Starting phenix.real_space_refine on Fri Mar 6 17:00:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l2e_23126/03_2026/7l2e_23126.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l2e_23126/03_2026/7l2e_23126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l2e_23126/03_2026/7l2e_23126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l2e_23126/03_2026/7l2e_23126.map" model { file = "/net/cci-nas-00/data/ceres_data/7l2e_23126/03_2026/7l2e_23126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l2e_23126/03_2026/7l2e_23126.cif" } resolution = 2.97 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= 0.041 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 138 5.16 5 C 20689 2.51 5 N 5349 2.21 5 O 6465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 252 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: 32641 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 8743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1119, 8729 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1119, 8729 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 2 bond proxies already assigned to first conformer: 8918 Chain: "B" Number of atoms: 8743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1119, 8729 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1119, 8729 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 2 bond proxies already assigned to first conformer: 8918 Chain: "C" Number of atoms: 8744 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1119, 8729 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1119, 8729 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 55, 'TRANS': 1063} Chain breaks: 2 bond proxies already assigned to first conformer: 8916 Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 948 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 825 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "G" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 948 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "J" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 825 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "I" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 948 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "K" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 825 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ATYR A 365 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 365 " occ=0.50 residue: pdb=" N ATYR B 365 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR B 365 " occ=0.50 residue: pdb=" N ATYR C 365 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR C 365 " occ=0.50 Time building chain proxies: 12.70, per 1000 atoms: 0.39 Number of scatterers: 32641 At special positions: 0 Unit cell: (194.74, 179.76, 184.04, 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 138 16.00 O 6465 8.00 N 5349 7.00 C 20689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=1.77 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=1.81 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=1.80 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 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 e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 149 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 343 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 603 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 149 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 343 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 603 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 149 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 343 " " NAG C1309 " - " ASN C 616 " " NAG C1310 " - " ASN C 603 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN A 122 " " NAG O 1 " - " ASN A 234 " " NAG P 1 " - " ASN A 17 " " NAG Q 1 " - " ASN A 165 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN B 122 " " NAG W 1 " - " ASN B 234 " " NAG X 1 " - " ASN B 17 " " NAG Y 1 " - " ASN B 165 " " NAG Z 1 " - " ASN C 717 " " NAG a 1 " - " ASN C 801 " " NAG b 1 " - " ASN C1098 " " NAG c 1 " - " ASN C1134 " " NAG d 1 " - " ASN C 122 " " NAG e 1 " - " ASN C 234 " " NAG f 1 " - " ASN C 17 " " NAG g 1 " - " ASN C 165 " Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 2.2 seconds 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7530 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 69 sheets defined 20.7% alpha, 34.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.961A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.107A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.433A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 619 through 625 Processing helix chain 'A' and resid 626 through 629 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 748 through 783 removed outlier: 6.085A pdb=" N SER A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N PHE A 759 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.519A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 838 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.576A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.230A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 948 through 966 removed outlier: 3.572A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.831A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.077A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.011A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.959A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.135A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.406A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 626 through 629 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 749 through 783 removed outlier: 6.140A pdb=" N SER B 758 " --> pdb=" O LEU B 754 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N PHE B 759 " --> pdb=" O GLN B 755 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.593A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 838 removed outlier: 4.185A pdb=" N GLN B 836 " --> pdb=" O GLY B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 removed outlier: 3.767A pdb=" N GLN B 853 " --> pdb=" O LEU B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.657A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.166A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 948 through 966 removed outlier: 3.590A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.851A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.113A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.989A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.983A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.143A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.447A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 625 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 749 through 783 removed outlier: 5.964A pdb=" N SER C 758 " --> pdb=" O LEU C 754 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE C 759 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.658A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 838 removed outlier: 4.266A pdb=" N GLN C 836 " --> pdb=" O GLY C 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 removed outlier: 3.843A pdb=" N GLN C 853 " --> pdb=" O LEU C 849 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS C 854 " --> pdb=" O ILE C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.575A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.195A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 948 through 966 removed outlier: 