Starting phenix.real_space_refine on Sat Mar 7 05:45:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kj4_22893/03_2026/7kj4_22893.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kj4_22893/03_2026/7kj4_22893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kj4_22893/03_2026/7kj4_22893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kj4_22893/03_2026/7kj4_22893.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kj4_22893/03_2026/7kj4_22893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kj4_22893/03_2026/7kj4_22893.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 192 5.16 5 C 24697 2.51 5 N 6307 2.21 5 O 7580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 278 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38776 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 7658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7658 Classifications: {'peptide': 981} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 48, 'TRANS': 932} Chain breaks: 10 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 7665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7665 Classifications: {'peptide': 981} Link IDs: {'PTRANS': 48, 'TRANS': 932} Chain breaks: 10 Chain: "C" Number of atoms: 7661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7661 Classifications: {'peptide': 981} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 48, 'TRANS': 932} Chain breaks: 10 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4844 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} Chain: "E" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4844 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} Chain: "F" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4844 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.24, per 1000 atoms: 0.24 Number of scatterers: 38776 At special positions: 0 Unit cell: (164.175, 164.175, 232.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 192 16.00 O 7580 8.00 N 6307 7.00 C 24697 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.00 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.06 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.00 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.51 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.73 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=2.05 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=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.18 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=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.05 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.01 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.51 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.06 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.02 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.05 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM38214 O5 NAG A1302 .*. O " rejected from bonding due to valence issues. Atom "HETATM38564 O5 NAG C1301 .*. O " rejected from bonding due to valence issues. Atom "HETATM38648 O5 NAG C1307 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " 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 a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A 717 " " NAG A1313 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 717 " " NAG B1312 " - " ASN B1074 " " NAG B1313 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C 717 " " NAG D 701 " - " ASN D 322 " " NAG E 701 " - " ASN E 322 " " NAG G 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1098 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " " NAG P 1 " - " ASN D 53 " " NAG Q 1 " - " ASN D 90 " " NAG R 1 " - " ASN D 103 " " NAG S 1 " - " ASN D 432 " " NAG T 1 " - " ASN D 546 " " NAG U 1 " - " ASN E 53 " " NAG V 1 " - " ASN E 90 " " NAG W 1 " - " ASN E 103 " " NAG X 1 " - " ASN E 432 " " NAG Y 1 " - " ASN E 546 " " NAG Z 1 " - " ASN F 53 " " NAG a 1 " - " ASN F 90 " " NAG b 1 " - " ASN F 103 " " NAG c 1 " - " ASN F 432 " " NAG d 1 " - " ASN F 546 " Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 1.6 seconds 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8886 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 51 sheets defined 43.0% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 364 through 371 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.056A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.695A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.121A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.554A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.667A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.522A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.655A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.740A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.384A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.131A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.711A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 4.362A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.924A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.841A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.419A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.664A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.593A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.526A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.616A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.751A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.603A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.003A 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 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.976A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.864A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.506A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.329A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 782 removed outlier: 4.058A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.227A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 941 removed outlier: 3.628A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 977 through 982 removed outlier: 3.577A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.816A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR C 998 " --> pdb=" O ASP C 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.011A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 53 removed outlier: 5.449A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 82 removed outlier: 4.199A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 4.103A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.942A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.699A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 194 removed outlier: 4.044A pdb=" N LEU D 176 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG D 177 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.665A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.621A pdb=" N TYR D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TRP D 203 " --> pdb=" O TYR D 199 " (cutoff:3.500A) 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 252 