Starting phenix.real_space_refine on Mon Mar 25 06:13:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5q_0141/03_2024/6h5q_0141.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5q_0141/03_2024/6h5q_0141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5q_0141/03_2024/6h5q_0141.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5q_0141/03_2024/6h5q_0141.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5q_0141/03_2024/6h5q_0141.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5q_0141/03_2024/6h5q_0141.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 ------------------------------------------------------------------------------- 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= 0.005 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: 5 Type Number sf(0) Gaussians P 75 5.49 5 S 180 5.16 5 C 29370 2.51 5 N 8115 2.21 5 O 8910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 42": "OD1" <-> "OD2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B ARG 194": "NH1" <-> "NH2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B ARG 204": "NH1" <-> "NH2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B ARG 222": "NH1" <-> "NH2" Residue "B ARG 230": "NH1" <-> "NH2" Residue "B ARG 370": "NH1" <-> "NH2" Residue "A ASP 42": "OD1" <-> "OD2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A ARG 194": "NH1" <-> "NH2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 204": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "D ASP 42": "OD1" <-> "OD2" Residue "D ARG 48": "NH1" <-> "NH2" Residue "D ARG 54": "NH1" <-> "NH2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "D ARG 194": "NH1" <-> "NH2" Residue "D ARG 195": "NH1" <-> "NH2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "D ARG 204": "NH1" <-> "NH2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "D ARG 222": "NH1" <-> "NH2" Residue "D ARG 230": "NH1" <-> "NH2" Residue "D ARG 370": "NH1" <-> "NH2" Residue "F ASP 42": "OD1" <-> "OD2" Residue "F ARG 48": "NH1" <-> "NH2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F ARG 57": "NH1" <-> "NH2" Residue "F ARG 100": "NH1" <-> "NH2" Residue "F ARG 194": "NH1" <-> "NH2" Residue "F ARG 195": "NH1" <-> "NH2" Residue "F ARG 203": "NH1" <-> "NH2" Residue "F ARG 204": "NH1" <-> "NH2" Residue "F ARG 213": "NH1" <-> "NH2" Residue "F ARG 222": "NH1" <-> "NH2" Residue "F ARG 230": "NH1" <-> "NH2" Residue "F ARG 370": "NH1" <-> "NH2" Residue "H ASP 42": "OD1" <-> "OD2" Residue "H ARG 48": "NH1" <-> "NH2" Residue "H ARG 54": "NH1" <-> "NH2" Residue "H ARG 57": "NH1" <-> "NH2" Residue "H ARG 100": "NH1" <-> "NH2" Residue "H ARG 194": "NH1" <-> "NH2" Residue "H ARG 195": "NH1" <-> "NH2" Residue "H ARG 203": "NH1" <-> "NH2" Residue "H ARG 204": "NH1" <-> "NH2" Residue "H ARG 213": "NH1" <-> "NH2" Residue "H ARG 222": "NH1" <-> "NH2" Residue "H ARG 230": "NH1" <-> "NH2" Residue "H ARG 370": "NH1" <-> "NH2" Residue "J ASP 42": "OD1" <-> "OD2" Residue "J ARG 48": "NH1" <-> "NH2" Residue "J ARG 54": "NH1" <-> "NH2" Residue "J ARG 57": "NH1" <-> "NH2" Residue "J ARG 100": "NH1" <-> "NH2" Residue "J ARG 194": "NH1" <-> "NH2" Residue "J ARG 195": "NH1" <-> "NH2" Residue "J ARG 203": "NH1" <-> "NH2" Residue "J ARG 204": "NH1" <-> "NH2" Residue "J ARG 213": "NH1" <-> "NH2" Residue "J ARG 222": "NH1" <-> "NH2" Residue "J ARG 230": "NH1" <-> "NH2" Residue "J ARG 370": "NH1" <-> "NH2" Residue "L ASP 42": "OD1" <-> "OD2" Residue "L ARG 48": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ARG 57": "NH1" <-> "NH2" Residue "L ARG 100": "NH1" <-> "NH2" Residue "L ARG 194": "NH1" <-> "NH2" Residue "L ARG 195": "NH1" <-> "NH2" Residue "L ARG 203": "NH1" <-> "NH2" Residue "L ARG 204": "NH1" <-> "NH2" Residue "L ARG 213": "NH1" <-> "NH2" Residue "L ARG 222": "NH1" <-> "NH2" Residue "L ARG 230": "NH1" <-> "NH2" Residue "L ARG 370": "NH1" <-> "NH2" Residue "N ASP 42": "OD1" <-> "OD2" Residue "N ARG 48": "NH1" <-> "NH2" Residue "N ARG 54": "NH1" <-> "NH2" Residue "N ARG 57": "NH1" <-> "NH2" Residue "N ARG 100": "NH1" <-> "NH2" Residue "N ARG 194": "NH1" <-> "NH2" Residue "N ARG 195": "NH1" <-> "NH2" Residue "N ARG 203": "NH1" <-> "NH2" Residue "N ARG 204": "NH1" <-> "NH2" Residue "N ARG 213": "NH1" <-> "NH2" Residue "N ARG 222": "NH1" <-> "NH2" Residue "N ARG 230": "NH1" <-> "NH2" Residue "N ARG 370": "NH1" <-> "NH2" Residue "P ASP 42": "OD1" <-> "OD2" Residue "P ARG 48": "NH1" <-> "NH2" Residue "P ARG 54": "NH1" <-> "NH2" Residue "P ARG 57": "NH1" <-> "NH2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 194": "NH1" <-> "NH2" Residue "P ARG 195": "NH1" <-> "NH2" Residue "P ARG 203": "NH1" <-> "NH2" Residue "P ARG 204": "NH1" <-> "NH2" Residue "P ARG 213": "NH1" <-> "NH2" Residue "P ARG 222": "NH1" <-> "NH2" Residue "P ARG 230": "NH1" <-> "NH2" Residue "P ARG 370": "NH1" <-> "NH2" Residue "S ASP 42": "OD1" <-> "OD2" Residue "S ARG 48": "NH1" <-> "NH2" Residue "S ARG 54": "NH1" <-> "NH2" Residue "S ARG 57": "NH1" <-> "NH2" Residue "S ARG 100": "NH1" <-> "NH2" Residue "S ARG 194": "NH1" <-> "NH2" Residue "S ARG 195": "NH1" <-> "NH2" Residue "S ARG 203": "NH1" <-> "NH2" Residue "S ARG 204": "NH1" <-> "NH2" Residue "S ARG 213": "NH1" <-> "NH2" Residue "S ARG 222": "NH1" <-> "NH2" Residue "S ARG 230": "NH1" <-> "NH2" Residue "S ARG 370": "NH1" <-> "NH2" Residue "U ASP 42": "OD1" <-> "OD2" Residue "U ARG 48": "NH1" <-> "NH2" Residue "U ARG 54": "NH1" <-> "NH2" Residue "U ARG 57": "NH1" <-> "NH2" Residue "U ARG 100": "NH1" <-> "NH2" Residue "U ARG 194": "NH1" <-> "NH2" Residue "U ARG 195": "NH1" <-> "NH2" Residue "U ARG 203": "NH1" <-> "NH2" Residue "U ARG 204": "NH1" <-> "NH2" Residue "U ARG 213": "NH1" <-> "NH2" Residue "U ARG 222": "NH1" <-> "NH2" Residue "U ARG 230": "NH1" <-> "NH2" Residue "U ARG 370": "NH1" <-> "NH2" Residue "W ASP 42": "OD1" <-> "OD2" Residue "W ARG 48": "NH1" <-> "NH2" Residue "W ARG 54": "NH1" <-> "NH2" Residue "W ARG 57": "NH1" <-> "NH2" Residue "W ARG 100": "NH1" <-> "NH2" Residue "W ARG 194": "NH1" <-> "NH2" Residue "W ARG 195": "NH1" <-> "NH2" Residue "W ARG 203": "NH1" <-> "NH2" Residue "W ARG 204": "NH1" <-> "NH2" Residue "W ARG 213": "NH1" <-> "NH2" Residue "W ARG 222": "NH1" <-> "NH2" Residue "W ARG 230": "NH1" <-> "NH2" Residue "W ARG 370": "NH1" <-> "NH2" Residue "Y ASP 42": "OD1" <-> "OD2" Residue "Y ARG 48": "NH1" <-> "NH2" Residue "Y ARG 54": "NH1" <-> "NH2" Residue "Y ARG 57": "NH1" <-> "NH2" Residue "Y ARG 100": "NH1" <-> "NH2" Residue "Y ARG 194": "NH1" <-> "NH2" Residue "Y ARG 195": "NH1" <-> "NH2" Residue "Y ARG 203": "NH1" <-> "NH2" Residue "Y ARG 204": "NH1" <-> "NH2" Residue "Y ARG 213": "NH1" <-> "NH2" Residue "Y ARG 222": "NH1" <-> "NH2" Residue "Y ARG 230": "NH1" <-> "NH2" Residue "Y ARG 370": "NH1" <-> "NH2" Residue "0 ASP 42": "OD1" <-> "OD2" Residue "0 ARG 48": "NH1" <-> "NH2" Residue "0 ARG 54": "NH1" <-> "NH2" Residue "0 ARG 57": "NH1" <-> "NH2" Residue "0 ARG 100": "NH1" <-> "NH2" Residue "0 ARG 194": "NH1" <-> "NH2" Residue "0 ARG 195": "NH1" <-> "NH2" Residue "0 ARG 203": "NH1" <-> "NH2" Residue "0 ARG 204": "NH1" <-> "NH2" Residue "0 ARG 213": "NH1" <-> "NH2" Residue "0 ARG 222": "NH1" <-> "NH2" Residue "0 ARG 230": "NH1" <-> "NH2" Residue "0 ARG 370": "NH1" <-> "NH2" Residue "2 ASP 42": "OD1" <-> "OD2" Residue "2 ARG 48": "NH1" <-> "NH2" Residue "2 ARG 54": "NH1" <-> "NH2" Residue "2 ARG 57": "NH1" <-> "NH2" Residue "2 ARG 100": "NH1" <-> "NH2" Residue "2 ARG 194": "NH1" <-> "NH2" Residue "2 ARG 195": "NH1" <-> "NH2" Residue "2 ARG 203": "NH1" <-> "NH2" Residue "2 ARG 204": "NH1" <-> "NH2" Residue "2 ARG 213": "NH1" <-> "NH2" Residue "2 ARG 222": "NH1" <-> "NH2" Residue "2 ARG 230": "NH1" <-> "NH2" Residue "2 ARG 370": "NH1" <-> "NH2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 46650 Number of models: 1 Model: "" Number of chains: 30 Chain: "B" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "R" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "A" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "D" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "E" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "F" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "G" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "H" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "I" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "J" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "K" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "L" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "M" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "N" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "O" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "P" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "Q" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "S" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "T" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "U" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "V" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "W" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "X" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "Y" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "Z" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "0" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "1" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "2" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "3" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} Time building chain proxies: 24.50, per 1000 atoms: 0.53 Number of scatterers: 46650 At special positions: 0 Unit cell: (203.184, 203.184, 135.456, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 180 16.00 P 75 15.00 O 8910 8.00 N 8115 7.00 C 29370 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Time building additional restraints: 18.03 Conformation dependent library (CDL) restraints added in 8.3 seconds 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10530 Finding SS restraints... Secondary structure from input PDB file: 330 helices and 15 sheets defined 59.1% alpha, 4.7% beta 0 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 16.56 Creating SS restraints... Processing helix chain 'B' and resid 