3.555A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.753A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.050A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.967A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.763A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.762A pdb=" N THR G 87 " --> pdb=" O ALA G 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.763A pdb=" N THR I 87 " --> pdb=" O ALA I 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.288A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.559A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.649A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.099A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS A 136 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.882A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.683A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.263A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.909A pdb=" N PHE A 238 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 12.768A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.422A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.703A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.222A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.099A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS A 136 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.882A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.683A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.263A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.659A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.776A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.803A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.919A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 removed outlier: 5.901A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.584A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.584A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.229A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 789 removed outlier: 6.065A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.288A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.560A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 68 through 69 Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.649A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.099A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS B 136 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.881A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.682A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.263A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.910A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.768A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 12.422A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.702A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.222A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.099A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS B 136 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.881A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.682A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.263A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.766A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.827A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.956A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.578A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.578A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.253A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.288A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.560A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 68 through 69 Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.649A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.098A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS C 136 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.882A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.682A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.263A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.879A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.909A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 12.768A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.422A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.701A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 10.223A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.098A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS C 136 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.882A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.682A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.263A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.879A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.770A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.792A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.916A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.577A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.577A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF8, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.203A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AG1, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.560A pdb=" N TYR L 86 " --> pdb=" O THR L 102 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.560A pdb=" N TYR L 86 " --> pdb=" O THR L 102 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 21 through 24 Processing sheet with id=AG4, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AG5, first strand: chain 'G' and resid 11 through 12 removed outlier: 7.203A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AG7, first strand: chain 'J' and resid 9 through 12 removed outlier: 3.560A pdb=" N TYR J 86 " --> pdb=" O THR J 102 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 9 through 12 removed outlier: 3.560A pdb=" N TYR J 86 " --> pdb=" O THR J 102 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 21 through 24 Processing sheet with id=AH1, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AH2, first strand: chain 'I' and resid 11 through 12 removed outlier: 7.203A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AH4, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.561A pdb=" N TYR K 86 " --> pdb=" O THR K 102 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.561A pdb=" N TYR K 86 " --> pdb=" O THR K 102 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 21 through 24 1259 hydrogen bonds defined for protein. 3324 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: 8.31 Time building geometry restraints manager: 3.14 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: 5283 1.30 - 1.43: 9405 1.43 - 1.56: 18537 1.56 - 1.69: 2 1.69 - 1.82: 174 Bond restraints: 33401 Sorted by residual: bond pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 1.465 1.404 0.061 1.15e-02 7.56e+03 2.81e+01 bond pdb=" N PRO C 82 " pdb=" CA PRO C 82 " ideal model delta sigma weight residual 1.465 1.404 0.061 1.15e-02 7.56e+03 2.78e+01 bond pdb=" N PRO B 82 " pdb=" CA PRO B 82 " ideal model delta sigma weight residual 1.465 1.404 0.060 1.15e-02 7.56e+03 2.76e+01 bond pdb=" C TYR B 248 " pdb=" O TYR B 248 " ideal model delta sigma weight residual 1.236 1.174 0.062 1.26e-02 6.30e+03 2.46e+01 bond pdb=" C PRO B 82 " pdb=" O PRO B 82 " ideal model delta sigma weight residual 1.233 1.178 0.055 1.12e-02 7.97e+03 2.39e+01 ... (remaining 33396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 44505 3.40 - 6.80: 898 6.80 - 10.20: 68 10.20 - 13.59: 11 13.59 - 16.99: 5 Bond angle restraints: 45487 Sorted by residual: angle pdb=" CA ASP A 294 " pdb=" C ASP A 294 " pdb=" N PRO A 295 " ideal model delta sigma