removed outlier: 3.744A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.953A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 274 through 277 removed outlier: 4.551A pdb=" N ASN D 277 " --> pdb=" O PHE D 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 274 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.767A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 4.108A pdb=" N PHE D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 365 through 383 Processing helix chain 'D' and resid 384 through 388 removed outlier: 4.476A pdb=" N ALA D 387 " --> pdb=" O ALA D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 4.021A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.845A pdb=" N LYS D 441 " --> pdb=" O ASN D 437 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.653A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS D 465 " --> pdb=" O TRP D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.654A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.047A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.769A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU D 554 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 removed outlier: 3.746A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 599 removed outlier: 3.621A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Proline residue: D 590 - end of helix removed outlier: 3.954A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 53 removed outlier: 4.045A pdb=" N GLU E 37 " --> pdb=" O ASN E 33 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA E 46 " --> pdb=" O GLN E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 3.655A pdb=" N LYS E 68 " --> pdb=" O ASN E 64 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 83 No H-bonds generated for 'chain 'E' and resid 82 through 83' Processing helix chain 'E' and resid 84 through 88 Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.567A pdb=" N GLN E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 130 Processing helix chain 'E' and resid 147 through 155 removed outlier: 3.523A pdb=" N MET E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 172 removed outlier: 3.630A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 194 removed outlier: 3.920A pdb=" N LEU E 176 " --> pdb=" O VAL E 172 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG E 177 " --> pdb=" O GLY E 173 " (cutoff:3.500A) Proline residue: E 178 - end of helix removed outlier: 4.003A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN E 188 " --> pdb=" O VAL E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 218 through 252 removed outlier: 3.997A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE E 233 " --> pdb=" O THR E 229 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.741A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 277 No H-bonds generated for 'chain 'E' and resid 275 through 277' Processing helix chain 'E' and resid 278 through 283 Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 303 through 319 Processing helix chain 'E' and resid 326 through 331 Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.634A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 399 through 414 removed outlier: 4.543A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR E 414 " --> pdb=" O LEU E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.863A pdb=" N LYS E 441 " --> pdb=" O ASN E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.535A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU E 457 " --> pdb=" O THR E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 533 removed outlier: 4.149A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU E 529 " --> pdb=" O PHE E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 548 through 559 removed outlier: 3.920A pdb=" N LEU E 554 " --> pdb=" O ALA E 550 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 removed outlier: 4.136A pdb=" N GLU E 571 " --> pdb=" O THR E 567 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN E 572 " --> pdb=" O LEU E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 587 Processing helix chain 'E' and resid 588 through 599 removed outlier: 3.962A pdb=" N ASP E 597 " --> pdb=" O THR E 593 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 51 removed outlier: 3.805A pdb=" N PHE F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP F 30 " --> pdb=" O LYS F 26 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS F 31 " --> pdb=" O THR F 27 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 82 removed outlier: 3.600A pdb=" N THR F 78 " --> pdb=" O LYS F 74 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU F 79 " --> pdb=" O GLU F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 88 removed outlier: 6.094A pdb=" N GLN F 86 " --> pdb=" O TYR F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 102 Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 155 removed outlier: 3.557A pdb=" N ILE F 151 " --> pdb=" O GLY F 147 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 172 removed outlier: 3.553A pdb=" N ARG F 169 " --> pdb=" O TRP F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 194 Proline residue: F 178 - end of helix removed outlier: 3.690A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 204 removed outlier: 3.782A pdb=" N TYR F 202 " --> pdb=" O ASP F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 208 Processing helix chain 'F' and resid 220 through 252 removed outlier: 4.093A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR F 229 " --> pdb=" O ASP F 225 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLU F 232 " --> pdb=" O HIS F 228 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE F 233 " --> pdb=" O THR F 229 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 4.030A pdb=" N ASN F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 267 No H-bonds generated for 'chain 'F' and resid 265 through 267' Processing helix chain 'F' and resid 274 through 277 removed outlier: 4.524A pdb=" N ASN F 277 " --> pdb=" O PHE F 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 274 through 277' Processing helix chain 'F' and resid 278 through 283 Processing helix chain 'F' and resid 293 through 300 removed outlier: 3.604A pdb=" N MET F 297 " --> pdb=" O VAL F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.682A pdb=" N ALA F 311 " --> pdb=" O ILE F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 386 removed outlier: 3.582A pdb=" N HIS F 373 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR F 381 " --> pdb=" O GLY F 377 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA F 384 " --> pdb=" O GLN F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 388 No H-bonds generated for 'chain 'F' and resid 387 through 388' Processing helix chain 'F' and resid 389 through 393 Processing helix chain 'F' and resid 397 through 413 removed outlier: 3.722A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 removed outlier: 3.941A pdb=" N SER F 420 " --> pdb=" O LYS F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.571A pdb=" N GLU F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 465 removed outlier: 4.314A pdb=" N