2 through 17 removed outlier: 4.047A pdb=" N ARG B 6 " --> pdb=" O ALA B 2 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN B 14 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 15 " --> pdb=" O PHE B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG B 48 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG B 57 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 77 removed outlier: 3.537A pdb=" N LEU B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 removed outlier: 3.736A pdb=" N LEU B 87 " --> pdb=" O SER B 83 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN B 89 " --> pdb=" O GLY B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP B 128 " --> pdb=" O GLU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE B 170 " --> pdb=" O ILE B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA B 181 " --> pdb=" O LEU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA B 189 " --> pdb=" O PRO B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG B 195 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL B 218 " --> pdb=" O LYS B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 261 No H-bonds generated for 'chain 'B' and resid 259 through 261' Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN B 304 " --> pdb=" O MET B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 310 Processing helix chain 'B' and resid 325 through 328 removed outlier: 3.725A pdb=" N SER B 328 " --> pdb=" O SER B 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 325 through 328' Processing helix chain 'B' and resid 329 through 343 removed outlier: 4.462A pdb=" N GLU B 342 " --> pdb=" O GLY B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE B 362 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 369 " --> pdb=" O GLY B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.617A pdb=" N LEU B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 395 removed outlier: 3.833A pdb=" N LEU B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 394 " --> pdb=" O ASP B 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 17 removed outlier: 4.047A pdb=" N ARG A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN A 14 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 15 " --> pdb=" O PHE A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 77 removed outlier: 3.538A pdb=" N LEU A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 removed outlier: 3.736A pdb=" N LEU A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN A 89 " --> pdb=" O GLY A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 removed outlier: 3.850A pdb=" N ASP A 128 " --> pdb=" O GLU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 172 removed outlier: 3.646A pdb=" N ILE A 170 " --> pdb=" O ILE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA A 181 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA A 189 " --> pdb=" O PRO A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG A 195 " --> pdb=" O SER A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 224 removed outlier: 3.530A pdb=" N VAL A 218 " --> pdb=" O LYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 241 removed outlier: 3.627A pdb=" N PHE A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 237 " --> pdb=" O MET A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 269 through 276 Processing helix chain 'A' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN A 304 " --> pdb=" O MET A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 310 Processing helix chain 'A' and resid 325 through 328 removed outlier: 3.724A pdb=" N SER A 328 " --> pdb=" O SER A 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 325 through 328' Processing helix chain 'A' and resid 329 through 343 removed outlier: 4.463A pdb=" N GLU A 342 " --> pdb=" O GLY A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A 369 " --> pdb=" O GLY A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 385 removed outlier: 3.618A pdb=" N LEU A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 395 removed outlier: 3.832A pdb=" N LEU A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 394 " --> pdb=" O ASP A 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 17 removed outlier: 4.047A pdb=" N ARG D 6 " --> pdb=" O ALA D 2 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN D 14 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS D 15 " --> pdb=" O PHE D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG D 48 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG D 57 " --> pdb=" O ASP D 53 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY D 60 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 77 removed outlier: 3.538A pdb=" N LEU D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 92 removed outlier: 3.737A pdb=" N LEU D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 132 removed outlier: 3.850A pdb=" N ASP D 128 " --> pdb=" O GLU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 172 removed outlier: 3.646A pdb=" N ILE D 170 " --> pdb=" O ILE D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA D 181 " --> pdb=" O LEU D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA D 189 " --> pdb=" O PRO D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG D 195 " --> pdb=" O SER D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL D 218 " --> pdb=" O LYS D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE D 232 " --> pdb=" O SER D 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 258 removed outlier: 3.765A pdb=" N ASP D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 261 No H-bonds generated for 'chain 'D' and resid 259 through 261' Processing helix chain 'D' and resid 269 through 276 Processing helix chain 'D' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER D 298 " --> pdb=" O SER D 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN D 304 " --> pdb=" O MET D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 310 Processing helix chain 'D' and resid 325 through 328 removed outlier: 3.725A pdb=" N SER D 328 " --> pdb=" O SER D 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 325 through 328' Processing helix chain 'D' and resid 329 through 343 removed outlier: 4.462A pdb=" N GLU D 342 " --> pdb=" O GLY D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 350 Processing helix chain 'D' and resid 358 through 372 removed outlier: 3.602A pdb=" N PHE D 362 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL D 369 " --> pdb=" O GLY D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 385 removed outlier: 3.617A pdb=" N LEU D 384 " --> pdb=" O LEU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 395 removed outlier: 3.833A pdb=" N LEU D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D 394 " --> pdb=" O ASP D 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 17 removed outlier: 4.047A pdb=" N ARG F 6 " --> pdb=" O ALA F 2 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN F 14 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS F 15 " --> pdb=" O PHE F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG F 48 " --> pdb=" O SER F 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG F 57 " --> pdb=" O ASP F 53 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY F 60 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN F 61 " --> pdb=" O ARG F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 77 removed outlier: 3.537A pdb=" N LEU F 69 " --> pdb=" O SER F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 removed outlier: 3.735A pdb=" N LEU F 87 " --> pdb=" O SER F 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN F 89 " --> pdb=" O GLY F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP F 128 " --> pdb=" O GLU F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE F 170 " --> pdb=" O ILE F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA F 181 " --> pdb=" O LEU F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA F 189 " --> pdb=" O PRO F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG F 195 " --> pdb=" O SER F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 224 removed outlier: 3.530A pdb=" N VAL F 218 " --> pdb=" O LYS F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE F 232 " --> pdb=" O SER F 228 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE F 237 " --> pdb=" O MET F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 258 removed outlier: 3.765A pdb=" N ASP F 256 " --> pdb=" O GLU F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 261 No H-bonds generated for 'chain 'F' and resid 259 through 261' Processing helix chain 'F' and resid 269 through 276 Processing helix chain 'F' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER F 298 " --> pdb=" O SER F 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN F 304 " --> pdb=" O MET F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 310 Processing helix chain 'F' and resid 325 through 328 removed outlier: 3.725A pdb=" N SER F 328 " --> pdb=" O SER F 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 325 through 328' Processing helix chain 'F' and resid 329 through 343 removed outlier: 4.463A pdb=" N GLU F 342 " --> pdb=" O GLY F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 350 Processing helix chain 'F' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE F 362 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL F 369 " --> pdb=" O GLY F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 385 removed outlier: 3.616A pdb=" N LEU F 384 " --> pdb=" O LEU F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 395 removed outlier: 3.833A pdb=" N LEU F 393 " --> pdb=" O GLU F 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL F 394 " --> pdb=" O ASP F 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 17 removed outlier: 4.046A pdb=" N ARG H 6 " --> pdb=" O ALA H 2 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN H 14 " --> pdb=" O LEU H 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS H 15 " --> pdb=" O PHE H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG H 48 " --> pdb=" O SER H 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG H 57 " --> pdb=" O ASP H 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY H 60 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 77 removed outlier: 3.537A pdb=" N LEU H 69 " --> pdb=" O SER H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 92 removed outlier: 3.736A pdb=" N LEU H 87 " --> pdb=" O SER H 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN H 89 " --> pdb=" O GLY H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP H 128 " --> pdb=" O GLU H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 172 removed outlier: 3.646A pdb=" N ILE H 170 " --> pdb=" O ILE H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 181 removed outlier: 3.886A pdb=" N ALA H 181 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA H 189 " --> pdb=" O PRO H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG H 195 " --> pdb=" O SER H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL H 218 " --> pdb=" O LYS H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE H 232 " --> pdb=" O SER H 228 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE H 237 " --> pdb=" O MET H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP H 256 " --> pdb=" O GLU H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 261 No H-bonds generated for 'chain 'H' and resid 259 through 261' Processing helix chain 'H' and resid 269 through 276 Processing helix chain 'H' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU H 296 " --> pdb=" O GLU H 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER H 298 " --> pdb=" O SER H 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN H 304 " --> pdb=" O MET H 300 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 310 Processing helix chain 'H' and resid 325 through 328 removed outlier: 3.725A pdb=" N SER H 328 " --> pdb=" O SER H 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 325 through 328' Processing helix chain 'H' and resid 329 through 343 removed outlier: 4.462A pdb=" N GLU H 342 " --> pdb=" O GLY H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 350 Processing helix chain 'H' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE H 362 " --> pdb=" O ASP H 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL H 369 " --> pdb=" O GLY H 365 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 385 removed outlier: 3.617A pdb=" N LEU H 384 " --> pdb=" O LEU H 380 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 395 removed outlier: 3.833A pdb=" N LEU H 393 " --> pdb=" O GLU H 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL H 394 " --> pdb=" O ASP H 390 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 17 removed outlier: 4.047A pdb=" N ARG J 6 " --> pdb=" O ALA J 2 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN J 14 " --> pdb=" O LEU J 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS J 15 " --> pdb=" O PHE J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG J 48 " --> pdb=" O SER J 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG J 57 " --> pdb=" O ASP J 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY J 60 " --> pdb=" O VAL J 56 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN J 61 " --> pdb=" O ARG J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 77 removed outlier: 3.538A pdb=" N LEU J 69 " --> pdb=" O SER J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 92 removed outlier: 3.736A pdb=" N LEU J 87 " --> pdb=" O SER J 83 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN J 89 " --> pdb=" O GLY J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP J 128 " --> pdb=" O GLU J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE J 170 " --> pdb=" O ILE J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA J 181 " --> pdb=" O LEU J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA J 189 " --> pdb=" O PRO J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 202 removed outlier: 3.542A pdb=" N ARG J 195 " --> pdb=" O SER J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL J 218 " --> pdb=" O LYS J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE J 232 " --> pdb=" O SER J 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE J 237 " --> pdb=" O MET J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP J 256 " --> pdb=" O GLU J 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 259 through 261 No H-bonds generated for 'chain 'J' and resid 259 through 261' Processing helix chain 'J' and resid 269 through 276 Processing helix chain 'J' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU J 296 " --> pdb=" O GLU J 292 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER J 298 " --> pdb=" O SER J 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN J 304 " --> pdb=" O MET J 300 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 310 Processing helix chain 'J' and resid 325 through 328 removed outlier: 3.725A pdb=" N SER J 328 " --> pdb=" O SER J 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 325 through 328' Processing helix chain 'J' and resid 329 through 343 removed outlier: 4.462A pdb=" N GLU J 342 " --> pdb=" O GLY J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 346 through 350 Processing helix chain 'J' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE J 362 " --> pdb=" O ASP J 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL J 369 " --> pdb=" O GLY J 365 " (cutoff:3.500A) Processing helix chain 'J' and resid 380 through 385 removed outlier: 3.617A pdb=" N LEU J 384 " --> pdb=" O LEU J 380 " (cutoff:3.500A) Processing helix chain 'J' and resid 387 through 395 removed outlier: 3.833A pdb=" N LEU J 393 " --> pdb=" O GLU J 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL J 394 " --> pdb=" O ASP J 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 17 removed outlier: 4.048A pdb=" N ARG L 6 " --> pdb=" O ALA L 2 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN L 14 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS L 15 " --> pdb=" O PHE L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG L 48 " --> pdb=" O SER L 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG L 57 " --> pdb=" O ASP L 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY L 60 " --> pdb=" O VAL L 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN L 61 " --> pdb=" O ARG L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 77 removed outlier: 3.537A pdb=" N LEU L 69 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 92 removed outlier: 3.737A pdb=" N LEU L 87 " --> pdb=" O SER L 83 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN L 89 " --> pdb=" O GLY L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 132 removed outlier: 3.850A pdb=" N ASP L 128 " --> pdb=" O GLU L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE L 170 " --> pdb=" O ILE L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 177 through 181 removed outlier: 3.886A pdb=" N ALA L 181 " --> pdb=" O LEU L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA L 189 " --> pdb=" O PRO L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 202 removed outlier: 3.542A pdb=" N ARG L 195 " --> pdb=" O SER L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 212 through 224 removed outlier: 3.530A pdb=" N VAL L 218 " --> pdb=" O LYS L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE L 232 " --> pdb=" O SER L 228 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE L 237 " --> pdb=" O MET L 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 250 through 258 removed outlier: 3.765A pdb=" N ASP L 256 " --> pdb=" O GLU L 252 " (cutoff:3.500A) Processing helix chain 'L' and resid 259 through 261 No H-bonds generated for 'chain 'L' and resid 259 through 261' Processing helix chain 'L' and resid 269 through 276 Processing helix chain 'L' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU L 296 " --> pdb=" O GLU L 292 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER L 298 " --> pdb=" O SER L 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN L 304 " --> pdb=" O MET L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 307 through 310 Processing helix chain 'L' and resid 325 through 328 removed outlier: 3.725A pdb=" N SER L 328 " --> pdb=" O SER L 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 325 through 328' Processing helix chain 'L' and resid 329 through 343 removed outlier: 4.462A pdb=" N GLU L 342 " --> pdb=" O GLY L 338 " (cutoff:3.500A) Processing helix chain 'L' and resid 346 through 350 Processing helix chain 'L' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE L 362 " --> pdb=" O ASP L 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL L 369 " --> pdb=" O GLY L 365 " (cutoff:3.500A) Processing helix chain 'L' and resid 380 through 385 removed outlier: 3.618A pdb=" N LEU L 384 " --> pdb=" O LEU L 380 " (cutoff:3.500A) Processing helix chain 'L' and resid 387 through 395 removed outlier: 3.833A pdb=" N LEU L 393 " --> pdb=" O GLU L 389 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL L 394 " --> pdb=" O ASP L 390 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 17 removed outlier: 4.046A pdb=" N ARG N 6 " --> pdb=" O ALA N 2 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS N 15 " --> pdb=" O PHE N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG N 48 " --> pdb=" O SER N 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG N 57 " --> pdb=" O ASP N 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY N 60 " --> pdb=" O VAL N 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN N 61 " --> pdb=" O ARG N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 77 removed outlier: 3.538A pdb=" N LEU N 69 " --> pdb=" O SER N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 92 removed outlier: 3.736A pdb=" N LEU N 87 " --> pdb=" O SER N 83 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN N 89 " --> pdb=" O GLY N 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP N 128 " --> pdb=" O GLU N 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE N 170 " --> pdb=" O ILE N 166 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA N 181 " --> pdb=" O LEU N 178 " (cutoff:3.500A) Processing helix chain 