weight residual 117.59 134.58 -16.99 9.90e-01 1.02e+00 2.95e+02 angle pdb=" O ASP A 294 " pdb=" C ASP A 294 " pdb=" N PRO A 295 " ideal model delta sigma weight residual 121.32 107.49 13.83 8.50e-01 1.38e+00 2.65e+02 angle pdb=" O ASP B 294 " pdb=" C ASP B 294 " pdb=" N PRO B 295 " ideal model delta sigma weight residual 121.32 107.39 13.93 1.15e+00 7.56e-01 1.47e+02 angle pdb=" C ASP A 294 " pdb=" N PRO A 295 " pdb=" CA PRO A 295 " ideal model delta sigma weight residual 119.19 132.01 -12.82 1.06e+00 8.90e-01 1.46e+02 angle pdb=" C ASP B 294 " pdb=" N PRO B 295 " pdb=" CA PRO B 295 " ideal model delta sigma weight residual 119.19 131.65 -12.46 1.06e+00 8.90e-01 1.38e+02 ... (remaining 45482 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 19276 17.99 - 35.99: 1273 35.99 - 53.98: 209 53.98 - 71.98: 42 71.98 - 89.97: 25 Dihedral angle restraints: 20825 sinusoidal: 9051 harmonic: 11774 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -21.46 -64.54 1 1.00e+01 1.00e-02 5.47e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -22.19 -63.81 1 1.00e+01 1.00e-02 5.36e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -24.42 -61.58 1 1.00e+01 1.00e-02 5.03e+01 ... (remaining 20822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 4951 0.128 - 0.256: 289 0.256 - 0.383: 52 0.383 - 0.511: 11 0.511 - 0.639: 13 Chirality restraints: 5316 Sorted by residual: chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.33e+02 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.06e+02 ... (remaining 5313 not shown) Planarity restraints: 5851 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1303 " -0.318 2.00e-02 2.50e+03 2.74e-01 9.40e+02 pdb=" C7 NAG B1303 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B1303 " -0.153 2.00e-02 2.50e+03 pdb=" N2 NAG B1303 " 0.488 2.00e-02 2.50e+03 pdb=" O7 NAG B1303 " -0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1303 " 0.318 2.00e-02 2.50e+03 2.74e-01 9.38e+02 pdb=" C7 NAG C1303 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG C1303 " 0.153 2.00e-02 2.50e+03 pdb=" N2 NAG C1303 " -0.488 2.00e-02 2.50e+03 pdb=" O7 NAG C1303 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 2 " -0.258 2.00e-02 2.50e+03 2.17e-01 5.87e+02 pdb=" C7 NAG b 2 " 0.069 2.00e-02 2.50e+03 pdb=" C8 NAG b 2 " -0.174 2.00e-02 2.50e+03 pdb=" N2 NAG b 2 " 0.364 2.00e-02 2.50e+03 pdb=" O7 NAG b 2 " -0.001 2.00e-02 2.50e+03 ... (remaining 5848 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3623 2.75 - 3.29: 30062 3.29 - 3.83: 53304 3.83 - 4.36: 65376 4.36 - 4.90: 113550 Nonbonded interactions: 265915 Sorted by model distance: nonbonded pdb=" OH TYR K 36 " pdb=" OE1 GLN K 89 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR J 36 " pdb=" OE1 GLN J 89 " model vdw 2.218 3.040 nonbonded pdb=" O GLY A 545 " pdb=" OG SER B 982 " model vdw 2.236 3.040 nonbonded pdb=" OG1 THR A 553 " pdb=" OD1 ASP A 586 " model vdw 2.246 3.040 ... (remaining 265910 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 364 or resid 366 through 476 or resid 478 throu \ gh 1310)) selection = (chain 'B' and (resid 14 through 364 or resid 366 through 476 or resid 478 throu \ gh 1310)) selection = (chain 'C' and (resid 14 through 364 or resid 366 through 476 or resid 478 throu \ gh 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' 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' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.33 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: 6.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.710 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 38.710 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 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 : 0.007 0.259 33530 Z= 0.472 Angle : 1.131 16.992 45823 Z= 0.742 Chirality : 0.079 0.639 5316 Planarity : 0.015 0.274 5797 Dihedral : 12.297 89.973 13142 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.34 % Allowed : 2.54 % Favored : 97.11 % Cbeta Deviations : 0.66 % 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: -0.67 (0.13), residues: 4030 helix: -0.14 (0.18), residues: 717 sheet: 0.16 (0.16), residues: 1092 loop : -0.82 (0.13), residues: 2221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 34 TYR 0.043 0.002 TYR C 495 PHE 0.031 0.002 PHE A 906 TRP 0.024 0.003 TRP B 64 HIS 0.016 0.002 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00690 (33401) covalent geometry : angle 1.10980 (45487) SS BOND : bond 0.05734 ( 51) SS BOND : angle 1.21511 ( 102) hydrogen bonds : bond 0.16450 ( 1190) hydrogen bonds : angle 7.75260 ( 3324) link_BETA1-4 : bond 0.00442 ( 24) link_BETA1-4 : angle 1.61422 ( 72) link_NAG-ASN : bond 0.00845 ( 54) link_NAG-ASN : angle 3.74325 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 354 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.6526 (mtt) cc_final: 0.6301 (mtt) REVERT: A 697 MET cc_start: 0.7600 (ttt) cc_final: 0.7262 (ttt) REVERT: A 814 LYS cc_start: 0.8266 (tptt) cc_final: 0.8033 (mmmt) REVERT: A 817 PHE cc_start: 0.7995 (t80) cc_final: 0.7708 (t80) REVERT: A 841 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.6817 (mt) REVERT: B 817 PHE cc_start: 0.7729 (t80) cc_final: 0.7404 (t80) REVERT: C 200 TYR cc_start: 0.8336 (m-80) cc_final: 0.7904 (m-80) REVERT: C 854 LYS cc_start: 0.7369 (tptt) cc_final: 0.6897 (mttm) outliers start: 12 outliers final: 3 residues processed: 359 average time/residue: 0.6062 time to fit residues: 262.7912 Evaluate side-chains 219 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 215 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1092 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 211 ASN ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 957 GLN A 960 ASN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN B 804 GLN B 856 ASN B 935 GLN B 960 ASN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 207 HIS C 211 ASN C 804 GLN C 856 ASN C 960 ASN H 76 ASN H 105 GLN L 31 GLN L 42 GLN ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 105 GLN J 31 GLN J 42 GLN I 73 ASN I 76 ASN I 105 GLN K 31 GLN K 42 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.147620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.097560 restraints weight = 77073.784| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.29 r_work: 0.3104 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33530 Z= 0.149 Angle : 0.591 9.543 45823 Z= 0.305 Chirality : 0.045 0.182 5316 Planarity : 0.005 0.087 5797 Dihedral : 5.447 53.683 6033 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.89 % Allowed : 6.95 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.13), residues: 4030 helix: 0.61 (0.19), residues: 741 sheet: 0.13 (0.16), residues: 1068 loop : -0.77 (0.13), residues: 2221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 646 TYR 0.031 0.002 TYR G 52A PHE 0.024 0.002 PHE A 906 TRP 0.017 0.002 TRP A 64 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00341 (33401) covalent geometry : angle 0.58045 (45487) SS BOND : bond 0.00361 ( 51) SS BOND : angle 0.76992 ( 102) hydrogen bonds : bond 0.04481 ( 1190) hydrogen bonds : angle 5.88331 ( 3324) link_BETA1-4 : bond 0.00489 ( 24) link_BETA1-4 : angle 1.48677 ( 72) link_NAG-ASN : bond 0.00328 ( 54) link_NAG-ASN : angle 1.68955 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 240 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.6662 (mtt) cc_final: 0.6402 (mtp) REVERT: A 258 TRP cc_start: 0.6112 (m100) cc_final: 0.4999 (t60) REVERT: A 697 MET cc_start: 0.7766 (ttt) cc_final: 0.7336 (ttt) REVERT: A 765 ARG cc_start: 0.8266 (mtp85) cc_final: 0.7979 (ttm110) REVERT: A 789 TYR cc_start: 0.7457 (m-80) cc_final: 0.7253 (m-10) REVERT: A 814 LYS cc_start: 0.8251 (tptt) cc_final: 0.8046 (tppt) REVERT: A 841 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6742 (mt) REVERT: B 96 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7611 (pt0) REVERT: B 175 PHE cc_start: 0.7769 (m-10) cc_final: 0.7568 (m-10) REVERT: B 258 TRP cc_start: 0.6184 (m100) cc_final: 0.5106 (t60) REVERT: B 789 TYR cc_start: 0.7752 (m-80) cc_final: 0.7505 (m-80) REVERT: B 814 LYS cc_start: 0.8430 (tppt) cc_final: 0.7811 (mptp) REVERT: C 96 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7211 (pm20) REVERT: C 258 TRP cc_start: 0.6019 (m100) cc_final: 0.5122 (t60) REVERT: C 551 VAL cc_start: 0.7195 (p) cc_final: 0.6938 (m) REVERT: C 789 TYR cc_start: 0.7638 (m-80) cc_final: 0.7436 (m-10) REVERT: C 817 PHE cc_start: 0.8143 (t80) cc_final: 0.7926 (t80) REVERT: C 854 LYS cc_start: 0.7567 (tptt) cc_final: 0.7027 (mttp) REVERT: H 58 HIS cc_start: 0.6110 (OUTLIER) cc_final: 0.5177 (m-70) REVERT: H 94 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.7016 (pttm) REVERT: L 95 TYR cc_start: 0.8729 (m-80) cc_final: 0.8503 (m-80) REVERT: G 46 GLU cc_start: 0.7812 (tt0) cc_final: 0.7541 (tt0) REVERT: I 38 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7062 (ttm170) REVERT: I 46 GLU cc_start: 0.8001 (tt0) cc_final: 0.7486 (pt0) REVERT: I 94 LYS cc_start: 0.7589 (tttm) cc_final: 0.7367 (tttm) REVERT: K 5 THR cc_start: 0.7891 (m) cc_final: 0.7690 (t) outliers start: 66 outliers final: 22 residues processed: 282 average time/residue: 0.5347 time to fit residues: 187.0535 Evaluate side-chains 238 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 94 LYS Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 336 optimal weight: 10.0000 chunk 30 optimal weight: 0.0070 chunk 120 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 306 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 260 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 341 optimal weight: 6.9990 chunk 388 optimal weight: 7.9990 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 487 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN I 73 ASN I 76 ASN I 82AASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.143727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.093225 restraints weight = 78636.593| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.30 r_work: 0.3036 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33530 Z= 0.184 Angle : 0.580 7.713 45823 Z= 0.299 Chirality : 0.045 0.192 5316 Planarity : 0.005 0.070 5797 Dihedral : 5.023 53.556 6025 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.86 % Allowed : 9.06 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.13), residues: 4030 helix: 0.90 (0.19), residues: 726 sheet: 0.12 (0.16), residues: 1011 loop : -0.73 (0.12), residues: 2293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 646 TYR 0.033 0.002 TYR G 52A PHE 0.030 0.002 PHE A 906 TRP 0.019 0.002 TRP B 64 HIS 0.007 0.002 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00443 (33401) covalent geometry : angle 0.57144 (45487) SS BOND : bond 0.00388 ( 51) SS BOND : angle 0.77936 ( 102) hydrogen bonds : bond 0.04132 ( 1190) hydrogen bonds : angle 5.61361 ( 3324) link_BETA1-4 : bond 0.00320 ( 24) link_BETA1-4 : angle 1.37995 ( 72) link_NAG-ASN : bond 0.00248 ( 54) link_NAG-ASN : angle 1.49778 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 217 time to evaluate : 1.142 Fit side-chains revert: symmetry clash REVERT: A 24 LEU cc_start: 0.7876 (tp) cc_final: 0.7567 (tt) REVERT: A 96 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7607 (pt0) REVERT: A 153 MET cc_start: 0.6698 (mtt) cc_final: 0.6439 (mtp) REVERT: A 258 TRP cc_start: 0.6005 (OUTLIER) cc_final: 0.5169 (t60) REVERT: A 697 MET cc_start: 0.7708 (ttt) cc_final: 0.7353 (ttt) REVERT: A 765 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7972 (ttm110) REVERT: A 789 TYR cc_start: 0.7667 (m-80) cc_final: 0.7258 (m-10) REVERT: A 814 LYS cc_start: 0.8311 (tptt) cc_final: 0.8042 (tppt) REVERT: A 841 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.6848 (mt) REVERT: B 24 LEU cc_start: 0.7683 (tp) cc_final: 0.7361 (tt) REVERT: B 96 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7497 (pt0) REVERT: B 258 TRP cc_start: 0.6124 (m100) cc_final: 0.5115 (t60) REVERT: B 814 LYS cc_start: 0.8367 (tppt) cc_final: 0.7748 (mptp) REVERT: B 855 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7253 (m-10) REVERT: C 96 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7911 (pt0) REVERT: C 153 MET cc_start: 0.5856 (mtm) cc_final: 0.5579 (mtm) REVERT: C 258 TRP cc_start: 0.6007 (OUTLIER) cc_final: 0.5110 (t60) REVERT: C 532 ASN cc_start: 0.7457 (OUTLIER) cc_final: 0.7251 (p0) REVERT: C 789 TYR cc_start: 0.7877 (m-80) cc_final: 0.7606 (m-10) REVERT: C 814 LYS cc_start: 0.8313 (tppt) cc_final: 0.7775 (mptp) REVERT: C 841 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7385 (pt) REVERT: C 854 LYS cc_start: 0.7625 (tptt) cc_final: 0.7018 (mttp) REVERT: C 904 TYR cc_start: 0.6842 (m-80) cc_final: 0.6148 (t80) REVERT: H 32 TYR cc_start: 0.7952 (m-80) cc_final: 0.7608 (m-80) REVERT: H 58 HIS cc_start: 0.6336 (OUTLIER) cc_final: 0.5184 (m-70) REVERT: H 82 MET cc_start: 0.7478 (ttp) cc_final: 0.7168 (tpp) REVERT: G 46 GLU cc_start: 0.7849 (tt0) cc_final: 0.7450 (tt0) REVERT: J 32 TYR cc_start: 0.8076 (m-10) cc_final: 0.7792 (m-10) REVERT: I 58 HIS cc_start: 0.6430 (OUTLIER) cc_final: 0.6095 (m90) REVERT: I 94 LYS cc_start: 0.7678 (tttm) cc_final: 0.7437 (tttm) REVERT: K 5 THR cc_start: 0.7958 (m) cc_final: 0.7731 (t) outliers start: 65 outliers final: 25 residues processed: 257 average time/residue: 0.5621 time to fit residues: 177.4984 Evaluate side-chains 239 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain G residue 58 HIS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 244 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 197 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 224 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 GLN A 856 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 804 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN I 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.143196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.093320 restraints weight = 67235.376| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.11 r_work: 0.3043 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33530 Z= 0.175 Angle : 0.562 8.320 45823 Z= 0.288 Chirality : 0.045 0.194 5316 Planarity : 0.004 0.061 5797 Dihedral : 4.911 53.491 6025 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.83 % Allowed : 10.15 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.13), residues: 4030 helix: 1.04 (0.20), residues: 714 sheet: 0.08 (0.16), residues: 1044 loop : -0.70 (0.12), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 646 TYR 0.032 0.002 TYR G 52A PHE 0.024 0.002 PHE B 906 TRP 0.016 0.002 TRP H 103 HIS 0.008 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00422 (33401) covalent geometry : angle 0.55304 (45487) SS BOND : bond 0.00390 ( 51) SS BOND : angle 0.73814 ( 102) hydrogen bonds : bond 0.03899 ( 1190) hydrogen bonds : angle 5.49290 ( 3324) link_BETA1-4 : bond 0.00317 ( 24) link_BETA1-4 : angle 1.31896 ( 72) link_NAG-ASN : bond 0.00223 ( 54) link_NAG-ASN : angle 1.49617 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 205 time to evaluate : 1.196 Fit side-chains revert: symmetry clash REVERT: A 24 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7636 (tt) REVERT: A 96 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7629 (pt0) REVERT: A 153 MET cc_start: 0.6715 (mtt) cc_final: 0.6462 (mtp) REVERT: A 697 MET cc_start: 0.7729 (ttt) cc_final: 0.7394 (ttt) REVERT: A 789 TYR cc_start: 0.7602 (m-80) cc_final: 0.7237 (m-10) REVERT: A 814 LYS cc_start: 0.8348 (tptt) cc_final: 0.7940 (tppt) REVERT: B 24 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7338 (tt) REVERT: B 96 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7495 (pt0) REVERT: B 258 TRP cc_start: 0.6158 (m100) cc_final: 0.4982 (t60) REVERT: B 814 LYS cc_start: 0.8316 (tppt) cc_final: 0.7690 (mptp) REVERT: B 823 PHE cc_start: 0.8207 (m-10) cc_final: 0.7896 (m-80) REVERT: B 841 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7213 (pt) REVERT: B 855 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.7289 (m-10) REVERT: B 1029 MET cc_start: 0.9059 (tpp) cc_final: 0.8859 (ttm) REVERT: C 69 HIS cc_start: 0.6744 (OUTLIER) cc_final: 0.6511 (t-170) REVERT: C 258 TRP cc_start: 0.6025 (OUTLIER) cc_final: 0.5133 (t60) REVERT: C 532 ASN cc_start: 0.7498 (OUTLIER) cc_final: 0.7272 (p0) REVERT: C 789 TYR cc_start: 0.7903 (m-80) cc_final: 0.7683 (m-10) REVERT: C 841 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7400 (pt) REVERT: C 854 LYS cc_start: 0.7707 (tptt) cc_final: 0.7114 (mttp) REVERT: C 904 TYR cc_start: 0.6810 (m-80) cc_final: 0.6111 (t80) REVERT: C 1072 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7977 (mp0) REVERT: H 58 HIS cc_start: 0.6406 (OUTLIER) cc_final: 0.5136 (m-70) REVERT: H 82 MET cc_start: 0.7591 (ttp) cc_final: 0.7262 (tpp) REVERT: L 95 TYR cc_start: 0.8778 (m-80) cc_final: 0.8485 (m-80) REVERT: G 46 GLU cc_start: 0.7868 (tt0) cc_final: 0.7604 (tt0) REVERT: G 82 MET cc_start: 0.7281 (ttp) cc_final: 0.7027 (tpp) REVERT: G 94 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7464 (pttp) REVERT: I 58 HIS cc_start: 0.6458 (OUTLIER) cc_final: 0.6093 (m90) REVERT: I 82 MET cc_start: 0.6451 (OUTLIER) cc_final: 0.5831 (ptm) REVERT: K 5 THR cc_start: 0.7993 (m) cc_final: 0.7739 (t) REVERT: K 35 TRP cc_start: 0.6937 (m100) cc_final: 0.6641 (m100) outliers start: 64 outliers final: 33 residues processed: 245 average time/residue: 0.5673 time to fit residues: 170.5618 Evaluate side-chains 251 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 203 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain G residue 58 HIS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 191 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 339 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 333 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 392 optimal weight: 6.9990 chunk 291 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN G 76 ASN I 82AASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.142833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.091958 restraints weight = 84534.825| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.64 r_work: 0.3003 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33530 Z= 0.170 Angle : 0.550 9.230 45823 Z= 0.281 Chirality : 0.045 0.192 5316 Planarity : 0.004 0.055 5797 Dihedral : 4.843 53.452 6023 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.77 % Allowed : 10.78 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.13), residues: 4030 helix: 1.10 (0.20), residues: 714 sheet: -0.01 (0.15), residues: 1077 loop : -0.65 (0.13), residues: 2239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 646 TYR 0.036 0.002 TYR G 52A PHE 0.023 0.002 PHE C 759 TRP 0.017 0.002 TRP H 103 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00411 (33401) covalent geometry : angle 0.54155 (45487) SS BOND : bond 0.00364 ( 51) SS BOND : angle 0.69391 ( 102) hydrogen bonds : bond 0.03842 ( 1190) hydrogen bonds : angle 5.40541 ( 3324) link_BETA1-4 : bond 0.00341 ( 24) link_BETA1-4 : angle 1.29655 ( 72) link_NAG-ASN : bond 0.00201 ( 54) link_NAG-ASN : angle 1.44385 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 215 time to evaluate : 1.222 Fit side-chains revert: symmetry clash REVERT: A 24 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7604 (tt) REVERT: A 96 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7779 (pt0) REVERT: A 153 MET cc_start: 0.6759 (mtt) cc_final: 0.6423 (mtp) REVERT: A 697 MET cc_start: 0.7757 (ttt) cc_final: 0.7428 (ttt) REVERT: A 789 TYR cc_start: 0.7599 (m-80) cc_final: 0.7318 (m-10) REVERT: A 814 LYS cc_start: 0.8442 (tptt) cc_final: 0.7986 (tppt) REVERT: B 24 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7441 (tt) REVERT: B 96 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7640 (pt0) REVERT: B 814 LYS cc_start: 0.8230 (tppt) cc_final: 0.7986 (tptm) REVERT: B 823 PHE cc_start: 0.8246 (m-10) cc_final: 0.7950 (m-80) REVERT: B 841 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7383 (pt) REVERT: B 855 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7376 (m-10) REVERT: C 69 HIS cc_start: 0.6838 (OUTLIER) cc_final: 0.6558 (t-170) REVERT: C 96 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7159 (pm20) REVERT: C 258 TRP cc_start: 0.5937 (m100) cc_final: 0.5095 (t60) REVERT: C 532 ASN cc_start: 0.7523 (OUTLIER) cc_final: 0.7289 (p0) REVERT: C 789 TYR cc_start: 0.7929 (m-80) cc_final: 0.7703 (m-10) REVERT: C 841 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7306 (pt) REVERT: C 854 LYS cc_start: 0.7843 (tptt) cc_final: 0.7187 (mttp) REVERT: C 904 TYR cc_start: 0.6873 (m-80) cc_final: 0.6125 (t80) REVERT: H 32 TYR cc_start: 0.7841 (m-80) cc_final: 0.7633 (m-80) REVERT: H 34 MET cc_start: 0.7334 (mtp) cc_final: 0.6994 (tpp) REVERT: H 46 GLU cc_start: 0.7823 (tt0) cc_final: 0.7607 (pt0) REVERT: H 58 HIS cc_start: 0.6318 (OUTLIER) cc_final: 0.5011 (m-70) REVERT: H 82 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.7100 (tpp) REVERT: H 94 LYS cc_start: 0.7573 (pttp) cc_final: 0.7310 (pptt) REVERT: L 95 TYR cc_start: 0.8792 (m-80) cc_final: 0.8510 (m-80) REVERT: G 46 GLU cc_start: 0.7870 (tt0) cc_final: 0.7604 (tt0) REVERT: G 94 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7470 (pttp) REVERT: I 46 GLU cc_start: 0.7717 (tt0) cc_final: 0.7451 (pt0) REVERT: I 58 HIS cc_start: 0.6395 (OUTLIER) cc_final: 0.6067 (m90) REVERT: I 82 MET cc_start: 0.6486 (OUTLIER) cc_final: 0.5797 (ptm) REVERT: K 5 THR cc_start: 0.8019 (m) cc_final: 0.7760 (t) REVERT: K 35 TRP cc_start: 0.7022 (m100) cc_final: 0.6706 (m100) outliers start: 62 outliers final: 36 residues processed: 258 average time/residue: 0.5575 time to fit residues: 176.3488 Evaluate side-chains 253 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 202 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain G residue 58 HIS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 124 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 293 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 339 optimal weight: 5.9990 chunk 219 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 357 optimal weight: 0.0980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 935 GLN C 207 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 76 ASN G 76 ASN I 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.143670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.092831 restraints weight = 87536.356| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.48 r_work: 0.3025 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33530 Z= 0.133 Angle : 0.527 9.092 45823 Z= 0.269 Chirality : 0.044 0.196 5316 Planarity : 0.004 0.053 5797 Dihedral : 4.798 52.994 6023 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.94 % Allowed : 10.95 % Favored : 87.11 % 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 (0.13), residues: 4030 helix: 1.16 (0.20), residues: 729 sheet: 0.05 (0.16), residues: 1044 loop : -0.64 (0.13), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 