PHE F 452 " --> pdb=" O GLY F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 469 through 471 No H-bonds generated for 'chain 'F' and resid 469 through 471' Processing helix chain 'F' and resid 472 through 484 removed outlier: 3.848A pdb=" N TRP F 478 " --> pdb=" O MET F 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 502 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 512 through 534 removed outlier: 4.043A pdb=" N TYR F 516 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 548 through 559 removed outlier: 3.915A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 572 removed outlier: 4.213A pdb=" N GLU F 571 " --> pdb=" O THR F 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 598 removed outlier: 3.681A pdb=" N PHE F 588 " --> pdb=" O LEU F 584 " (cutoff:3.500A) Proline residue: F 590 - end of helix removed outlier: 3.837A pdb=" N TRP F 594 " --> pdb=" O PRO F 590 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.179A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.349A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.594A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.542A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.750A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.755A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.949A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.648A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.584A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.844A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 removed outlier: 6.500A pdb=" N ASN A 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.915A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.077A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.389A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.136A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.784A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.438A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.385A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.431A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.408A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.920A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (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 361 through 362 removed outlier: 6.566A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.202A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.026A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.870A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 789 through 790 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1123 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.972A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.516A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.528A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN C 125 " --> pdb=" O ASN C 122 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.392A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AD9, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.987A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.627A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.462A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.633A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE7, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AE8, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.130A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AF1, first strand: chain 'E' and resid 132 through 133 Processing sheet with id=AF2, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.180A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'E' and resid 347 through 350 Processing sheet with id=AF4, first strand: chain 'F' and resid 131 through 133 Processing sheet with id=AF5, first strand: chain 'F' and resid 262 through 263 removed outlier: 6.101A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'F' and resid 347 through 350 1738 hydrogen bonds defined for protein. 4878 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: 9.93 Time building geometry restraints manager: 4.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 6459 1.30 - 1.44: 10822 1.44 - 1.57: 22095 1.57 - 1.71: 39 1.71 - 1.84: 279 Bond restraints: 39694 Sorted by residual: bond pdb=" CG ASN C 717 " pdb=" ND2 ASN C 717 " ideal model delta sigma weight residual 1.328 1.203 0.125 2.10e-02 2.27e+03 3.53e+01 bond pdb=" CG ASN A 122 " pdb=" ND2 ASN A 122 " ideal model delta sigma weight residual 1.328 1.447 -0.119 2.10e-02 2.27e+03 3.23e+01 bond pdb=" CA CYS A 480 " pdb=" C CYS A 480 " ideal model delta sigma weight residual 1.519 1.581 -0.062 1.14e-02 7.69e+03 2.94e+01 bond pdb=" N CYS C 488 " pdb=" CA CYS C 488 " ideal model delta sigma weight residual 1.457 1.521 -0.064 1.24e-02 6.50e+03 2.68e+01 bond pdb=" N ASN C 343 " pdb=" CA ASN C 343 " ideal model delta sigma weight residual 1.458 1.513 -0.056 1.22e-02 6.72e+03 2.07e+01 ... (remaining 39689 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 44932 2.53 - 5.05: 8509 5.05 - 7.58: 477 7.58 - 10.11: 34 10.11 - 12.64: 7 Bond angle restraints: 53959 Sorted by residual: angle pdb=" N ARG B1107 " pdb=" CA ARG B1107 " pdb=" C ARG B1107 " ideal model delta sigma weight residual 111.71 122.03 -10.32 1.15e+00 7.56e-01 8.05e+01 angle pdb=" N SER F 547 " pdb=" CA SER F 547 " pdb=" C SER F 547 " ideal model delta sigma weight residual 112.89 123.32 -10.43 1.24e+00 6.50e-01 7.08e+01 angle pdb=" N ARG A1107 " pdb=" CA ARG A1107 " pdb=" C ARG A1107 " ideal model delta sigma weight residual 112.54 121.68 -9.14 1.22e+00 6.72e-01 5.61e+01 angle pdb=" N SER A 60 " pdb=" CA SER A 60 " pdb=" C SER A 60 " ideal model delta sigma weight residual 109.95 120.68 -10.73 1.44e+00 4.82e-01 5.56e+01 angle pdb=" N ARG C1107 " pdb=" CA ARG C1107 " pdb=" C ARG C1107 " ideal model delta sigma weight residual 111.75 121.22 -9.47 1.28e+00 6.10e-01 5.48e+01 ... (remaining 53954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 22487 18.00 - 35.99: 1698 35.99 - 53.99: 376 53.99 - 71.98: 105 71.98 - 89.98: 67 Dihedral angle restraints: 24733 sinusoidal: 10948 harmonic: 13785 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -172.94 86.94 1 1.00e+01 1.00e-02 9.09e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -170.78 84.78 1 1.00e+01 1.00e-02 8.73e+01 dihedral pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " pdb=" SG CYS E 141 " pdb=" CB CYS E 141 " ideal model delta sinusoidal sigma weight residual 93.00 9.52 83.48 1 1.00e+01 1.00e-02 8.51e+01 ... (remaining 24730 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.958: 6192 0.958 - 1.917: 3 1.917 - 2.875: 1 2.875 - 3.833: 0 3.833 - 4.792: 2 Chirality restraints: 6198 Sorted by residual: chirality pdb=" C1 NAG C1311 " pdb=" ND2 ASN C 717 " pdb=" C2 NAG C1311 " pdb=" O5 NAG C1311 " both_signs ideal model delta sigma weight residual False -2.40 2.39 -4.79 2.00e-01 2.50e+01 5.74e+02 chirality pdb=" C1 NAG C1309 " pdb=" ND2 ASN C 657 " pdb=" C2 NAG C1309 " pdb=" O5 NAG C1309 " both_signs ideal model delta sigma weight residual False -2.40 1.51 -3.91 2.00e-01 2.50e+01 3.82e+02 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 