'N' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA N 189 " --> pdb=" O PRO N 185 " (cutoff:3.500A) Processing helix chain 'N' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG N 195 " --> pdb=" O SER N 191 " (cutoff:3.500A) Processing helix chain 'N' and resid 212 through 224 removed outlier: 3.530A pdb=" N VAL N 218 " --> pdb=" O LYS N 214 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 241 removed outlier: 3.627A pdb=" N PHE N 232 " --> pdb=" O SER N 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE N 237 " --> pdb=" O MET N 233 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP N 256 " --> pdb=" O GLU N 252 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 261 No H-bonds generated for 'chain 'N' and resid 259 through 261' Processing helix chain 'N' and resid 269 through 276 Processing helix chain 'N' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU N 296 " --> pdb=" O GLU N 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER N 298 " --> pdb=" O SER N 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN N 304 " --> pdb=" O MET N 300 " (cutoff:3.500A) Processing helix chain 'N' and resid 307 through 310 Processing helix chain 'N' and resid 325 through 328 removed outlier: 3.724A pdb=" N SER N 328 " --> pdb=" O SER N 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 325 through 328' Processing helix chain 'N' and resid 329 through 343 removed outlier: 4.462A pdb=" N GLU N 342 " --> pdb=" O GLY N 338 " (cutoff:3.500A) Processing helix chain 'N' and resid 346 through 350 Processing helix chain 'N' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE N 362 " --> pdb=" O ASP N 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL N 369 " --> pdb=" O GLY N 365 " (cutoff:3.500A) Processing helix chain 'N' and resid 380 through 385 removed outlier: 3.617A pdb=" N LEU N 384 " --> pdb=" O LEU N 380 " (cutoff:3.500A) Processing helix chain 'N' and resid 387 through 395 removed outlier: 3.832A pdb=" N LEU N 393 " --> pdb=" O GLU N 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL N 394 " --> pdb=" O ASP N 390 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 17 removed outlier: 4.047A pdb=" N ARG P 6 " --> pdb=" O ALA P 2 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN P 14 " --> pdb=" O LEU P 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS P 15 " --> pdb=" O PHE P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG P 48 " --> pdb=" O SER P 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG P 57 " --> pdb=" O ASP P 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY P 60 " --> pdb=" O VAL P 56 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN P 61 " --> pdb=" O ARG P 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 77 removed outlier: 3.537A pdb=" N LEU P 69 " --> pdb=" O SER P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 92 removed outlier: 3.737A pdb=" N LEU P 87 " --> pdb=" O SER P 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN P 89 " --> pdb=" O GLY P 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 124 through 132 removed outlier: 3.850A pdb=" N ASP P 128 " --> pdb=" O GLU P 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE P 170 " --> pdb=" O ILE P 166 " (cutoff:3.500A) Processing helix chain 'P' and resid 177 through 181 removed outlier: 3.886A pdb=" N ALA P 181 " --> pdb=" O LEU P 178 " (cutoff:3.500A) Processing helix chain 'P' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA P 189 " --> pdb=" O PRO P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG P 195 " --> pdb=" O SER P 191 " (cutoff:3.500A) Processing helix chain 'P' and resid 212 through 224 removed outlier: 3.530A pdb=" N VAL P 218 " --> pdb=" O LYS P 214 " (cutoff:3.500A) Processing helix chain 'P' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE P 232 " --> pdb=" O SER P 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE P 237 " --> pdb=" O MET P 233 " (cutoff:3.500A) Processing helix chain 'P' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP P 256 " --> pdb=" O GLU P 252 " (cutoff:3.500A) Processing helix chain 'P' and resid 259 through 261 No H-bonds generated for 'chain 'P' and resid 259 through 261' Processing helix chain 'P' and resid 269 through 276 Processing helix chain 'P' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU P 296 " --> pdb=" O GLU P 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER P 298 " --> pdb=" O SER P 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN P 304 " --> pdb=" O MET P 300 " (cutoff:3.500A) Processing helix chain 'P' and resid 307 through 310 Processing helix chain 'P' and resid 325 through 328 removed outlier: 3.725A pdb=" N SER P 328 " --> pdb=" O SER P 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 325 through 328' Processing helix chain 'P' and resid 329 through 343 removed outlier: 4.462A pdb=" N GLU P 342 " --> pdb=" O GLY P 338 " (cutoff:3.500A) Processing helix chain 'P' and resid 346 through 350 Processing helix chain 'P' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE P 362 " --> pdb=" O ASP P 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL P 369 " --> pdb=" O GLY P 365 " (cutoff:3.500A) Processing helix chain 'P' and resid 380 through 385 removed outlier: 3.617A pdb=" N LEU P 384 " --> pdb=" O LEU P 380 " (cutoff:3.500A) Processing helix chain 'P' and resid 387 through 395 removed outlier: 3.833A pdb=" N LEU P 393 " --> pdb=" O GLU P 389 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL P 394 " --> pdb=" O ASP P 390 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 17 removed outlier: 4.047A pdb=" N ARG S 6 " --> pdb=" O ALA S 2 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN S 14 " --> pdb=" O LEU S 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS S 15 " --> pdb=" O PHE S 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG S 48 " --> pdb=" O SER S 44 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG S 57 " --> pdb=" O ASP S 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY S 60 " --> pdb=" O VAL S 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN S 61 " --> pdb=" O ARG S 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 77 removed outlier: 3.538A pdb=" N LEU S 69 " --> pdb=" O SER S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 92 removed outlier: 3.737A pdb=" N LEU S 87 " --> pdb=" O SER S 83 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN S 89 " --> pdb=" O GLY S 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP S 128 " --> pdb=" O GLU S 124 " (cutoff:3.500A) Processing helix chain 'S' and resid 159 through 172 removed outlier: 3.646A pdb=" N ILE S 170 " --> pdb=" O ILE S 166 " (cutoff:3.500A) Processing helix chain 'S' and resid 177 through 181 removed outlier: 3.886A pdb=" N ALA S 181 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing helix chain 'S' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA S 189 " --> pdb=" O PRO S 185 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG S 195 " --> pdb=" O SER S 191 " (cutoff:3.500A) Processing helix chain 'S' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL S 218 " --> pdb=" O LYS S 214 " (cutoff:3.500A) Processing helix chain 'S' and resid 227 through 241 removed outlier: 3.627A pdb=" N PHE S 232 " --> pdb=" O SER S 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE S 237 " --> pdb=" O MET S 233 " (cutoff:3.500A) Processing helix chain 'S' and resid 250 through 258 removed outlier: 3.765A pdb=" N ASP S 256 " --> pdb=" O GLU S 252 " (cutoff:3.500A) Processing helix chain 'S' and resid 259 through 261 No H-bonds generated for 'chain 'S' and resid 259 through 261' Processing helix chain 'S' and resid 269 through 276 Processing helix chain 'S' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU S 296 " --> pdb=" O GLU S 292 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER S 298 " --> pdb=" O SER S 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN S 304 " --> pdb=" O MET S 300 " (cutoff:3.500A) Processing helix chain 'S' and resid 307 through 310 Processing helix chain 'S' and resid 325 through 328 removed outlier: 3.725A pdb=" N SER S 328 " --> pdb=" O SER S 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 325 through 328' Processing helix chain 'S' and resid 329 through 343 removed outlier: 4.462A pdb=" N GLU S 342 " --> pdb=" O GLY S 338 " (cutoff:3.500A) Processing helix chain 'S' and resid 346 through 350 Processing helix chain 'S' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE S 362 " --> pdb=" O ASP S 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL S 369 " --> pdb=" O GLY S 365 " (cutoff:3.500A) Processing helix chain 'S' and resid 380 through 385 removed outlier: 3.618A pdb=" N LEU S 384 " --> pdb=" O LEU S 380 " (cutoff:3.500A) Processing helix chain 'S' and resid 387 through 395 removed outlier: 3.832A pdb=" N LEU S 393 " --> pdb=" O GLU S 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL S 394 " --> pdb=" O ASP S 390 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 17 removed outlier: 4.046A pdb=" N ARG U 6 " --> pdb=" O ALA U 2 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN U 14 " --> pdb=" O LEU U 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS U 15 " --> pdb=" O PHE U 11 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 61 removed outlier: 3.573A pdb=" N ARG U 48 " --> pdb=" O SER U 44 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG U 57 " --> pdb=" O ASP U 53 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY U 60 " --> pdb=" O VAL U 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN U 61 " --> pdb=" O ARG U 57 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 77 removed outlier: 3.537A pdb=" N LEU U 69 " --> pdb=" O SER U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 92 removed outlier: 3.737A pdb=" N LEU U 87 " --> pdb=" O SER U 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN U 89 " --> pdb=" O GLY U 85 " (cutoff:3.500A) Processing helix chain 'U' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP U 128 " --> pdb=" O GLU U 124 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE U 170 " --> pdb=" O ILE U 166 " (cutoff:3.500A) Processing helix chain 'U' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA U 181 " --> pdb=" O LEU U 178 " (cutoff:3.500A) Processing helix chain 'U' and resid 184 through 189 removed outlier: 4.436A pdb=" N ALA U 189 " --> pdb=" O PRO U 185 " (cutoff:3.500A) Processing helix chain 'U' and resid 191 through 202 removed outlier: 3.542A pdb=" N ARG U 195 " --> pdb=" O SER U 191 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL U 218 " --> pdb=" O LYS U 214 " (cutoff:3.500A) Processing helix chain 'U' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE U 232 " --> pdb=" O SER U 228 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE U 237 " --> pdb=" O MET U 233 " (cutoff:3.500A) Processing helix chain 'U' and resid 250 through 258 removed outlier: 3.765A pdb=" N ASP U 256 " --> pdb=" O GLU U 252 " (cutoff:3.500A) Processing helix chain 'U' and resid 259 through 261 No H-bonds generated for 'chain 'U' and resid 259 through 261' Processing helix chain 'U' and resid 269 through 276 Processing helix chain 'U' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU U 296 " --> pdb=" O GLU U 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER U 298 " --> pdb=" O SER U 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN U 304 " --> pdb=" O MET U 300 " (cutoff:3.500A) Processing helix chain 'U' and resid 307 through 310 Processing helix chain 'U' and resid 325 through 328 removed outlier: 3.725A pdb=" N SER U 328 " --> pdb=" O SER U 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 325 through 328' Processing helix chain 'U' and resid 329 through 343 removed outlier: 4.463A pdb=" N GLU U 342 " --> pdb=" O GLY U 338 " (cutoff:3.500A) Processing helix chain 'U' and resid 346 through 350 Processing helix chain 'U' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE U 362 " --> pdb=" O ASP U 358 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL U 369 " --> pdb=" O GLY U 365 " (cutoff:3.500A) Processing helix chain 'U' and resid 380 through 385 removed outlier: 3.616A pdb=" N LEU U 384 " --> pdb=" O LEU U 380 " (cutoff:3.500A) Processing helix chain 'U' and resid 387 through 395 removed outlier: 3.832A pdb=" N LEU U 393 " --> pdb=" O GLU U 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL U 394 " --> pdb=" O ASP U 390 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 17 removed outlier: 4.046A pdb=" N ARG W 6 " --> pdb=" O ALA W 2 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN W 14 " --> pdb=" O LEU W 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS W 15 " --> pdb=" O PHE W 11 " (cutoff:3.500A) Processing helix chain 'W' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG W 48 " --> pdb=" O SER W 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG W 57 " --> pdb=" O ASP W 53 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY W 60 " --> pdb=" O VAL W 56 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN W 61 " --> pdb=" O ARG W 57 " (cutoff:3.500A) Processing helix chain 'W' and resid 65 through 77 removed outlier: 3.537A pdb=" N LEU W 69 " --> pdb=" O SER W 65 " (cutoff:3.500A) Processing helix chain 'W' and resid 83 through 92 removed outlier: 3.735A pdb=" N LEU W 87 " --> pdb=" O SER W 83 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN W 89 " --> pdb=" O GLY W 85 " (cutoff:3.500A) Processing helix chain 'W' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP W 128 " --> pdb=" O GLU W 124 " (cutoff:3.500A) Processing helix chain 'W' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE W 170 " --> pdb=" O ILE W 166 " (cutoff:3.500A) Processing helix chain 'W' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA W 181 " --> pdb=" O LEU W 178 " (cutoff:3.500A) Processing helix chain 'W' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA W 189 " --> pdb=" O PRO W 185 " (cutoff:3.500A) Processing helix chain 'W' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG W 195 " --> pdb=" O SER W 191 " (cutoff:3.500A) Processing helix chain 'W' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL W 218 " --> pdb=" O LYS W 214 " (cutoff:3.500A) Processing helix chain 'W' and resid 227 through 241 removed outlier: 3.627A pdb=" N PHE W 232 " --> pdb=" O SER W 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE W 237 " --> pdb=" O MET W 233 " (cutoff:3.500A) Processing helix chain 'W' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP W 256 " --> pdb=" O GLU W 252 " (cutoff:3.500A) Processing helix chain 'W' and resid 259 through 261 No H-bonds generated for 'chain 'W' and resid 259 through 261' Processing helix chain 'W' and resid 269 through 276 Processing helix chain 'W' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU W 296 " --> pdb=" O GLU W 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER W 298 " --> pdb=" O SER W 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN W 304 " --> pdb=" O MET W 300 " (cutoff:3.500A) Processing helix chain 'W' and resid 307 through 310 Processing helix chain 'W' and resid 325 through 328 removed outlier: 3.724A pdb=" N SER W 328 " --> pdb=" O SER W 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 325 through 328' Processing helix chain 'W' and resid 329 through 343 removed outlier: 4.461A pdb=" N GLU W 342 " --> pdb=" O GLY W 338 " (cutoff:3.500A) Processing helix chain 'W' and resid 346 through 350 Processing helix chain 'W' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE W 362 " --> pdb=" O ASP W 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL W 369 " --> pdb=" O GLY W 365 " (cutoff:3.500A) Processing helix chain 'W' and resid 380 through 385 removed outlier: 3.618A pdb=" N LEU W 384 " --> pdb=" O LEU W 380 " (cutoff:3.500A) Processing helix chain 'W' and resid 387 through 395 removed outlier: 3.833A pdb=" N LEU W 393 " --> pdb=" O GLU W 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL W 394 " --> pdb=" O ASP W 390 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 17 removed outlier: 4.046A pdb=" N ARG Y 6 " --> pdb=" O ALA Y 2 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN Y 14 " --> pdb=" O LEU Y 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS Y 15 " --> pdb=" O PHE Y 11 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG Y 48 " --> pdb=" O SER Y 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG Y 57 " --> pdb=" O ASP Y 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY Y 60 " --> pdb=" O VAL Y 56 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN Y 61 " --> pdb=" O ARG Y 57 " (cutoff:3.500A) Processing helix chain 'Y' and resid 65 through 77 removed outlier: 3.538A pdb=" N LEU Y 69 " --> pdb=" O SER Y 65 " (cutoff:3.500A) Processing helix chain 'Y' and resid 83 through 92 removed outlier: 3.737A pdb=" N LEU Y 87 " --> pdb=" O SER Y 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN Y 89 " --> pdb=" O GLY Y 85 " (cutoff:3.500A) Processing helix chain 'Y' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP Y 128 " --> pdb=" O GLU Y 124 " (cutoff:3.500A) Processing helix chain 'Y' and resid 159 through 172 removed outlier: 3.646A pdb=" N ILE Y 170 " --> pdb=" O ILE Y 166 " (cutoff:3.500A) Processing helix chain 'Y' and resid 177 through 181 removed outlier: 3.886A pdb=" N ALA Y 181 " --> pdb=" O LEU Y 178 " (cutoff:3.500A) Processing helix chain 'Y' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA Y 189 " --> pdb=" O PRO Y 185 " (cutoff:3.500A) Processing helix chain 'Y' and resid 191 through 202 removed outlier: 3.542A pdb=" N ARG Y 195 " --> pdb=" O SER Y 191 " (cutoff:3.500A) Processing helix chain 'Y' and resid 212 through 224 removed outlier: 3.530A pdb=" N VAL Y 218 " --> pdb=" O LYS Y 214 " (cutoff:3.500A) Processing helix chain 'Y' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE Y 232 " --> pdb=" O SER Y 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE Y 237 " --> pdb=" O MET Y 233 " (cutoff:3.500A) Processing helix chain 'Y' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP Y 256 " --> pdb=" O GLU Y 252 " (cutoff:3.500A) Processing helix chain 'Y' and resid 259 through 261 No H-bonds generated for 'chain 'Y' and resid 259 through 261' Processing helix chain 'Y' and resid 269 through 276 Processing helix chain 'Y' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU Y 296 " --> pdb=" O GLU Y 292 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER Y 298 " --> pdb=" O SER Y 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN Y 304 " --> pdb=" O MET Y 300 " (cutoff:3.500A) Processing helix chain 'Y' and resid 307 through 310 Processing helix chain 'Y' and resid 325 through 328 removed outlier: 3.725A pdb=" N SER Y 328 " --> pdb=" O SER Y 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 325 through 328' Processing helix chain 'Y' and resid 329 through 343 removed outlier: 4.462A pdb=" N GLU Y 342 " --> pdb=" O GLY Y 338 " (cutoff:3.500A) Processing helix chain 'Y' and resid 346 through 350 Processing helix chain 'Y' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE Y 362 " --> pdb=" O ASP Y 358 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL Y 369 " --> pdb=" O GLY Y 365 " (cutoff:3.500A) Processing helix chain 'Y' and resid 380 through 385 removed outlier: 3.617A pdb=" N LEU Y 384 " --> pdb=" O LEU Y 380 " (cutoff:3.500A) Processing helix chain 'Y' and resid 387 through 395 removed outlier: 3.833A pdb=" N LEU Y 393 " --> pdb=" O GLU Y 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL Y 394 " --> pdb=" O ASP Y 390 " (cutoff:3.500A) Processing helix chain '0' and resid 2 through 17 removed outlier: 4.047A pdb=" N ARG 0 6 " --> pdb=" O ALA 0 2 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN 0 14 " --> pdb=" O LEU 0 10 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS 0 15 " --> pdb=" O PHE 0 11 " (cutoff:3.500A) Processing helix chain '0' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG 0 48 " --> pdb=" O SER 0 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG 0 57 " --> pdb=" O ASP 0 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY 0 60 " --> pdb=" O VAL 0 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN 0 61 " --> pdb=" O ARG 0 57 " (cutoff:3.500A) Processing