646 TYR 0.037 0.001 TYR G 52A PHE 0.021 0.001 PHE A 759 TRP 0.018 0.002 TRP L 35 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00315 (33401) covalent geometry : angle 0.51911 (45487) SS BOND : bond 0.00315 ( 51) SS BOND : angle 0.64671 ( 102) hydrogen bonds : bond 0.03631 ( 1190) hydrogen bonds : angle 5.27981 ( 3324) link_BETA1-4 : bond 0.00328 ( 24) link_BETA1-4 : angle 1.25022 ( 72) link_NAG-ASN : bond 0.00166 ( 54) link_NAG-ASN : angle 1.35338 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 215 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: A 24 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7699 (tt) REVERT: A 150 LYS cc_start: 0.8034 (mptt) cc_final: 0.7674 (mppt) REVERT: A 153 MET cc_start: 0.6680 (mtt) cc_final: 0.6363 (mtp) REVERT: A 697 MET cc_start: 0.7756 (ttt) cc_final: 0.7435 (ttt) REVERT: A 740 MET cc_start: 0.8996 (ttp) cc_final: 0.8613 (tpp) REVERT: A 765 ARG cc_start: 0.8256 (mtp85) cc_final: 0.7984 (ttm110) REVERT: A 789 TYR cc_start: 0.7494 (m-80) cc_final: 0.7210 (m-10) REVERT: A 814 LYS cc_start: 0.8466 (tptt) cc_final: 0.7977 (tppt) REVERT: A 843 ASP cc_start: 0.5962 (OUTLIER) cc_final: 0.5584 (p0) REVERT: B 24 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7399 (tt) REVERT: B 96 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7624 (pt0) REVERT: B 281 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8373 (pm20) REVERT: B 814 LYS cc_start: 0.8211 (tppt) cc_final: 0.7948 (tptm) REVERT: B 823 PHE cc_start: 0.8252 (m-10) cc_final: 0.7965 (m-80) REVERT: B 841 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7321 (pt) REVERT: B 855 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7248 (m-10) REVERT: C 258 TRP cc_start: 0.5928 (m100) cc_final: 0.5078 (t60) REVERT: C 532 ASN cc_start: 0.7512 (OUTLIER) cc_final: 0.7274 (p0) REVERT: C 814 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7222 (tmtm) REVERT: C 841 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7245 (pt) REVERT: C 854 LYS cc_start: 0.7886 (tptt) cc_final: 0.7201 (mttp) REVERT: C 1072 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: H 82 MET cc_start: 0.7625 (ttp) cc_final: 0.7188 (tpp) REVERT: G 46 GLU cc_start: 0.7880 (tt0) cc_final: 0.7640 (tt0) REVERT: J 35 TRP cc_start: 0.6961 (m100) cc_final: 0.6692 (m100) REVERT: I 46 GLU cc_start: 0.7703 (tt0) cc_final: 0.7394 (pt0) REVERT: I 58 HIS cc_start: 0.6498 (OUTLIER) cc_final: 0.6090 (m90) REVERT: I 82 MET cc_start: 0.6494 (OUTLIER) cc_final: 0.5792 (ptm) REVERT: K 5 THR cc_start: 0.7909 (m) cc_final: 0.7656 (t) REVERT: K 35 TRP cc_start: 0.7002 (m100) cc_final: 0.6679 (m100) REVERT: K 95 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.8117 (t) outliers start: 68 outliers final: 36 residues processed: 261 average time/residue: 0.5622 time to fit residues: 179.9518 Evaluate side-chains 257 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 207 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain G residue 58 HIS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 83 optimal weight: 0.8980 chunk 178 optimal weight: 0.9990 chunk 290 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 226 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN G 76 ASN J 31 GLN I 73 ASN I 82AASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.143509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.093046 restraints weight = 82203.833| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.60 r_work: 0.3017 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33530 Z= 0.134 Angle : 0.525 9.093 45823 Z= 0.268 Chirality : 0.044 0.195 5316 Planarity : 0.004 0.051 5797 Dihedral : 4.790 54.560 6023 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.06 % Allowed : 11.55 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.13), residues: 4030 helix: 1.20 (0.20), residues: 729 sheet: 0.06 (0.16), residues: 1044 loop : -0.63 (0.13), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 646 TYR 0.035 0.001 TYR H 52A PHE 0.025 0.001 PHE C 759 TRP 0.018 0.002 TRP K 96 HIS 0.007 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00319 (33401) covalent geometry : angle 0.51791 (45487) SS BOND : bond 0.00295 ( 51) SS BOND : angle 0.63504 ( 102) hydrogen bonds : bond 0.03613 ( 1190) hydrogen bonds : angle 5.24679 ( 3324) link_BETA1-4 : bond 0.00323 ( 24) link_BETA1-4 : angle 1.24355 ( 72) link_NAG-ASN : bond 0.00161 ( 54) link_NAG-ASN : angle 1.33110 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 211 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: A 69 HIS cc_start: 0.6668 (OUTLIER) cc_final: 0.5334 (t-170) REVERT: A 96 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7749 (pt0) REVERT: A 150 LYS cc_start: 0.8069 (mptt) cc_final: 0.7706 (mppt) REVERT: A 153 MET cc_start: 0.6719 (mtt) cc_final: 0.6389 (mtp) REVERT: A 697 MET cc_start: 0.7796 (ttt) cc_final: 0.7470 (ttt) REVERT: A 740 MET cc_start: 0.8998 (ttp) cc_final: 0.8601 (tpp) REVERT: A 765 ARG cc_start: 0.8259 (mtp85) cc_final: 0.7988 (ttm110) REVERT: A 789 TYR cc_start: 0.7439 (m-80) cc_final: 0.7160 (m-10) REVERT: A 814 LYS cc_start: 0.8473 (tptt) cc_final: 0.7958 (tppt) REVERT: A 843 ASP cc_start: 0.5990 (OUTLIER) cc_final: 0.5607 (p0) REVERT: B 24 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7351 (tt) REVERT: B 96 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7607 (pt0) REVERT: B 814 LYS cc_start: 0.8200 (tppt) cc_final: 0.7688 (mptp) REVERT: B 823 PHE cc_start: 0.8273 (m-10) cc_final: 0.7996 (m-80) REVERT: B 841 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7351 (pt) REVERT: B 855 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.7278 (m-10) REVERT: C 69 HIS cc_start: 0.6791 (OUTLIER) cc_final: 0.6547 (t-170) REVERT: C 96 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7023 (pm20) REVERT: C 258 TRP cc_start: 0.5943 (m100) cc_final: 0.5128 (t60) REVERT: C 340 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8070 (tp30) REVERT: C 532 ASN cc_start: 0.7568 (OUTLIER) cc_final: 0.7348 (p0) REVERT: C 814 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7206 (tmtm) REVERT: C 841 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7250 (pt) REVERT: C 854 LYS cc_start: 0.7911 (tptt) cc_final: 0.7220 (mttp) REVERT: C 1072 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: H 46 GLU cc_start: 0.7646 (pt0) cc_final: 0.7425 (pt0) REVERT: H 58 HIS cc_start: 0.6270 (OUTLIER) cc_final: 0.4916 (m-70) REVERT: H 82 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7149 (tpp) REVERT: H 94 LYS cc_start: 0.8077 (pptt) cc_final: 0.7589 (pptt) REVERT: G 46 GLU cc_start: 0.7842 (tt0) cc_final: 0.7601 (tt0) REVERT: J 35 TRP cc_start: 0.6889 (m100) cc_final: 0.6630 (m100) REVERT: I 46 GLU cc_start: 0.7724 (tt0) cc_final: 0.7489 (pt0) REVERT: I 58 HIS cc_start: 0.6493 (OUTLIER) cc_final: 0.6120 (m90) REVERT: I 71 ARG cc_start: 0.7520 (ptm160) cc_final: 0.7284 (ptm160) REVERT: I 82 MET cc_start: 0.6535 (OUTLIER) cc_final: 0.5849 (ptm) REVERT: K 35 TRP cc_start: 0.7046 (m100) cc_final: 0.6744 (m100) REVERT: K 95 THR cc_start: 0.8310 (OUTLIER) cc_final: 0.8085 (t) outliers start: 72 outliers final: 37 residues processed: 264 average time/residue: 0.5802 time to fit residues: 187.4210 Evaluate side-chains 260 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 205 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain G residue 58 HIS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 143 optimal weight: 0.6980 chunk 323 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 290 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 300 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 