0.05 -2.45 2.00e-01 2.50e+01 1.51e+02 ... (remaining 6195 not shown) Planarity restraints: 6912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 546 " 0.261 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" CG ASN D 546 " -0.093 2.00e-02 2.50e+03 pdb=" OD1 ASN D 546 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN D 546 " -0.519 2.00e-02 2.50e+03 pdb=" C1 NAG T 1 " 0.354 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " -0.353 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG R 2 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " -0.107 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " 0.543 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " -0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 616 " 0.076 2.00e-02 2.50e+03 2.79e-01 9.72e+02 pdb=" CG ASN B 616 " -0.082 2.00e-02 2.50e+03 pdb=" OD1 ASN B 616 " 0.158 2.00e-02 2.50e+03 pdb=" ND2 ASN B 616 " -0.488 2.00e-02 2.50e+03 pdb=" C1 NAG B1308 " 0.336 2.00e-02 2.50e+03 ... (remaining 6909 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 53 2.50 - 3.10: 25699 3.10 - 3.70: 57619 3.70 - 4.30: 88235 4.30 - 4.90: 142912 Nonbonded interactions: 314518 Sorted by model distance: nonbonded pdb=" OD1 ASN B1134 " pdb=" C1 NAG L 1 " model vdw 1.904 2.776 nonbonded pdb=" NE2 GLN C 115 " pdb=" O ASN C 165 " model vdw 1.957 3.120 nonbonded pdb=" ND2 ASN C 603 " pdb=" O5 NAG C1307 " model vdw 1.970 3.120 nonbonded pdb=" ND2 ASN C 165 " pdb=" C1 NAG C1313 " model vdw 1.991 3.550 nonbonded pdb=" ND2 ASN B 603 " pdb=" C1 NAG B1307 " model vdw 1.992 3.550 ... (remaining 314513 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 223 or (resid 224 and (name N or name CA or nam \ e C or name O or name CB )) or resid 225 through 1313)) selection = (chain 'B' and (resid 27 through 124 or (resid 125 and (name N or name CA or nam \ e C or name O or name CB )) or resid 126 through 223 or (resid 224 and (name N o \ r name CA or name C or name O or name CB )) or resid 225 through 505 or (resid 5 \ 06 and (name N or name CA or name C or name O or name CB )) or resid 507 through \ 1313)) selection = (chain 'C' and (resid 27 through 124 or (resid 125 and (name N or name CA or nam \ e C or name O or name CB )) or resid 126 through 505 or (resid 506 and (name N o \ r name CA or name C or name O or name CB )) or resid 507 through 1313)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = 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' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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: 7.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.900 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 36.970 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.140 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 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 : 0.016 0.699 39820 Z= 0.907 Angle : 2.001 46.851 54289 Z= 1.262 Chirality : 0.141 4.792 6198 Planarity : 0.014 0.305 6858 Dihedral : 14.391 89.981 15703 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.09 % Favored : 93.40 % Rotamer: Outliers : 2.36 % Allowed : 4.43 % Favored : 93.20 % Cbeta Deviations : 0.32 % 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: -2.39 (0.11), residues: 4650 helix: -2.20 (0.09), residues: 1697 sheet: 0.38 (0.22), residues: 492 loop : -1.50 (0.12), residues: 2461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 460 TYR 0.119 0.021 TYR B 380 PHE 0.100 0.016 PHE A 592 TRP 0.184 0.029 TRP D 349 HIS 0.014 0.004 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.01360 (39694) covalent geometry : angle 1.83561 (53959) SS BOND : bond 0.14308 ( 48) SS BOND : angle 7.89198 ( 96) hydrogen bonds : bond 0.18678 ( 1738) hydrogen bonds : angle 8.50490 ( 4878) link_BETA1-4 : bond 0.03172 ( 24) link_BETA1-4 : angle 4.08895 ( 72) link_NAG-ASN : bond 0.19683 ( 54) link_NAG-ASN : angle 13.24456 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 752 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ASN cc_start: 0.2970 (OUTLIER) cc_final: 0.2573 (m-40) REVERT: A 1000 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8830 (mmt90) REVERT: B 140 PHE cc_start: 0.5461 (p90) cc_final: 0.5099 (p90) REVERT: B 1092 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.5537 (mt-10) REVERT: C 1101 HIS cc_start: 0.5033 (m90) cc_final: 0.4766 (m170) REVERT: E 140 GLU cc_start: 0.1894 (pt0) cc_final: 0.1400 (tp30) REVERT: E 309 LYS cc_start: 0.6881 (mmtt) cc_final: 0.6534 (tptm) REVERT: E 446 ILE cc_start: 0.5342 (mm) cc_final: 0.4695 (mm) REVERT: E 557 MET cc_start: 0.5635 (tmm) cc_final: 0.5166 (tmm) REVERT: F 148 LEU cc_start: -0.0449 (tp) cc_final: -0.1561 (tp) REVERT: F 180 TYR cc_start: 0.1822 (t80) cc_final: 0.1461 (t80) REVERT: F 270 MET cc_start: -0.3363 (tpp) cc_final: -0.3858 (tpp) REVERT: F 273 ARG cc_start: 0.0706 (ttt180) cc_final: 0.0196 (mmm-85) REVERT: F 278 LEU cc_start: 0.3771 (mt) cc_final: 0.2870 (tp) REVERT: F 358 ILE cc_start: 0.3482 (mt) cc_final: 0.3250 (mm) REVERT: F 367 ASP cc_start: 0.2153 (t0) cc_final: 0.1932 (m-30) REVERT: F 449 THR cc_start: 0.0249 (OUTLIER) cc_final: -0.0023 (t) REVERT: F 455 MET cc_start: 0.4020 (tmm) cc_final: 0.3605 (tmm) REVERT: F 462 MET cc_start: 0.3010 (mtp) cc_final: 0.2580 (mmt) REVERT: F 539 LEU cc_start: 0.1242 (tp) cc_final: 0.0698 (tp) REVERT: F 560 LEU cc_start: 0.2426 (mt) cc_final: 0.2105 (tt) REVERT: F 582 ARG cc_start: -0.1721 (OUTLIER) cc_final: -0.2135 (mmt90) outliers start: 98 outliers final: 20 residues processed: 836 average time/residue: 0.2663 time to fit residues: 351.0426 Evaluate side-chains 372 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 347 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 1000 ARG Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain E residue 133 CYS Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 571 GLU Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 582 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 470 optimal weight: 10.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 607 GLN A 913 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 125 ASN B 207 HIS B 394 ASN B 460 ASN B 474 GLN B 675 GLN B 755 GLN B 779 GLN C 115 GLN C 271 GLN C 501 ASN C 762 GLN C 907 ASN C1005 GLN C1048 HIS C1071 GLN D 42 GLN D 63 ASN D 117 ASN D 330 ASN E 58 ASN E 63 ASN E 101 GLN E 345 HIS E 373 HIS E 378 HIS E 388 GLN E 417 HIS E 505 HIS E 508 ASN F 63 ASN F 89 GLN F 134 ASN F 149 ASN F 241 HIS ** F 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 572 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.201129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.184430 restraints weight = 88870.494| |-----------------------------------------------------------------------------| r_work (start): 0.4422 rms_B_bonded: 1.87 r_work: 0.4266 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4237 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.4237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 39820 Z= 0.187 Angle : 0.815 21.227 54289 Z= 0.402 Chirality : 0.052 1.019 6198 Planarity : 0.005 0.073 6858 Dihedral : 7.831 59.997 6985 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.16 % Favored : 96.75 % Rotamer: Outliers : 2.19 % Allowed : 9.23 % Favored : 88.58 % Cbeta Deviations : 0.02 % 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: -0.95 (0.12), residues: 4650 helix: -0.31 (0.12), residues: 1757 sheet: 0.20 (0.19), residues: 620 loop : -1.05 (0.13), residues: 2273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 466 TYR 0.031 0.002 TYR F 199 PHE 0.033 0.002 PHE A 559 TRP 0.028 0.002 TRP F 271 HIS 0.009 0.001 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00405 (39694) covalent geometry : angle 0.75122 (53959) SS BOND : bond 0.00546 ( 48) SS BOND : angle 2.17408 ( 96) hydrogen bonds : bond 0.05305 ( 1738) hydrogen bonds : angle 5.93179 ( 4878) link_BETA1-4 : bond 0.01025 ( 24) link_BETA1-4 : angle 2.40013 ( 72) link_NAG-ASN : bond 0.01071 ( 54) link_NAG-ASN : angle 5.42977 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 400 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 ASN cc_start: -0.0774 (OUTLIER) cc_final: -0.1220 (p0) REVERT: A 460 ASN cc_start: 0.2860 (OUTLIER) cc_final: 0.2522 (m-40) REVERT: A 900 MET cc_start: 0.7597 (mtp) cc_final: 0.7304 (mtp) REVERT: B 140 PHE cc_start: 0.5381 (p90) cc_final: 0.5021 (p90) REVERT: B 1005 GLN cc_start: 0.7961 (tp40) cc_final: 0.7750 (tp40) REVERT: C 567 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.7013 (mtt180) REVERT: F 273 ARG cc_start: 0.0197 (ttt180) cc_final: -0.1430 (mmt180) REVERT: F 462 MET cc_start: 0.1395 (mtp) cc_final: 0.0723 (mmt) REVERT: F 557 MET cc_start: 0.2883 (tmm) cc_final: 0.2672 (tmm) outliers start: 91 outliers final: 48 residues processed: 472 average time/residue: 0.2493 time to fit residues: 190.7842 Evaluate side-chains 328 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 277 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 357 ARG Chi-restraints excluded: chain E residue 455 MET Chi-restraints excluded: chain E residue 571 GLU Chi-restraints excluded: chain E residue 589 GLU Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 344 CYS Chi-restraints excluded: chain F residue 431 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 315 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 308 optimal weight: 30.0000 chunk 321 optimal weight: 0.6980 chunk 311 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1048 HIS B 360 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1048 HIS C 87 ASN C 762 GLN C 907 ASN C1005 GLN D 51 ASN D 154 ASN E 76 GLN ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 417 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.202596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.190794 restraints weight = 88582.008| |-----------------------------------------------------------------------------| r_work (start): 0.4510 rms_B_bonded: 1.11 r_work: 0.4383 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.4352 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6206 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 39820 Z= 0.145 Angle : 0.691 16.582 54289 Z= 0.342 Chirality : 0.047 0.739 6198 Planarity : 0.004 0.055 6858 Dihedral : 6.837 59.882 6948 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.35 % Favored : 96.56 % Rotamer: Outliers : 1.74 % Allowed : 11.57 % Favored : 86.70 % 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: -0.51 (0.12), residues: 4650 helix: 0.30 (0.12), residues: 1750 sheet: 0.23 (0.19), residues: 635 loop : -0.98 (0.13), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 328 TYR 0.024 0.002 TYR A1138 PHE 0.023 0.002 PHE D 274 TRP 0.039 0.002 TRP F 271 HIS 0.006 0.001 HIS C1101 Details of bonding type rmsd covalent geometry : bond 0.00314 (39694) covalent geometry : angle 0.64214 (53959) SS BOND : bond 0.00399 ( 48) SS BOND : angle 1.89344 ( 96) hydrogen bonds : bond 0.04442 ( 1738) hydrogen bonds : angle 5.51643 ( 4878) link_BETA1-4 : bond 0.00643 ( 24) link_BETA1-4 : angle 2.12390 ( 72) link_NAG-ASN : bond 0.00680 ( 54) link_NAG-ASN : angle 4.32181 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 318 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.7472 (m-80) cc_final: 0.7023 (m-80) REVERT: A 460 ASN cc_start: 0.3089 (OUTLIER) cc_final: 0.2661 (m-40) REVERT: B 1005 GLN cc_start: 0.7806 (tp40) cc_final: 0.7544 (tp40) REVERT: C 567 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6968 (mtt180) REVERT: D 62 MET cc_start: 0.4077 (ppp) cc_final: 0.3779 (ppp) REVERT: D 345 HIS cc_start: 0.5565 (t70) cc_final: 0.5111 (t70) REVERT: F 462 MET cc_start: 0.1416 (mtp) cc_final: 0.0882 (mmt) outliers start: 72 outliers final: 42 residues processed: 369 average time/residue: 0.2459 time to fit residues: 150.1543 Evaluate side-chains 304 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 260 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 455 MET Chi-restraints excluded: chain E residue 571 GLU Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 339 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 123 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 213 optimal weight: 8.9990 chunk 24 optimal weight: 0.2980 chunk 460 optimal weight: 0.0370 chunk 138 optimal weight: 10.0000 chunk 378 optimal weight: 20.0000 chunk 370 optimal weight: 4.9990 chunk 424 optimal weight: 7.9990 chunk 435 optimal weight: 9.9990 chunk 447 optimal weight: 50.0000 overall best weight: 1.4662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B1010 GLN C 501 ASN C 762 GLN C 907 ASN C1005 GLN D 49 ASN ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.201623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.189653 restraints weight = 88240.860| |-----------------------------------------------------------------------------| r_work (start): 0.4496 rms_B_bonded: 1.10 r_work: 0.4369 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.4338 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 39820 Z= 0.160 Angle : 0.658 15.004 54289 Z= 0.324 Chirality : 0.046 0.741 6198 Planarity : 0.004 0.058 6858 Dihedral : 6.385 59.535 6947 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.14 % Favored : 96.77 % Rotamer: Outliers : 2.31 % Allowed : 12.03 % Favored : 85.66 % 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: -0.34 (0.12), residues: 4650 helix: 0.51 (0.12), residues: 1749 sheet: 0.19 (0.19), residues: 651 loop : -0.89 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 460 TYR 0.021 0.001 TYR B1067 PHE 0.023 0.002 PHE A 559 TRP 0.023 0.001 TRP C 436 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00360 (39694) covalent geometry : angle 0.61634 (53959) SS BOND : bond 0.00945 ( 48) SS BOND : angle 1.82555 ( 96) hydrogen bonds : bond 0.04186 ( 1738) hydrogen bonds : angle 5.34911 ( 4878) link_BETA1-4 : bond 0.00612 ( 24) link_BETA1-4 : angle 2.00941 ( 72) link_NAG-ASN : bond 0.00557 ( 54) link_NAG-ASN : angle 3.83379 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 289 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.7450 (m-80) cc_final: 0.7005 (m-80) REVERT: A 460 ASN cc_start: 0.3230 (OUTLIER) cc_final: 0.2782 (m-40) REVERT: B 1005 GLN cc_start: 0.7844 (tp40) cc_final: 0.7615 (tp40) REVERT: C 61 ASN cc_start: 0.5405 (OUTLIER) cc_final: 0.4654 (p0) REVERT: C 567 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6990 (mtt180) REVERT: D 270 MET cc_start: 0.3614 (mmm) cc_final: 0.3344 (mmp) REVERT: D 345 HIS cc_start: 0.5509 (t70) cc_final: 0.5155 (t70) REVERT: E 224 GLU cc_start: 0.4609 (OUTLIER) cc_final: 0.4038 (tm-30) REVERT: F 344 CYS cc_start: 0.4640 (OUTLIER) cc_final: 0.4431 (p) REVERT: F 462 MET cc_start: 0.1855 (mtp) cc_final: 0.1152 (mmt) REVERT: F 477 TRP cc_start: 0.1880 (t-100) cc_final: 0.1672 (t-100) outliers start: 96 outliers final: 56 residues processed: 365 average time/residue: 0.2357 time to fit residues: 143.4368 Evaluate side-chains 314 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 253 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 571 GLU Chi-restraints excluded: chain E residue 589 GLU Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 344 CYS Chi-restraints excluded: chain F residue 567 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 267 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 300 optimal weight: 30.0000 chunk 91 optimal weight: 4.9990 chunk 257 optimal weight: 0.9990 chunk 407 optimal weight: 30.0000 chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 335 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C1005 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.199086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.182141 restraints weight = 87880.862| |-----------------------------------------------------------------------------| r_work (start): 0.4395 rms_B_bonded: 1.85 r_work: 0.4236 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4195 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 39820 Z= 0.188 Angle : 0.669 15.943 54289 Z= 0.329 Chirality : 0.046 0.751 6198 Planarity : 0.004 0.053 6858 Dihedral : 6.266 59.347 6947 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Rotamer: Outliers : 2.55 % Allowed : 12.58 % Favored : 84.86 % 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: -0.32 (0.12), residues: 4650 helix: 0.59 (0.12), residues: 1745 sheet: 0.21 (0.19), residues: 635 loop : -0.95 (0.13), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 567 TYR 0.022 0.002 TYR A1138 PHE 0.021 0.002 PHE C 135 TRP 0.024 0.001 TRP C 436 HIS 0.007 0.001 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00434 (39694) covalent geometry : angle 0.63100 (53959) SS BOND : bond 0.00405 ( 48) SS BOND : angle 1.87456 ( 96) hydrogen bonds : bond 0.04130 ( 1738) hydrogen bonds : angle 5.31009 ( 4878) link_BETA1-4 : bond 0.00632 ( 24) link_BETA1-4 : angle 1.93575 ( 72) link_NAG-ASN : bond 0.00526 ( 54) link_NAG-ASN : angle 3.70100 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 275 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ASN cc_start: 0.3217 (OUTLIER) cc_final: 0.2877 (m-40) REVERT: B 1005 GLN cc_start: 0.8017 (tp40) cc_final: 0.7788 (tp40) REVERT: D 270 MET cc_start: 0.4042 (mmm) cc_final: 0.3803 (mmp) REVERT: D 345 HIS cc_start: 0.5824 (t70) cc_final: 0.5422 (t70) REVERT: E 224 GLU cc_start: 0.4687 (OUTLIER) cc_final: 0.4003 (tm-30) REVERT: F 344 CYS cc_start: 0.4828 (OUTLIER) cc_final: 0.4439 (p) REVERT: F 462 MET cc_start: 0.2420 (mtp) cc_final: 0.1265 (mmt) REVERT: F 477 TRP cc_start: 0.2182 (t-100) cc_final: 0.1910 (t-100) outliers start: 106 outliers final: 71 residues processed: 358 average time/residue: 0.2334 time to fit residues: 139.8344 Evaluate side-chains 321 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 247 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 571 GLU Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 344 CYS Chi-restraints excluded: chain F residue 567 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 450 optimal weight: 30.0000 chunk 240 optimal weight: 9.9990 chunk 326 optimal weight: 0.9980 chunk 47 optimal weight: 0.0000 chunk 400 optimal weight: 20.0000 chunk 370 optimal weight: 20.0000 chunk 360 optimal weight: 7.9990 chunk 267 optimal weight: 1.9990 chunk 306 optimal weight: 30.0000 chunk 64 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1010 GLN C 907 ASN C1005 GLN E 51 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.199457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.182525 restraints weight = 88188.141| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 1.85 r_work: 0.4240 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.4212 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 39820 Z= 0.158 Angle : 0.641 15.118 54289 Z= 0.315 Chirality : 0.045 0.675 6198 Planarity : 0.004 0.051 6858 Dihedral : 6.056 58.825 6947 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.35 % Favored : 96.56 % Rotamer: Outliers : 2.41 % Allowed : 13.28 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.12), residues: 4650 helix: 0.71 (0.12), residues: 1748 sheet: 0.25 (0.19), residues: 628 loop : -0.88 (0.13), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 115 TYR 0.031 0.001 TYR B 495 PHE 0.032 0.002 PHE C 135 TRP 0.028 0.001 TRP A 353 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00362 (39694) covalent geometry : angle 0.60638 (53959) SS BOND : bond 0.00311 ( 48) SS BOND : angle 1.60244 ( 96) hydrogen bonds : bond 0.03883 ( 1738) hydrogen bonds : angle 5.21200 ( 4878) link_BETA1-4 : bond 0.00590 ( 24) link_BETA1-4 : angle 1.89269 ( 72) link_NAG-ASN : bond 0.00444 ( 54) link_NAG-ASN : angle 3.46404 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 273 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ASN cc_start: 0.3347 (OUTLIER) cc_final: 0.2940 (m-40) REVERT: C 1005 GLN cc_start: 0.8122 (tp40) cc_final: 0.7843 (mm-40) REVERT: D 62 MET cc_start: 0.4594 (ppp) cc_final: 0.3847 (ppp) REVERT: D 249 MET cc_start: 0.3557 (tpt) cc_final: 0.3223 (tpt) REVERT: D 270 MET cc_start: 0.4031 (mmm) cc_final: 0.3746 (mmp) REVERT: E 100 LEU cc_start: 0.4613 (tp) cc_final: 0.4041 (mt) REVERT: E 224 GLU cc_start: 0.4779 (OUTLIER) cc_final: 0.4050 (tm-30) REVERT: F 462 MET cc_start: 0.2433 (mtp) cc_final: 0.1291 (mmt) REVERT: F 474 MET cc_start: 0.1536 (mmm) cc_final: 0.1202 (mmm) REVERT: F 477 TRP cc_start: 0.2074 (t-100) cc_final: 0.1813 (t-100) outliers start: 100 outliers final: 73 residues processed: 349 average time/residue: 0.2312 time to fit residues: 134.8322 Evaluate side-chains 318 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 243 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 343 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 263 optimal weight: 0.5980 chunk 268 optimal weight: 1.9990 chunk 274 optimal weight: 2.9990 chunk 290 optimal weight: 0.1980 chunk 35 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 chunk 151 optimal weight: 0.9990 chunk 304 optimal weight: 5.9990 chunk 463 optimal weight: 10.0000 chunk 449 optimal weight: 40.0000 chunk 90 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1005 GLN B1010 GLN B1113 GLN C 907 ASN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS E 101 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.198161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.173373 restraints weight = 82894.066| |-----------------------------------------------------------------------------| r_work (start): 0.4324 