helix chain '0' and resid 65 through 77 removed outlier: 3.537A pdb=" N LEU 0 69 " --> pdb=" O SER 0 65 " (cutoff:3.500A) Processing helix chain '0' and resid 83 through 92 removed outlier: 3.736A pdb=" N LEU 0 87 " --> pdb=" O SER 0 83 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN 0 89 " --> pdb=" O GLY 0 85 " (cutoff:3.500A) Processing helix chain '0' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP 0 128 " --> pdb=" O GLU 0 124 " (cutoff:3.500A) Processing helix chain '0' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE 0 170 " --> pdb=" O ILE 0 166 " (cutoff:3.500A) Processing helix chain '0' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA 0 181 " --> pdb=" O LEU 0 178 " (cutoff:3.500A) Processing helix chain '0' and resid 184 through 189 removed outlier: 4.436A pdb=" N ALA 0 189 " --> pdb=" O PRO 0 185 " (cutoff:3.500A) Processing helix chain '0' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG 0 195 " --> pdb=" O SER 0 191 " (cutoff:3.500A) Processing helix chain '0' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL 0 218 " --> pdb=" O LYS 0 214 " (cutoff:3.500A) Processing helix chain '0' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE 0 232 " --> pdb=" O SER 0 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE 0 237 " --> pdb=" O MET 0 233 " (cutoff:3.500A) Processing helix chain '0' and resid 250 through 258 removed outlier: 3.765A pdb=" N ASP 0 256 " --> pdb=" O GLU 0 252 " (cutoff:3.500A) Processing helix chain '0' and resid 259 through 261 No H-bonds generated for 'chain '0' and resid 259 through 261' Processing helix chain '0' and resid 269 through 276 Processing helix chain '0' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU 0 296 " --> pdb=" O GLU 0 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER 0 298 " --> pdb=" O SER 0 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN 0 304 " --> pdb=" O MET 0 300 " (cutoff:3.500A) Processing helix chain '0' and resid 307 through 310 Processing helix chain '0' and resid 325 through 328 removed outlier: 3.724A pdb=" N SER 0 328 " --> pdb=" O SER 0 325 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 325 through 328' Processing helix chain '0' and resid 329 through 343 removed outlier: 4.461A pdb=" N GLU 0 342 " --> pdb=" O GLY 0 338 " (cutoff:3.500A) Processing helix chain '0' and resid 346 through 350 Processing helix chain '0' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE 0 362 " --> pdb=" O ASP 0 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL 0 369 " --> pdb=" O GLY 0 365 " (cutoff:3.500A) Processing helix chain '0' and resid 380 through 385 removed outlier: 3.617A pdb=" N LEU 0 384 " --> pdb=" O LEU 0 380 " (cutoff:3.500A) Processing helix chain '0' and resid 387 through 395 removed outlier: 3.832A pdb=" N LEU 0 393 " --> pdb=" O GLU 0 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL 0 394 " --> pdb=" O ASP 0 390 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 17 removed outlier: 4.046A pdb=" N ARG 2 6 " --> pdb=" O ALA 2 2 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN 2 14 " --> pdb=" O LEU 2 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS 2 15 " --> pdb=" O PHE 2 11 " (cutoff:3.500A) Processing helix chain '2' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG 2 48 " --> pdb=" O SER 2 44 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG 2 57 " --> pdb=" O ASP 2 53 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY 2 60 " --> pdb=" O VAL 2 56 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN 2 61 " --> pdb=" O ARG 2 57 " (cutoff:3.500A) Processing helix chain '2' and resid 65 through 77 removed outlier: 3.537A pdb=" N LEU 2 69 " --> pdb=" O SER 2 65 " (cutoff:3.500A) Processing helix chain '2' and resid 83 through 92 removed outlier: 3.737A pdb=" N LEU 2 87 " --> pdb=" O SER 2 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN 2 89 " --> pdb=" O GLY 2 85 " (cutoff:3.500A) Processing helix chain '2' and resid 124 through 132 removed outlier: 3.850A pdb=" N ASP 2 128 " --> pdb=" O GLU 2 124 " (cutoff:3.500A) Processing helix chain '2' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE 2 170 " --> pdb=" O ILE 2 166 " (cutoff:3.500A) Processing helix chain '2' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA 2 181 " --> pdb=" O LEU 2 178 " (cutoff:3.500A) Processing helix chain '2' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA 2 189 " --> pdb=" O PRO 2 185 " (cutoff:3.500A) Processing helix chain '2' and resid 191 through 202 removed outlier: 3.542A pdb=" N ARG 2 195 " --> pdb=" O SER 2 191 " (cutoff:3.500A) Processing helix chain '2' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL 2 218 " --> pdb=" O LYS 2 214 " (cutoff:3.500A) Processing helix chain '2' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE 2 232 " --> pdb=" O SER 2 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE 2 237 " --> pdb=" O MET 2 233 " (cutoff:3.500A) Processing helix chain '2' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP 2 256 " --> pdb=" O GLU 2 252 " (cutoff:3.500A) Processing helix chain '2' and resid 259 through 261 No H-bonds generated for 'chain '2' and resid 259 through 261' Processing helix chain '2' and resid 269 through 276 Processing helix chain '2' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU 2 296 " --> pdb=" O GLU 2 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER 2 298 " --> pdb=" O SER 2 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN 2 304 " --> pdb=" O MET 2 300 " (cutoff:3.500A) Processing helix chain '2' and resid 307 through 310 Processing helix chain '2' and resid 325 through 328 removed outlier: 3.725A pdb=" N SER 2 328 " --> pdb=" O SER 2 325 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 325 through 328' Processing helix chain '2' and resid 329 through 343 removed outlier: 4.461A pdb=" N GLU 2 342 " --> pdb=" O GLY 2 338 " (cutoff:3.500A) Processing helix chain '2' and resid 346 through 350 Processing helix chain '2' and resid 358 through 372 removed outlier: 3.604A pdb=" N PHE 2 362 " --> pdb=" O ASP 2 358 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL 2 369 " --> pdb=" O GLY 2 365 " (cutoff:3.500A) Processing helix chain '2' and resid 380 through 385 removed outlier: 3.617A pdb=" N LEU 2 384 " --> pdb=" O LEU 2 380 " (cutoff:3.500A) Processing helix chain '2' and resid 387 through 395 removed outlier: 3.832A pdb=" N LEU 2 393 " --> pdb=" O GLU 2 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL 2 394 " --> pdb=" O ASP 2 390 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS B 33 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG B 100 " --> pdb=" O HIS B 33 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE B 35 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU B 102 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL B 37 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL B 104 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE B 39 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN B 106 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS A 33 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG A 100 " --> pdb=" O HIS A 33 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE A 35 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU A 102 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL A 37 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 104 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE A 39 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN A 106 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'D' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS D 33 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG D 100 " --> pdb=" O HIS D 33 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE D 35 " --> pdb=" O ARG D 100 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU D 102 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL D 37 " --> pdb=" O LEU D 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL D 104 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE D 39 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N GLN D 106 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'F' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS F 33 " --> pdb=" O SER F 98 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG F 100 " --> pdb=" O HIS F 33 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE F 35 " --> pdb=" O ARG F 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU F 102 " --> pdb=" O ILE F 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL F 37 " --> pdb=" O LEU F 102 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL F 104 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE F 39 " --> pdb=" O VAL F 104 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N GLN F 106 " --> pdb=" O ILE F 39 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'H' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS H 33 " --> pdb=" O SER H 98 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG H 100 " --> pdb=" O HIS H 33 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE H 35 " --> pdb=" O ARG H 100 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU H 102 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL H 37 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL H 104 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE H 39 " --> pdb=" O VAL H 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN H 106 " --> pdb=" O ILE H 39 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'J' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS J 33 " --> pdb=" O SER J 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG J 100 " --> pdb=" O HIS J 33 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE J 35 " --> pdb=" O ARG J 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU J 102 " --> pdb=" O ILE J 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL J 37 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL J 104 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE J 39 " --> pdb=" O VAL J 104 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N