328 optimal weight: 0.5980 chunk 232 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 76 ASN G 39 GLN G 76 ASN J 31 GLN I 39 GLN K 31 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.143740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.093867 restraints weight = 74142.205| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.22 r_work: 0.3046 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33530 Z= 0.128 Angle : 0.522 9.128 45823 Z= 0.266 Chirality : 0.043 0.195 5316 Planarity : 0.004 0.049 5797 Dihedral : 4.732 52.915 6023 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.97 % Allowed : 12.04 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.13), residues: 4030 helix: 1.23 (0.20), residues: 729 sheet: 0.07 (0.16), residues: 1044 loop : -0.61 (0.13), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 38 TYR 0.038 0.001 TYR H 52A PHE 0.022 0.001 PHE A 759 TRP 0.020 0.002 TRP K 96 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00304 (33401) covalent geometry : angle 0.51510 (45487) SS BOND : bond 0.00275 ( 51) SS BOND : angle 0.61521 ( 102) hydrogen bonds : bond 0.03568 ( 1190) hydrogen bonds : angle 5.18556 ( 3324) link_BETA1-4 : bond 0.00329 ( 24) link_BETA1-4 : angle 1.22300 ( 72) link_NAG-ASN : bond 0.00153 ( 54) link_NAG-ASN : angle 1.30380 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 211 time to evaluate : 1.247 Fit side-chains revert: symmetry clash REVERT: A 69 HIS cc_start: 0.6522 (OUTLIER) cc_final: 0.5244 (t-170) REVERT: A 150 LYS cc_start: 0.8025 (mptt) cc_final: 0.7677 (mppt) REVERT: A 153 MET cc_start: 0.6706 (mtt) cc_final: 0.6386 (mtp) REVERT: A 697 MET cc_start: 0.7782 (ttt) cc_final: 0.7461 (ttt) REVERT: A 740 MET cc_start: 0.8996 (ttp) cc_final: 0.8594 (tpp) REVERT: A 765 ARG cc_start: 0.8221 (mtp85) cc_final: 0.7976 (ttm110) REVERT: A 789 TYR cc_start: 0.7408 (m-80) cc_final: 0.7119 (m-10) REVERT: A 814 LYS cc_start: 0.8440 (tptt) cc_final: 0.7916 (tppt) REVERT: A 843 ASP cc_start: 0.6009 (OUTLIER) cc_final: 0.5618 (p0) REVERT: B 24 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7318 (tt) REVERT: B 96 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7607 (pt0) REVERT: B 741 TYR cc_start: 0.9112 (t80) cc_final: 0.8875 (t80) REVERT: B 814 LYS cc_start: 0.8206 (tppt) cc_final: 0.7686 (mptp) REVERT: B 823 PHE cc_start: 0.8257 (m-10) cc_final: 0.7996 (m-80) REVERT: B 841 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7338 (pt) REVERT: B 855 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7261 (m-10) REVERT: C 69 HIS cc_start: 0.6786 (OUTLIER) cc_final: 0.6470 (t-170) REVERT: C 96 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7027 (pm20) REVERT: C 258 TRP cc_start: 0.5918 (m100) cc_final: 0.5117 (t60) REVERT: C 340 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8038 (tp30) REVERT: C 532 ASN cc_start: 0.7523 (OUTLIER) cc_final: 0.7299 (p0) REVERT: C 814 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7160 (tmtm) REVERT: C 841 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7245 (pt) REVERT: C 854 LYS cc_start: 0.7930 (tptt) cc_final: 0.7236 (mttp) REVERT: C 1072 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8072 (mp0) REVERT: H 46 GLU cc_start: 0.7949 (pt0) cc_final: 0.7745 (pt0) REVERT: H 58 HIS cc_start: 0.6341 (OUTLIER) cc_final: 0.4980 (m-70) REVERT: H 82 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7224 (tpp) REVERT: H 94 LYS cc_start: 0.8057 (pptt) cc_final: 0.7663 (pptt) REVERT: H 100 PHE cc_start: 0.5630 (OUTLIER) cc_final: 0.5376 (m-80) REVERT: J 35 TRP cc_start: 0.6852 (m100) cc_final: 0.6563 (m100) REVERT: J 49 TYR cc_start: 0.7583 (p90) cc_final: 0.7367 (p90) REVERT: I 38 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7074 (ttm170) REVERT: I 58 HIS cc_start: 0.6534 (OUTLIER) cc_final: 0.6159 (m90) REVERT: I 94 LYS cc_start: 0.7599 (pttp) cc_final: 0.7353 (pptt) REVERT: K 35 TRP cc_start: 0.6983 (m100) cc_final: 0.6718 (m100) outliers start: 69 outliers final: 42 residues processed: 260 average time/residue: 0.5700 time to fit residues: 181.5969 Evaluate side-chains 266 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 207 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain G residue 58 HIS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 366 optimal weight: 7.9990 chunk 369 optimal weight: 0.2980 chunk 353 optimal weight: 7.9990 chunk 236 optimal weight: 0.2980 chunk 180 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 305 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 225 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C1083 HIS C1106 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN G 76 ASN J 31 GLN I 39 GLN I 82AASN K 31 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.144210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.094307 restraints weight = 65392.255| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.24 r_work: 0.3095 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33530 Z= 0.108 Angle : 0.508 9.118 45823 Z= 0.260 Chirality : 0.043 0.196 5316 Planarity : 0.004 0.050 5797 Dihedral : 4.639 52.452 6023 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.80 % Allowed : 12.49 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.13), residues: 4030 helix: 1.30 (0.20), residues: 729 sheet: 0.10 (0.16), residues: 1050 loop : -0.62 (0.13), residues: 2251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 646 TYR 0.042 0.001 TYR H 52A PHE 0.017 0.001 PHE B 759 TRP 0.034 0.002 TRP K 96 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00252 (33401) covalent geometry : angle 0.50199 (45487) SS BOND : bond 0.00238 ( 51) SS BOND : angle 0.56078 ( 102) hydrogen bonds : bond 0.03409 ( 1190) hydrogen bonds : angle 5.08555 ( 3324) link_BETA1-4 : bond 0.00337 ( 24) link_BETA1-4 : angle 1.19746 ( 72) link_NAG-ASN : bond 0.00149 ( 54) link_NAG-ASN : angle 1.23524 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 218 time to evaluate : 1.217 Fit side-chains revert: symmetry clash REVERT: A 69 HIS cc_start: 0.6323 (OUTLIER) cc_final: 0.5128 (t-170) REVERT: A 99 ASN cc_start: 0.8282 (m110) cc_final: 0.7794 (m-40) REVERT: A 150 LYS cc_start: 0.7991 (mptt) cc_final: 0.7692 (mppt) REVERT: A 153 MET cc_start: 0.6621 (mtt) cc_final: 0.6306 (mtp) REVERT: A 697 MET cc_start: 0.7637 (ttt) cc_final: 0.7311 (ttt) REVERT: A 740 MET cc_start: 0.8931 (ttp) cc_final: 0.8536 (tpp) REVERT: A 765 ARG cc_start: 0.8147 (mtp85) cc_final: 0.7889 (ttm110) REVERT: A 789 TYR cc_start: 0.7214 (m-80) cc_final: 0.6730 (m-10) REVERT: A 814 LYS cc_start: 0.8471 (tptt) cc_final: 0.7919 (tppt) REVERT: A 843 ASP cc_start: 0.5928 (OUTLIER) cc_final: 0.5526 (p0) REVERT: B 24 LEU cc_start: 0.7703 (tp) cc_final: 0.7419 (tt) REVERT: B 96 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7593 (pt0) REVERT: B 220 PHE cc_start: 0.8803 (t80) cc_final: 0.8343 (t80) REVERT: B 814 LYS cc_start: 0.8177 (tppt) cc_final: 0.7602 (mptp) REVERT: B 817 PHE cc_start: 0.8217 (t80) cc_final: 0.7961 (t80) REVERT: B 823 PHE cc_start: 0.8252 (m-10) cc_final: 0.8009 (m-80) REVERT: B 841 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7203 (pt) REVERT: B 855 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7174 (m-10) REVERT: C 69 HIS cc_start: 0.6718 (OUTLIER) cc_final: 0.6395 (t-170) REVERT: C 258 TRP cc_start: 0.5921 (m100) cc_final: 0.5073 (t60) REVERT: C 340 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7957 (tp30) REVERT: C 532 ASN cc_start: 0.7514 (OUTLIER) cc_final: 0.7296 (p0) REVERT: C 740 MET cc_start: 0.9167 (mmm) cc_final: 0.8960 (tpp) REVERT: C 814 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7124 (tmtm) REVERT: C 841 