 2.36 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 203 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.8661 (OUTLIER) cc_final: 0.8411 (m) REVERT: A 52 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7685 (tm-30) REVERT: A 226 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.6794 (pt) REVERT: A 365 TYR cc_start: 0.7961 (OUTLIER) cc_final: 0.7367 (m-80) REVERT: A 583 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7510 (pm20) REVERT: B 239 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: B 661 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8361 (tt0) REVERT: B 820 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8228 (m-30) REVERT: C 41 LYS cc_start: 0.7239 (OUTLIER) cc_final: 0.6206 (mmtp) REVERT: C 226 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7321 (pt) REVERT: C 752 LEU cc_start: 0.8009 (tt) cc_final: 0.7606 (tp) REVERT: C 779 GLN cc_start: 0.8841 (tp40) cc_final: 0.8608 (tp40) REVERT: C 964 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8250 (mtmp) REVERT: C 1002 GLN cc_start: 0.8743 (tp40) cc_final: 0.8422 (tp40) REVERT: D 62 MET cc_start: 0.3060 (mtt) cc_final: 0.2772 (mtt) REVERT: D 165 TRP cc_start: 0.0559 (t60) cc_final: 0.0236 (t60) REVERT: D 249 MET cc_start: 0.1669 (mmm) cc_final: 0.0552 (ptt) REVERT: D 270 MET cc_start: 0.2285 (mtp) cc_final: 0.0664 (tpt) REVERT: D 383 MET cc_start: 0.4376 (ppp) cc_final: 0.4096 (ppp) REVERT: D 474 MET cc_start: -0.0215 (mmm) cc_final: -0.0922 (ttt) REVERT: D 581 VAL cc_start: 0.0562 (OUTLIER) cc_final: 0.0184 (t) outliers start: 64 outliers final: 35 residues processed: 254 average time/residue: 0.5821 time to fit residues: 179.7460 Evaluate side-chains 242 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 195 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 581 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 293 optimal weight: 0.5980 chunk 129 optimal weight: 0.9980 chunk 232 optimal weight: 20.0000 chunk 343 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 262 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 238 optimal weight: 0.0570 chunk 351 optimal weight: 6.9990 overall best weight: 1.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 417 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS D 397 ASN D 493 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.213065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.160550 restraints weight = 38378.854| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.46 r_work: 0.3291 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.890 31612 Z= 0.244 Angle : 0.689 24.151 43140 Z= 0.341 Chirality : 0.049 0.351 4984 Planarity : 0.005 0.053 5448 Dihedral : 4.556 28.744 4060 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.66 % Favored : 94.26 % Rotamer: Outliers : 1.90 % Allowed : 14.02 % Favored : 84.08 % 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: -0.19 (0.14), residues: 3728 helix: 1.62 (0.17), residues: 991 sheet: 1.04 (0.20), residues: 656 loop : -1.48 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 518 TYR 0.030 0.002 TYR C 453 PHE 0.017 0.002 PHE A 898 TRP 0.021 0.001 TRP B 633 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (31502) covalent geometry : angle 0.65219 / 0.33 (42857) SS BOND : bond 0.00442 / 0.29 ( 41) SS BOND : angle 1.92360 / 1.35 ( 82) hydrogen bonds : bond 0.06470 / 4.25 ( 1252) hydrogen bonds : angle 5.08935 / 3.47 ( 3546) metal coordination : bond 0.62904 / 33.11 ( 2) link_BETA1-4 : bond 0.00736 / 0.50 ( 22) link_BETA1-4 : angle 2.12825 / 1.29 ( 66) link_NAG-ASN : bond 0.00395 / 0.25 ( 45) link_NAG-ASN : angle 3.51127 / 2.60 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 200 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8269 (m) REVERT: A 52 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7486 (tm-30) REVERT: A 226 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.6743 (pt) REVERT: A 241 LEU cc_start: 0.6067 (OUTLIER) cc_final: 0.5826 (mt) REVERT: A 365 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.7510 (m-80) REVERT: A 583 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7535 (pm20) REVERT: B 239 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: B 661 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8166 (tt0) REVERT: B 820 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.7975 (m-30) REVERT: C 41 LYS cc_start: 0.7285 (OUTLIER) cc_final: 0.6299 (mmtp) REVERT: C 226 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7331 (pt) REVERT: C 462 LYS cc_start: 0.8003 (mtpt) cc_final: 0.7721 (mttm) REVERT: C 752 LEU cc_start: 0.8139 (tt) cc_final: 0.7820 (tp) REVERT: C 1002 GLN cc_start: 0.8558 (tp40) cc_final: 0.8251 (tp40) REVERT: D 62 MET cc_start: 0.3256 (mtt) cc_final: 0.3026 (mtt) REVERT: D 165 TRP cc_start: 0.0666 (t60) cc_final: 0.0446 (t60) REVERT: D 249 MET cc_start: 0.1535 (mmm) cc_final: 0.0368 (ptt) REVERT: D 270 MET cc_start: 0.2463 (mtp) cc_final: 0.0810 (tpt) REVERT: D 297 MET cc_start: -0.0006 (mtp) cc_final: -0.0412 (mtt) REVERT: D 383 MET cc_start: 0.4579 (ppp) cc_final: 0.4126 (ppp) REVERT: D 474 MET cc_start: -0.0392 (mmm) cc_final: -0.1078 (ttt) REVERT: D 581 VAL cc_start: 0.0654 (OUTLIER) cc_final: 0.0297 (t) outliers start: 63 outliers final: 35 residues processed: 252 average time/residue: 0.5891 time to fit residues: 181.0061 Evaluate side-chains 246 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 293 optimal weight: 0.5980 chunk 209 