GLN J 106 " --> pdb=" O ILE J 39 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'L' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS L 33 " --> pdb=" O SER L 98 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG L 100 " --> pdb=" O HIS L 33 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE L 35 " --> pdb=" O ARG L 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU L 102 " --> pdb=" O ILE L 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL L 37 " --> pdb=" O LEU L 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL L 104 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE L 39 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN L 106 " --> pdb=" O ILE L 39 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'N' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS N 33 " --> pdb=" O SER N 98 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG N 100 " --> pdb=" O HIS N 33 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE N 35 " --> pdb=" O ARG N 100 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU N 102 " --> pdb=" O ILE N 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL N 37 " --> pdb=" O LEU N 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL N 104 " --> pdb=" O VAL N 37 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE N 39 " --> pdb=" O VAL N 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN N 106 " --> pdb=" O ILE N 39 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'P' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS P 33 " --> pdb=" O SER P 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG P 100 " --> pdb=" O HIS P 33 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE P 35 " --> pdb=" O ARG P 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU P 102 " --> pdb=" O ILE P 35 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL P 37 " --> pdb=" O LEU P 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL P 104 " --> pdb=" O VAL P 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE P 39 " --> pdb=" O VAL P 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN P 106 " --> pdb=" O ILE P 39 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'S' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS S 33 " --> pdb=" O SER S 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG S 100 " --> pdb=" O HIS S 33 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE S 35 " --> pdb=" O ARG S 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU S 102 " --> pdb=" O ILE S 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL S 37 " --> pdb=" O LEU S 102 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL S 104 " --> pdb=" O VAL S 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE S 39 " --> pdb=" O VAL S 104 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N GLN S 106 " --> pdb=" O ILE S 39 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'U' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS U 33 " --> pdb=" O SER U 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG U 100 " --> pdb=" O HIS U 33 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE U 35 " --> pdb=" O ARG U 100 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU U 102 " --> pdb=" O ILE U 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL U 37 " --> pdb=" O LEU U 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL U 104 " --> pdb=" O VAL U 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE U 39 " --> pdb=" O VAL U 104 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N GLN U 106 " --> pdb=" O ILE U 39 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'W' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS W 33 " --> pdb=" O SER W 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG W 100 " --> pdb=" O HIS W 33 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE W 35 " --> pdb=" O ARG W 100 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU W 102 " --> pdb=" O ILE W 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL W 37 " --> pdb=" O LEU W 102 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL W 104 " --> pdb=" O VAL W 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE W 39 " --> pdb=" O VAL W 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN W 106 " --> pdb=" O ILE W 39 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'Y' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS Y 33 " --> pdb=" O SER Y 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG Y 100 " --> pdb=" O HIS Y 33 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE Y 35 " --> pdb=" O ARG Y 100 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU Y 102 " --> pdb=" O ILE Y 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL Y 37 " --> pdb=" O LEU Y 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL Y 104 " --> pdb=" O VAL Y 37 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE Y 39 " --> pdb=" O VAL Y 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN Y 106 " --> pdb=" O ILE Y 39 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '0' and resid 33 through 40 removed outlier: 5.818A pdb=" N HIS 0 33 " --> pdb=" O SER 0 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG 0 100 " --> pdb=" O HIS 0 33 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE 0 35 " --> pdb=" O ARG 0 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU 0 102 " --> pdb=" O ILE 0 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL 0 37 " --> pdb=" O LEU 0 102 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL 0 104 " --> pdb=" O VAL 0 37 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE 0 39 " --> pdb=" O VAL 0 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN 0 106 " --> pdb=" O ILE 0 39 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain '2' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS 2 33 " --> pdb=" O SER 2 98 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG 2 100 " --> pdb=" O HIS 2 33 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE 2 35 " --> pdb=" O ARG 2 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU 2 102 " --> pdb=" O ILE 2 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL 2 37 " --> pdb=" O LEU 2 102 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL 2 104 " --> pdb=" O VAL 2 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE 2 39 " --> pdb=" O VAL 2 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN 2 106 " --> pdb=" O ILE 2 39 " (cutoff:3.500A) 1725 hydrogen bonds defined for protein. 4995 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 17.61 Time building geometry restraints manager: 19.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13736 1.33 - 1.45: 8355 1.45 - 1.57: 25084 1.57 - 1.69: 150 1.69 - 1.81: 345 Bond restraints: 47670 Sorted by residual: bond pdb=" CB PRO A 311 " pdb=" CG PRO A 311 " ideal model delta sigma weight residual 1.492 1.409 0.083 5.00e-02 4.00e+02 2.74e+00 bond pdb=" CB PRO L 311 " pdb=" CG PRO L 311 " ideal model delta sigma weight residual 1.492 1.409 0.083 5.00e-02 4.00e+02 2.74e+00 bond pdb=" CB PRO 0 311 " pdb=" CG PRO 0 311 " ideal model delta sigma weight residual 1.492 1.409 0.083 5.00e-02 4.00e+02 2.73e+00 bond pdb=" CB PRO H 311 " pdb=" CG PRO H 311 " ideal model delta sigma weight residual 1.492 1.409 0.083 5.00e-02 4.00e+02 2.73e+00 bond pdb=" CB PRO F 311 " pdb=" CG PRO F 311 " ideal model delta sigma weight residual 1.492 1.409 0.083 5.00e-02 4.00e+02 2.73e+00 ... (remaining 47665 not shown) Histogram of bond angle deviations from ideal: 98.02 - 105.23: 1335 105.23 - 112.43: 23658 112.43 - 119.64: 17300 119.64 - 126.84: 21663 126.84 - 134.04: 904 Bond angle restraints: 64860 Sorted by residual: angle pdb=" C ASN 2 61 " pdb=" N PRO 2 62 " pdb=" CA PRO 2 62 " ideal model delta sigma weight residual 119.28 129.33 -10.05 1.10e+00 8.26e-01 8.35e+01 angle pdb=" C ASN H 61 " pdb=" N PRO H 62 " pdb=" CA PRO H 62 " ideal model delta sigma weight residual 119.28 129.33 -10.05 1.10e+00 8.26e-01 8.34e+01 angle pdb=" C ASN U 61 " pdb=" N PRO U 62 " pdb=" CA PRO U 62 " ideal model delta sigma weight residual 119.28 129.32 -10.04 1.10e+00 8.26e-01 8.32e+01 angle pdb=" C ASN N 61 " pdb=" N PRO N 62 " pdb=" CA PRO N 62 " ideal model delta sigma weight residual 119.28 129.31 -10.03 1.10e+00 8.26e-01 8.32e+01 angle pdb=" C ASN S 61 " pdb=" N PRO S 62 " pdb=" CA PRO S 62 " ideal model delta sigma weight residual 119.28 129.31 -10.03 1.10e+00 8.26e-01 8.32e+01 ... (remaining 64855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.07: 25486 13.07 - 26.14: 2194 26.14 - 39.21: 655 39.21 - 52.28: 195 52.28 - 65.35: 90 Dihedral angle restraints: 28620 sinusoidal: 12270 harmonic: 16350 Sorted by residual: dihedral pdb=" CA THR J 187 " pdb=" C THR J 187 " pdb=" N ALA J 188 " pdb=" CA ALA J 188 " ideal model delta harmonic sigma weight residual 180.00 -158.40 -21.60 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA THR Y 187 " pdb=" C THR Y 187 " pdb=" N ALA Y 188 " pdb=" CA ALA Y 188 " ideal model delta harmonic sigma weight residual -180.00 -158.42 -21.58 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA THR 0 187 " pdb=" C THR 0 187 " pdb=" N ALA 0 188 " pdb=" CA ALA 0 188 " ideal model delta harmonic sigma weight residual -180.00 -158.43 -21.57 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 28617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 5069 0.055 - 0.110: 1905 0.110 - 0.166: 411 0.166 - 0.221: 70 0.221 - 0.276: 15 Chirality restraints: 7470 Sorted by residual: chirality pdb=" CB VAL J 314 " pdb=" CA VAL J 314 " pdb=" CG1 VAL J 314 " pdb=" CG2 VAL J 314 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CB VAL 2 314 " pdb=" CA VAL 2 314 " pdb=" CG1 VAL 2 314 " pdb=" CG2 VAL 2 314 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB VAL 0 314 " pdb=" CA VAL 0 314 " pdb=" CG1 VAL 0 314 " pdb=" CG2 VAL 0 314 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 7467 not shown) Planarity restraints: 7980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS N 375 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.70e+00 pdb=" C LYS N 375 