rms_B_bonded: 2.52 r_work: 0.4122 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.4090 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39820 Z= 0.145 Angle : 0.631 15.354 54289 Z= 0.310 Chirality : 0.045 0.799 6198 Planarity : 0.004 0.044 6858 Dihedral : 5.865 58.640 6944 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.55 % Favored : 96.37 % Rotamer: Outliers : 2.29 % Allowed : 14.10 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.11 (0.12), residues: 4650 helix: 0.84 (0.12), residues: 1740 sheet: 0.23 (0.19), residues: 640 loop : -0.87 (0.13), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 273 TYR 0.020 0.001 TYR F 199 PHE 0.029 0.001 PHE B 429 TRP 0.033 0.001 TRP D 478 HIS 0.006 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00327 (39694) covalent geometry : angle 0.59789 (53959) SS BOND : bond 0.00370 ( 48) SS BOND : angle 1.56489 ( 96) hydrogen bonds : bond 0.03768 ( 1738) hydrogen bonds : angle 5.13653 ( 4878) link_BETA1-4 : bond 0.00556 ( 24) link_BETA1-4 : angle 1.89615 ( 72) link_NAG-ASN : bond 0.00528 ( 54) link_NAG-ASN : angle 3.35145 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 270 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ASN cc_start: 0.3192 (OUTLIER) cc_final: 0.2808 (m-40) REVERT: B 387 LEU cc_start: 0.7574 (mp) cc_final: 0.7331 (mp) REVERT: C 1005 GLN cc_start: 0.8302 (tp40) cc_final: 0.8013 (mm-40) REVERT: D 62 MET cc_start: 0.4943 (ppp) cc_final: 0.4268 (ppp) REVERT: D 270 MET cc_start: 0.4360 (mmm) cc_final: 0.4152 (mmp) REVERT: D 438 PHE cc_start: 0.3689 (t80) cc_final: 0.3441 (t80) REVERT: D 477 TRP cc_start: 0.4185 (t-100) cc_final: 0.3965 (t-100) REVERT: E 100 LEU cc_start: 0.4808 (tp) cc_final: 0.4217 (mt) REVERT: E 224 GLU cc_start: 0.4670 (OUTLIER) cc_final: 0.3920 (tm-30) REVERT: E 323 MET cc_start: 0.3256 (mmm) cc_final: 0.2878 (tmm) REVERT: F 306 ARG cc_start: 0.5200 (ttt180) cc_final: 0.4164 (tpt170) REVERT: F 343 VAL cc_start: 0.3713 (OUTLIER) cc_final: 0.2975 (t) REVERT: F 345 HIS cc_start: 0.1192 (t70) cc_final: 0.0443 (t-170) REVERT: F 462 MET cc_start: 0.2606 (mtp) cc_final: 0.1397 (mmt) REVERT: F 474 MET cc_start: 0.1549 (mmm) cc_final: 0.1272 (mmm) REVERT: F 477 TRP cc_start: 0.2004 (t-100) cc_final: 0.1718 (t-100) outliers start: 95 outliers final: 76 residues processed: 346 average time/residue: 0.2369 time to fit residues: 136.2312 Evaluate side-chains 324 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 245 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 567 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 385 optimal weight: 4.9990 chunk 271 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 422 optimal weight: 10.0000 chunk 257 optimal weight: 2.9990 chunk 401 optimal weight: 30.0000 chunk 216 optimal weight: 2.9990 chunk 376 optimal weight: 30.0000 chunk 74 optimal weight: 0.8980 chunk 462 optimal weight: 20.0000 chunk 259 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN B 239 GLN B1005 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C1083 HIS ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 556 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.198660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.181661 restraints weight = 87808.488| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 1.83 r_work: 0.4230 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.4197 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 39820 Z= 0.190 Angle : 0.665 15.859 54289 Z= 0.328 Chirality : 0.046 0.720 6198 Planarity : 0.004 0.068 6858 Dihedral : 5.924 59.575 6944 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.70 % Favored : 96.22 % Rotamer: Outliers : 2.39 % Allowed : 14.36 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.12), residues: 4650 helix: 0.78 (0.12), residues: 1743 sheet: 0.08 (0.19), residues: 658 loop : -0.91 (0.13), residues: 2249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 346 TYR 0.029 0.002 TYR B 495 PHE 0.029 0.002 PHE B 429 TRP 0.030 0.001 TRP C 436 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00441 (39694) covalent geometry : angle 0.63057 (53959) SS BOND : bond 0.00347 ( 48) SS BOND : angle 2.29392 ( 96) hydrogen bonds : bond 0.03901 ( 1738) hydrogen bonds : angle 5.21662 ( 4878) link_BETA1-4 : bond 0.00585 ( 24) link_BETA1-4 : angle 1.87111 ( 72) link_NAG-ASN : bond 0.00445 ( 54) link_NAG-ASN : angle 3.32008 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 260 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ASN cc_start: 0.3062 (OUTLIER) cc_final: 0.2736 (m-40) REVERT: C 1005 GLN cc_start: 0.8156 (tp40) cc_final: 0.7879 (mm-40) REVERT: D 62 MET cc_start: 0.4401 (ppp) cc_final: 0.3711 (ppp) REVERT: E 100 LEU cc_start: 0.4559 (tp) cc_final: 0.4087 (mt) REVERT: E 224 GLU cc_start: 0.4541 (OUTLIER) cc_final: 0.3987 (tm-30) REVERT: E 323 MET cc_start: 0.3365 (mmm) cc_final: 0.2883 (tmm) REVERT: E 376 MET cc_start: 0.5286 (mpp) cc_final: 0.5055 (mpp) REVERT: E 606 TRP cc_start: -0.0546 (p90) cc_final: -0.1186 (p90) REVERT: F 306 ARG cc_start: 0.5217 (ttt180) cc_final: 0.4202 (tpt170) REVERT: F 345 HIS cc_start: 0.0960 (t70) cc_final: 0.0630 (t-170) REVERT: F 360 MET cc_start: 0.0052 (mtt) cc_final: -0.0597 (ttm) REVERT: F 398 GLU cc_start: 0.3680 (OUTLIER) cc_final: 0.3260 (mt-10) REVERT: F 462 MET cc_start: 0.2559 (mtp) cc_final: 0.1667 (mmt) REVERT: F 474 MET cc_start: 0.1702 (mmm) cc_final: 0.1411 (mmp) REVERT: F 477 TRP cc_start: 0.1961 (t-100) cc_final: 0.1697 (t-100) outliers start: 99 outliers final: 80 residues processed: 337 average time/residue: 0.2294 time to fit residues: 129.2587 Evaluate side-chains 317 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 234 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain F residue 567 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 259 optimal weight: 0.8980 chunk 192 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 chunk 119 optimal weight: 0.0030 chunk 422 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 367 optimal weight: 9.9990 chunk 233 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B1005 GLN B1010 GLN C 655 HIS C 907 ASN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN E 401 HIS ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN F 277 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.198659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.181615 restraints weight = 87739.488| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 1.84 r_work: 0.4231 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4196 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 39820 Z= 0.179 Angle : 0.661 15.672 54289 Z= 0.326 Chirality : 0.045 0.683 6198 Planarity : 0.004 0.072 6858 Dihedral : 5.929 58.943 6944 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.96 % Favored : 95.98 % Rotamer: Outliers : 2.36 % Allowed : 14.65 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.12), residues: 4650 helix: 0.81 (0.12), residues: 1740 sheet: 0.05 (0.19), residues: 642 loop : -0.94 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 346 TYR 0.030 0.002 TYR C 453 PHE 0.027 0.002 PHE B 429 TRP 0.025 0.001 TRP C 436 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00413 (39694) covalent geometry : angle 0.62900 (53959) SS BOND : bond 0.00394 ( 48) SS BOND : angle 2.12590 ( 96) hydrogen bonds : bond 0.03854 ( 1738) hydrogen bonds : angle 5.21005 ( 4878) link_BETA1-4 : bond 0.00592 ( 24) link_BETA1-4 : angle 1.86321 ( 72) link_NAG-ASN : bond 0.00434 ( 54) link_NAG-ASN : angle 3.24646 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 251 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ASN cc_start: 0.3040 (OUTLIER) cc_final: 0.2688 (m-40) REVERT: C 296 LEU cc_start: 0.8896 (tp) cc_final: 0.8687 (mt) REVERT: C 1005 GLN cc_start: 0.8134 (tp40) cc_final: 0.7847 (mm-40) REVERT: C 1077 THR cc_start: 0.8163 (t) cc_final: 0.7908 (t) REVERT: D 55 THR cc_start: 0.5740 (OUTLIER) cc_final: 0.5328 (m) REVERT: D 62 MET cc_start: 0.4336 (ppp) cc_final: 0.3564 (ppp) REVERT: E 100 LEU cc_start: 0.4515 (tp) cc_final: 0.4053 (mt) REVERT: E 224 GLU cc_start: 0.4583 (OUTLIER) cc_final: 0.4004 (tm-30) REVERT: E 323 MET cc_start: 0.3330 (mmm) cc_final: 0.2798 (tmm) REVERT: E 606 TRP cc_start: -0.0503 (p90) cc_final: -0.1124 (p90) REVERT: F 37 GLU cc_start: 0.3083 (mm-30) cc_final: 0.2056 (mt-10) REVERT: F 306 ARG cc_start: 0.5215 (ttt180) cc_final: 0.4201 (tpt170) REVERT: F 360 MET cc_start: 0.0093 (mtt) cc_final: -0.0341 (ttm) REVERT: F 398 GLU cc_start: 0.3633 (OUTLIER) cc_final: 0.3301 (mt-10) REVERT: F 462 MET cc_start: 0.2484 (mtp) cc_final: 0.1709 (mmt) REVERT: F 477 TRP cc_start: 0.1918 (t-100) cc_final: 0.1645 (t-100) outliers start: 98 outliers final: 81 residues processed: 326 average time/residue: 0.2305 time to fit residues: 126.9115 Evaluate side-chains 322 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 237 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 574 VAL Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain F residue 567 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 86 optimal weight: 0.5980 chunk 37 optimal weight: 50.0000 chunk 375 optimal weight: 30.0000 chunk 152 optimal weight: 5.9990 chunk 164 optimal weight: 0.9990 chunk 420 optimal weight: 30.0000 chunk 305 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 418 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 256 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1005 GLN C 907 ASN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.198295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.181287 restraints weight = 87725.553| |-----------------------------------------------------------------------------| r_work (start): 0.4335 rms_B_bonded: 1.83 r_work: 0.4065 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.4014 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 39820 Z= 0.188 Angle : 0.675 15.790 54289 Z= 0.331 Chirality : 0.046 0.683 6198 Planarity : 0.004 0.071 6858 Dihedral : 6.171 68.969 6944 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.06 % Favored : 95.87 % Rotamer: Outliers : 2.17 % Allowed : 14.92 % Favored : 82.91 % 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: -0.28 (0.12), residues: 4650 helix: 0.77 (0.12), residues: 1745 sheet: -0.04 (0.19), residues: 652 loop : -0.96 (0.13), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 346 TYR 0.030 0.002 TYR B 904 PHE 0.027 0.002 PHE B 429 TRP 0.022 0.001 TRP C 436 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00437 (39694) covalent geometry : angle 0.64598 (53959) SS BOND : bond 0.00354 ( 48) SS BOND : angle 1.89552 ( 96) hydrogen bonds : bond 0.03913 ( 1738) hydrogen bonds : angle 5.25140 ( 4878) link_BETA1-4 : bond 0.00568 ( 24) link_BETA1-4 : angle 1.90032 ( 72) link_NAG-ASN : bond 0.00431 ( 54) link_NAG-ASN : angle 3.17569 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 246 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 ASN cc_start: 0.3234 (OUTLIER) cc_final: 0.2915 (m-40) REVERT: B 453 TYR cc_start: 0.5822 (OUTLIER) cc_final: 0.5199 (p90) REVERT: B 1005 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.6834 (mp-120) REVERT: C 296 LEU cc_start: 0.8976 (tp) cc_final: 0.8768 (mt) REVERT: C 1005 GLN cc_start: 0.8052 (tp40) cc_final: 0.7752 (mm-40) REVERT: C 1077 THR cc_start: 0.8211 (t) cc_final: 0.7982 (t) REVERT: D 55 THR cc_start: 0.6101 (OUTLIER) cc_final: 0.5670 (m) REVERT: D 62 MET cc_start: 0.4769 (ppp) cc_final: 0.4035 (ppp) REVERT: D 455 MET cc_start: 0.4235 (ppp) cc_final: 0.4008 (ppp) REVERT: E 100 LEU cc_start: 0.4805 (tp) cc_final: 0.4180 (mt) REVERT: E 190 MET cc_start: 0.2621 (pmm) cc_final: 0.2420 (pmm) REVERT: E 224 GLU cc_start: 0.4496 (OUTLIER) cc_final: 0.3911 (tm-30) REVERT: E 323 MET cc_start: 0.3186 (mmm) cc_final: 0.2393 (tmm) REVERT: E 606 TRP cc_start: -0.0318 (p90) cc_final: -0.0549 (p90) REVERT: F 37 GLU cc_start: 0.3274 (mm-30) cc_final: 0.2030 (mt-10) REVERT: F 190 MET cc_start: 0.1867 (ptm) cc_final: 0.1033 (mtt) REVERT: F 306 ARG cc_start: 0.5190 (ttt180) cc_final: 0.4136 (tpt170) REVERT: F 360 MET cc_start: -0.0464 (mtt) cc_final: -0.0888 (mtm) REVERT: F 398 GLU cc_start: 0.3595 (OUTLIER) cc_final: 0.3241 (mt-10) REVERT: F 462 MET cc_start: 0.2833 (mtp) cc_final: 0.2032 (mmt) outliers start: 90 outliers final: 75 residues processed: 318 average time/residue: 0.2302 time to fit residues: 123.7173 Evaluate side-chains 311 residues out of total 4152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 230 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 224 GLU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 53 ASN Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain F residue 567 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 260 optimal weight: 0.7980 chunk 386 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 381 optimal weight: 8.9990 chunk 441 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.194641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.169792 restraints weight = 83501.615| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 2.52 r_work: 0.4004 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3961 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.398 39820 Z= 0.279 Angle : 0.847 59.147 54289 Z= 0.423 Chirality : 0.047 0.722 6198 Planarity : 0.004 0.065 6858 Dihedral : 6.239 68.014 6944 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.06 % Favored : 95.87 % Rotamer: Outliers : 2.31 % Allowed : 15.23 % Favored : 82.45 % Cbeta Deviations : 0.02 % 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: -0.28 (0.12), residues: 4650 helix: 0.77 (0.12), residues: 1745 sheet: -0.04 (0.19), residues: 652 loop : -0.97 (0.13), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C1107 TYR 0.036 0.002 TYR B 904 PHE 0.027 0.002 PHE B 429 TRP 0.020 0.001 TRP C 436 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00587 (39694) covalent geometry : angle 0.79990 (53959) SS BOND : bond 0.01160 ( 48) SS BOND : angle 3.74043 ( 96) hydrogen bonds : bond 0.03918 ( 1738) hydrogen bonds : angle 5.25176 ( 4878) link_BETA1-4 : bond 0.00587 ( 24) link_BETA1-4 : angle 1.90748 ( 72) link_NAG-ASN : bond 0.05435 ( 54) link_NAG-ASN : angle 4.15228 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10216.97 seconds wall clock time: 176 minutes 13.27 seconds (10573.27 seconds total)