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 246 optimal weight: 6.9990 chunk 330 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 312 optimal weight: 0.9980 chunk 257 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN C 422 ASN ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.213771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.161612 restraints weight = 38330.877| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.44 r_work: 0.3314 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31612 Z= 0.150 Angle : 0.660 20.830 43140 Z= 0.326 Chirality : 0.047 0.310 4984 Planarity : 0.005 0.053 5448 Dihedral : 4.481 27.724 4060 Min Nonbonded Distance : 1.633 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.34 % Favored : 94.58 % Rotamer: Outliers : 1.66 % Allowed : 14.35 % Favored : 83.99 % 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 (0.14), residues: 3728 helix: 1.66 (0.17), residues: 991 sheet: 1.06 (0.19), residues: 669 loop : -1.48 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 518 TYR 0.022 0.001 TYR C1067 PHE 0.018 0.001 PHE C 392 TRP 0.021 0.001 TRP C 633 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (31502) covalent geometry : angle 0.62678 / 0.32 (42857) SS BOND : bond 0.00410 / 0.26 ( 41) SS BOND : angle 1.76054 / 1.22 ( 82) hydrogen bonds : bond 0.05880 / 3.87 ( 1252) hydrogen bonds : angle 5.01822 / 3.42 ( 3546) metal coordination : bond 0.00075 / 0.04 ( 2) link_BETA1-4 : bond 0.00734 / 0.50 ( 22) link_BETA1-4 : angle 2.06277 / 1.23 ( 66) link_NAG-ASN : bond 0.00398 / 0.27 ( 45) link_NAG-ASN : angle 3.24112 / 2.39 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 201 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.8687 (OUTLIER) cc_final: 0.8403 (m) REVERT: A 52 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7697 (tm-30) REVERT: A 226 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.6903 (pt) REVERT: A 241 LEU cc_start: 0.6360 (OUTLIER) cc_final: 0.6062 (mt) REVERT: A 365 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.7488 (m-80) REVERT: A 583 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7563 (pm20) REVERT: B 239 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8178 (tt0) REVERT: B 574 ASP cc_start: 0.8049 (t0) cc_final: 0.7825 (t0) REVERT: B 661 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8303 (tt0) REVERT: B 820 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.8281 (m-30) REVERT: C 41 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.6262 (mmtp) REVERT: C 403 ARG cc_start: 0.7766 (ttt-90) cc_final: 0.7501 (ttt-90) REVERT: C 752 LEU cc_start: 0.8125 (tt) cc_final: 0.7751 (tp) REVERT: C 1002 GLN cc_start: 0.8772 (tp40) cc_final: 0.8469 (tp40) REVERT: D 62 MET cc_start: 0.3025 (mtt) cc_final: 0.2766 (mtt) REVERT: D 165 TRP cc_start: 0.0515 (t60) cc_final: 0.0158 (t60) REVERT: D 249 MET cc_start: 0.1468 (mmm) cc_final: 0.0437 (ptt) REVERT: D 270 MET cc_start: 0.2503 (mtp) cc_final: 0.0600 (tpt) REVERT: D 297 MET cc_start: -0.0241 (mtp) cc_final: -0.0546 (mtt) REVERT: D 383 MET cc_start: 0.4334 (ppp) cc_final: 0.4029 (ppp) REVERT: D 474 MET cc_start: -0.0175 (mmm) cc_final: -0.0861 (ttt) REVERT: D 581 VAL cc_start: 0.0477 (OUTLIER) cc_final: 0.0181 (t) outliers start: 55 outliers final: 36 residues processed: 246 average time/residue: 0.5969 time to fit residues: 178.3876 Evaluate side-chains 244 residues out of total 3316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 197 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 103 optimal weight: 1.9990 chunk 360 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 351 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.0000 chunk 176 optimal weight: 1.9990 chunk 233 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 365 optimal weight: 0.0370 chunk 245 optimal weight: 0.0980 overall best weight: 0.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN B 81 ASN B 125 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS D 397 ASN D 493 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.215563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.164112 restraints weight = 38726.029| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.39 r_work: 0.3364 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.901 31612 Z= 0.203 Angle : 0.604 16.779 43140 Z= 0.298 Chirality : 0.045 0.312 4984 Planarity : 0.004 0.054 5448 Dihedral : 4.237 26.139 4060 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.07 % Favored : 94.85 % Rotamer: Outliers : 1.66 % Allowed : 14.41 % Favored : 83.93 % 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: 0.01 (0.14), residues: 3728 helix: 1.82 (0.17), residues: 991 sheet: 1.13 (0.20), residues: 644 loop : -1.35 (0.13), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 518 TYR 0.029 0.001 TYR C 453 PHE 0.018 0.001 PHE C 392 TRP 0.019 0.001 TRP C 633 HIS 0.004 0.001 HIS C 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (31502) covalent geometry : angle 0.57730 / 0.29 (42857) SS BOND : bond 0.00365 / 0.23 ( 41) SS BOND : angle 1.45830 / 0.98 ( 82) hydrogen bonds : bond 0.04741 / 3.12 ( 1252) hydrogen bonds : angle 4.81405 / 3.29 ( 3546) metal coordination : bond 0.63704 / 33.53 ( 2) link_BETA1-4 : bond 0.00741 / 0.51 ( 22) link_BETA1-4 : angle 1.99031 / 1.17 ( 66) link_NAG-ASN : bond 0.00395 / 0.28 ( 45) link_NAG-ASN : angle 2.76174 / 1.97 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12076.44 seconds wall clock time: 206 minutes 7.25 seconds (12367.25 seconds total)