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7180 (pt) REVERT: C 854 LYS cc_start: 0.7905 (tptt) cc_final: 0.7200 (mttp) REVERT: C 1072 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: H 58 HIS cc_start: 0.6241 (OUTLIER) cc_final: 0.4840 (m-70) REVERT: H 82 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7408 (tpp) REVERT: H 94 LYS cc_start: 0.7950 (pptt) cc_final: 0.7427 (pptt) REVERT: H 100 PHE cc_start: 0.5445 (OUTLIER) cc_final: 0.5181 (m-80) REVERT: G 94 LYS cc_start: 0.7594 (pttp) cc_final: 0.7091 (pptt) REVERT: J 35 TRP cc_start: 0.6780 (m100) cc_final: 0.6522 (m100) REVERT: J 49 TYR cc_start: 0.7393 (p90) cc_final: 0.7173 (p90) REVERT: I 58 HIS cc_start: 0.6429 (OUTLIER) cc_final: 0.6101 (m90) REVERT: I 71 ARG cc_start: 0.7431 (ptm160) cc_final: 0.7163 (ptm160) REVERT: I 79 TYR cc_start: 0.7083 (m-80) cc_final: 0.6825 (m-10) REVERT: K 35 TRP cc_start: 0.6839 (m100) cc_final: 0.6556 (m100) REVERT: K 95 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.8003 (t) outliers start: 63 outliers final: 37 residues processed: 263 average time/residue: 0.5668 time to fit residues: 182.6422 Evaluate side-chains 263 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 211 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain G residue 58 HIS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 157 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 150 optimal weight: 0.0770 chunk 178 optimal weight: 0.4980 chunk 9 optimal weight: 0.0060 chunk 387 optimal weight: 0.0370 chunk 318 optimal weight: 0.8980 chunk 276 optimal weight: 3.9990 chunk 246 optimal weight: 8.9990 chunk 213 optimal weight: 0.8980 chunk 271 optimal weight: 0.6980 overall best weight: 0.2632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1083 HIS B1119 ASN C 625 HIS C1002 GLN C1106 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 76 ASN G 76 ASN J 31 GLN K 31 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.145194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.094292 restraints weight = 81474.185| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.59 r_work: 0.3087 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 33530 Z= 0.094 Angle : 0.500 12.631 45823 Z= 0.256 Chirality : 0.043 0.195 5316 Planarity : 0.004 0.048 5797 Dihedral : 4.549 52.666 6023 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.46 % Allowed : 12.98 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.13), residues: 4030 helix: 1.37 (0.20), residues: 732 sheet: 0.21 (0.16), residues: 1044 loop : -0.61 (0.13), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 646 TYR 0.032 0.001 TYR H 52A PHE 0.013 0.001 PHE G 67 TRP 0.024 0.001 TRP K 96 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00212 (33401) covalent geometry : angle 0.49446 (45487) SS BOND : bond 0.00200 ( 51) SS BOND : angle 0.52915 ( 102) hydrogen bonds : bond 0.03287 ( 1190) hydrogen bonds : angle 4.99200 ( 3324) link_BETA1-4 : bond 0.00351 ( 24) link_BETA1-4 : angle 1.18357 ( 72) link_NAG-ASN : bond 0.00156 ( 54) link_NAG-ASN : angle 1.18052 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8060 Ramachandran restraints generated. 4030 Oldfield, 0 Emsley, 4030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 220 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 HIS cc_start: 0.6303 (OUTLIER) cc_final: 0.5127 (t-170) REVERT: A 99 ASN cc_start: 0.8237 (m110) cc_final: 0.7748 (m-40) REVERT: A 150 LYS cc_start: 0.8009 (mptt) cc_final: 0.7671 (mppt) REVERT: A 153 MET cc_start: 0.6643 (mtt) cc_final: 0.6303 (mtp) REVERT: A 697 MET cc_start: 0.7664 (ttt) cc_final: 0.7319 (ttt) REVERT: A 740 MET cc_start: 0.8955 (ttp) cc_final: 0.8634 (tpp) REVERT: A 765 ARG cc_start: 0.8164 (mtp85) cc_final: 0.7913 (ttm110) REVERT: A 814 LYS cc_start: 0.8493 (tptt) cc_final: 0.7934 (tppt) REVERT: A 843 ASP cc_start: 0.5917 (OUTLIER) cc_final: 0.5534 (p0) REVERT: B 220 PHE cc_start: 0.8780 (t80) cc_final: 0.8331 (t80) REVERT: B 551 VAL cc_start: 0.7469 (OUTLIER) cc_final: 0.7186 (m) REVERT: B 814 LYS cc_start: 0.8163 (tppt) cc_final: 0.7594 (mptp) REVERT: B 817 PHE cc_start: 0.8204 (t80) cc_final: 0.7934 (t80) REVERT: B 823 PHE cc_start: 0.8222 (m-10) cc_final: 0.7967 (m-80) REVERT: B 841 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7427 (pt) REVERT: C 258 TRP cc_start: 0.5735 (m100) cc_final: 0.4904 (t60) REVERT: C 340 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7904 (tp30) REVERT: C 532 ASN cc_start: 0.7503 (OUTLIER) cc_final: 0.7293 (p0) REVERT: C 740 MET cc_start: 0.9187 (mmm) cc_final: 0.8981 (tpp) REVERT: C 759 PHE cc_start: 0.8429 (t80) cc_final: 0.8158 (t80) REVERT: C 814 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7056 (tmtm) REVERT: C 1072 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: H 38 ARG cc_start: 0.7938 (tmm160) cc_final: 0.7602 (tmm160) REVERT: H 58 HIS cc_start: 0.6230 (OUTLIER) cc_final: 0.4842 (m-70) REVERT: H 82 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7365 (tpp) REVERT: H 94 LYS cc_start: 0.7914 (pptt) cc_final: 0.7492 (pptt) REVERT: G 94 LYS cc_start: 0.7661 (pttp) cc_final: 0.7147 (pptt) REVERT: J 49 TYR cc_start: 0.7356 (p90) cc_final: 0.7144 (p90) REVERT: I 58 HIS cc_start: 0.6428 (OUTLIER) cc_final: 0.6101 (m90) REVERT: I 71 ARG cc_start: 0.7398 (ptm160) cc_final: 0.7148 (ptm160) REVERT: I 79 TYR cc_start: 0.7117 (m-80) cc_final: 0.6819 (m-10) REVERT: I 82 MET cc_start: 0.6495 (OUTLIER) cc_final: 0.5801 (ptm) REVERT: K 35 TRP cc_start: 0.6751 (m100) cc_final: 0.6494 (m100) REVERT: K 95 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7953 (t) outliers start: 51 outliers final: 29 residues processed: 258 average time/residue: 0.5606 time to fit residues: 177.1692 Evaluate side-chains 256 residues out of total 3486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 215 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain I residue 58 HIS Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 336 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 135 optimal weight: 6.9990 chunk 360 optimal weight: 4.9990 chunk 179 optimal weight: 0.8980 chunk 240 optimal weight: 1.9990 chunk 282 optimal weight: 0.7980 chunk 206 optimal weight: 0.9990 chunk 183 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 235 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82AASN G 76 ASN J 31 GLN I 82AASN K 31 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.143791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.093026 restraints weight = 77244.795| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.50 r_work: 0.3068 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33530 Z= 0.138 Angle : 0.522 11.475 45823 Z= 0.265 Chirality : 0.043 0.190 5316 Planarity : 0.004 0.058 5797 Dihedral : 4.573 52.692 6023 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.37 % Allowed : 13.21 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.13), residues: 4030 helix: 1.30 (0.20), residues: 732 sheet: 0.20 (0.16), residues: 1068 loop : -0.61 (0.13), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 646 TYR 0.037 0.001 TYR H 52A PHE 0.018 0.001 PHE B 759 TRP 0.023 0.001 TRP K 96 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00332 (33401) covalent geometry : angle 0.51526 (45487) SS BOND : bond 0.00276 ( 51) SS BOND : angle 0.58002 ( 102) hydrogen bonds : bond 0.03466 ( 1190) hydrogen bonds : angle 5.05145 ( 3324) link_BETA1-4 : bond 0.00343 ( 24) link_BETA1-4 : angle 1.20321 ( 72) link_NAG-ASN : bond 0.00144 ( 54) link_NAG-ASN : angle 1.25483 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11553.39 seconds wall clock time: 197 minutes 10.20 seconds (11830.20 seconds total)