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS N 375 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL N 376 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS L 375 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C LYS L 375 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS L 375 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL L 376 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS U 375 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.67e+00 pdb=" C LYS U 375 " -0.041 2.00e-02 2.50e+03 pdb=" O LYS U 375 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL U 376 " 0.014 2.00e-02 2.50e+03 ... (remaining 7977 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 54 2.28 - 2.94: 20209 2.94 - 3.59: 68204 3.59 - 4.25: 116601 4.25 - 4.90: 190536 Nonbonded interactions: 395604 Sorted by model distance: nonbonded pdb=" N GLY A 26 " pdb=" ND2 ASN 0 345 " model vdw 1.628 3.200 nonbonded pdb=" N GLY D 26 " pdb=" ND2 ASN 2 345 " model vdw 1.628 3.200 nonbonded pdb=" C GLY D 25 " pdb=" ND2 ASN 2 345 " model vdw 1.880 3.350 nonbonded pdb=" C GLY A 25 " pdb=" ND2 ASN 0 345 " model vdw 1.881 3.350 nonbonded pdb=" CA GLY D 26 " pdb=" ND2 ASN 2 345 " model vdw 2.105 3.520 ... (remaining 395599 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '2' selection = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain '1' selection = chain '3' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 9.510 Check model and map are aligned: 0.690 Set scattering table: 0.400 Process input model: 130.030 Find NCS groups from input model: 3.320 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 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 : 0.010 0.083 47670 Z= 0.631 Angle : 1.145 12.492 64860 Z= 0.660 Chirality : 0.059 0.276 7470 Planarity : 0.007 0.049 7980 Dihedral : 11.787 65.352 18090 Min Nonbonded Distance : 1.628 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.54 % Allowed : 3.40 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.31 (0.09), residues: 5625 helix: -3.84 (0.05), residues: 3150 sheet: -0.57 (0.25), residues: 375 loop : -1.25 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP U 146 HIS 0.008 0.004 HIS P 287 PHE 0.028 0.004 PHE N 352 TYR 0.024 0.004 TYR 2 281 ARG 0.014 0.001 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1580 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1505 time to evaluate : 5.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.9027 (pp) cc_final: 0.8816 (pp) REVERT: B 53 ASP cc_start: 0.8114 (t0) cc_final: 0.7720 (t0) REVERT: B 239 ASP cc_start: 0.7647 (t0) cc_final: 0.7391 (t0) REVERT: B 263 GLU cc_start: 0.7839 (mp0) cc_final: 0.7301 (mp0) REVERT: B 288 GLU cc_start: 0.7861 (mp0) cc_final: 0.7453 (mp0) REVERT: B 318 ASN cc_start: 0.8503 (t0) cc_final: 0.8233 (t0) REVERT: A 6 ARG cc_start: 0.7735 (ttp-110) cc_final: 0.7084 (mtm110) REVERT: A 217 ASP cc_start: 0.7725 (m-30) cc_final: 0.7317 (m-30) REVERT: A 288 GLU cc_start: 0.7662 (mp0) cc_final: 0.7361 (mp0) REVERT: A 318 ASN cc_start: 0.8462 (t0) cc_final: 0.8141 (t0) REVERT: A 323 LYS cc_start: 0.9024 (ttmp) cc_final: 0.8784 (ttmm) REVERT: A 358 ASP cc_start: 0.8324 (t70) cc_final: 0.8069 (t70) REVERT: D 61 ASN cc_start: 0.7696 (OUTLIER) cc_final: 0.7450 (p0) REVERT: D 103 GLU cc_start: 0.8031 (mp0) cc_final: 0.7570 (mp0) REVERT: D 213 ARG cc_start: 0.6964 (mtm110) cc_final: 0.6757 (ttp-110) REVERT: D 217 ASP cc_start: 0.7597 (m-30) cc_final: 0.6978 (m-30) REVERT: D 221 ASN cc_start: 0.8385 (m110) cc_final: 0.8123 (m110) REVERT: D 239 ASP cc_start: 0.7823 (t0) cc_final: 0.7535 (t0) REVERT: D 288 GLU cc_start: 0.7685 (mp0) cc_final: 0.7309 (mp0) REVERT: D 318 ASN cc_start: 0.8582 (t0) cc_final: 0.8325 (t0) REVERT: F 86 GLN cc_start: 0.8577 (mt0) cc_final: 0.8338 (mt0) REVERT: F 213 ARG cc_start: 0.7122 (mtm110) cc_final: 0.6918 (ttp-110) REVERT: F 217 ASP cc_start: 0.7774 (m-30) cc_final: 0.7204 (m-30) REVERT: F 239 ASP cc_start: 0.7834 (t0) cc_final: 0.7584 (t0) REVERT: F 263 GLU cc_start: 0.8014 (mp0) cc_final: 0.7487 (mp0) REVERT: F 318 ASN cc_start: 0.8653 (t0) cc_final: 0.8355 (t0) REVERT: F 358 ASP cc_start: 0.8203 (t70) cc_final: 0.7927 (t70) REVERT: H 7 SER cc_start: 0.9315 (t) cc_final: 0.9041 (t) REVERT: H 209 PHE cc_start: 0.8943 (m-80) cc_final: 0.8706 (m-80) REVERT: H 217 ASP cc_start: 0.7667 (m-30) cc_final: 0.7186 (m-30) REVERT: H 221 ASN cc_start: 0.8475 (m110) cc_final: 0.8263 (m110) REVERT: H 239 ASP cc_start: 0.7645 (t0) cc_final: 0.7280 (t0) REVERT: H 263 GLU cc_start: 0.7945 (mp0) cc_final: 0.7566 (mp0) REVERT: H 288 GLU cc_start: 0.7781 (mp0) cc_final: 0.7493 (mp0) REVERT: H 318 ASN cc_start: 0.8565 (t0) cc_final: 0.8273 (t0) REVERT: J 217 ASP cc_start: 0.7616 (m-30) cc_final: 0.7061 (m-30) REVERT: J 221 ASN cc_start: 0.8436 (m110) cc_final: 0.7977 (m110) REVERT: J 239 ASP cc_start: 0.7666 (t0) cc_final: 0.7359 (t0) REVERT: J 263 GLU cc_start: 0.7906 (mp0) cc_final: 0.7575 (mp0) REVERT: J 288 GLU cc_start: 0.7746 (mp0) cc_final: 0.7448 (mp0) REVERT: J 318 ASN cc_start: 0.8476 (t0) cc_final: 0.8101 (t0) REVERT: J 375 LYS cc_start: 0.8055 (ttmp) cc_final: 0.7728 (mptt) REVERT: L 100 ARG cc_start: 0.8246 (ppp80) cc_final: 0.8015 (ptt90) REVERT: L 109 GLN cc_start: 0.7976 (pt0) cc_final: 0.7607 (mm-40) REVERT: L 239 ASP cc_start: 0.7846 (t0) cc_final: 0.7544 (t0) REVERT: L 263 GLU cc_start: 0.7946 (mp0) cc_final: 0.7573 (mp0) REVERT: L 318 ASN cc_start: 0.8464 (t0) cc_final: 0.8204 (t0) REVERT: N 318 ASN cc_start: 0.8420 (t0) cc_final: 0.8211 (t0) REVERT: N 361 TYR cc_start: 0.8368 (m-80) cc_final: 0.8165 (m-80) REVERT: P 32 LYS cc_start: 0.8118 (mttm) cc_final: 0.7872 (mmtt) REVERT: P 86 GLN cc_start: 0.8665 (mt0) cc_final: 0.8438 (mt0) REVERT: P 150 LYS cc_start: 0.8251 (mppt) cc_final: 0.8045 (mppt) REVERT: P 217 ASP cc_start: 0.7661 (m-30) cc_final: 0.7151 (m-30) REVERT: P 239 ASP cc_start: 0.7741 (t0) cc_final: 0.7337 (t0) REVERT: P 263 GLU cc_start: 0.7916 (mp0) cc_final: 0.7539 (mp0) REVERT: P 288 GLU cc_start: 0.7783 (mp0) cc_final: 0.7409 (mp0) REVERT: P 318 ASN cc_start: 0.8392 (t0) cc_final: 0.8074 (t0) REVERT: S 126 GLU cc_start: 0.7551 (tt0) cc_final: 0.7333 (tt0) REVERT: S 150 LYS cc_start: 0.8432 (mppt) cc_final: 0.8214 (mppt) REVERT: S 221 ASN cc_start: 0.8353 (m110) cc_final: 0.8119 (m110) REVERT: S 239 ASP cc_start: 0.7743 (t0) cc_final: 0.7497 (t0) REVERT: S 280 MET cc_start: 0.7702 (mtm) cc_final: 0.7405 (mpp) REVERT: S 318 ASN cc_start: 0.8424 (t0) cc_final: 0.8109 (t0) REVERT: U 164 ASN cc_start: 0.8608 (t0) cc_final: 0.8034 (t0) REVERT: U 239 ASP cc_start: 0.7839 (t0) cc_final: 0.7552 (t0) REVERT: U 288 GLU cc_start: 0.7716 (mp0) cc_final: 0.7327 (mp0) REVERT: U 318 ASN cc_start: 0.8433 (t0) cc_final: 0.8139 (t0) REVERT: W 32 LYS cc_start: 0.8228 (mttm) cc_final: 0.8027 (mmtt) REVERT: W 144 PHE cc_start: 0.7924 (m-80) cc_final: 0.7681 (m-10) REVERT: W 150 LYS cc_start: 0.8726 (mppt) cc_final: 0.8387 (mppt) REVERT: W 217 ASP cc_start: 0.7726 (m-30) cc_final: 0.7145 (m-30) REVERT: W 221 ASN cc_start: 0.8308 (m110) cc_final: 0.7942 (m110) REVERT: W 239 ASP cc_start: 0.7741 (t0) cc_final: 0.7530 (t0) REVERT: W 288 GLU cc_start: 0.7768 (mp0) cc_final: 0.7543 (mp0) REVERT: Y 86 GLN cc_start: 0.8744 (mt0) cc_final: 0.8474 (mt0) REVERT: Y 129 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7886 (tm-30) REVERT: Y 164 ASN cc_start: 0.8650 (t0) cc_final: 0.8401 (t0) REVERT: Y 239 ASP cc_start: 0.7793 (t0) cc_final: 0.7521 (t0) REVERT: Y 260 TYR cc_start: 0.9069 (m-80) cc_final: 0.8811 (m-80) REVERT: Y 263 GLU cc_start: 0.7928 (mp0) cc_final: 0.7609 (mp0) REVERT: Y 288 GLU cc_start: 0.7777 (mp0) cc_final: 0.7439 (mp0) REVERT: Y 318 ASN cc_start: 0.8415 (t0) cc_final: 0.8188 (t0) REVERT: Y 361 TYR cc_start: 0.8266 (m-80) cc_final: 0.7750 (m-80) REVERT: 0 7 SER cc_start: 0.9394 (t) cc_final: 0.9087 (m) REVERT: 0 53 ASP cc_start: 0.8186 (t0) cc_final: 0.7917 (t0) REVERT: 0 239 ASP cc_start: 0.7655 (t0) cc_final: 0.7360 (t0) REVERT: 0 263 GLU cc_start: 0.7818 (mp0) cc_final: 0.7445 (mp0) REVERT: 0 288 GLU cc_start: 0.7645 (mp0) cc_final: 0.7236 (mp0) REVERT: 0 318 ASN cc_start: 0.8452 (t0) cc_final: 0.8097 (t0) REVERT: 2 86 GLN cc_start: 0.8731 (mt0) cc_final: 0.8477 (mt0) REVERT: 2 115 THR cc_start: 0.8555 (p) cc_final: 0.8275 (t) REVERT: 2 144 PHE cc_start: 0.8043 (m-80) cc_final: 0.7771 (m-80) REVERT: 2 217 ASP cc_start: 0.7515 (m-30) cc_final: 0.7234 (m-30) REVERT: 2 239 ASP cc_start: 0.7704 (t0) cc_final: 0.7357 (t0) REVERT: 2 288 GLU cc_start: 0.7705 (mp0) cc_final: 0.7211 (mp0) REVERT: 2 318 ASN cc_start: 0.8405 (t0) cc_final: 0.8011 (t0) REVERT: 2 361 TYR cc_start: 0.8284 (m-80) cc_final: 0.8009 (m-80) outliers start: 75 outliers final: 18 residues processed: 1553 average time/residue: 0.6231 time to fit residues: 1547.1618 Evaluate side-chains 1173 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1154 time to evaluate : 5.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 236 LEU Chi-restraints excluded: chain S residue 236 LEU Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 236 LEU Chi-restraints excluded: chain W residue 236 LEU Chi-restraints excluded: chain Y residue 236 LEU Chi-restraints excluded: chain 0 residue 236 LEU Chi-restraints excluded: chain 2 residue 236 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 481 optimal weight: 1.9990 chunk 432 optimal weight: 9.9990 chunk 239 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 291 optimal weight: 0.9990 chunk 230 optimal weight: 10.0000 chunk 446 optimal weight: 0.8980 chunk 172 optimal weight: 0.8980 chunk 271 optimal weight: 2.9990 chunk 332 optimal weight: 0.9990 chunk 517 optimal weight: 8.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 ASN B 322 ASN B 351 ASN A 61 ASN A 221 ASN A 322 ASN A 351 ASN ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN D 221 ASN D 305 GLN D 322 ASN D 351 ASN F 305 GLN F 351 ASN H 149 ASN ** H 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 221 ASN H 351 ASN J 149 ASN J 164 ASN J 345 ASN J 351 ASN L 221 ASN L 322 ASN L 351 ASN N 221 ASN N 322 ASN N 351 ASN P 221 ASN P 322 ASN P 351 ASN S 322 ASN S 351 ASN U 149 ASN U 221 ASN U 322 ASN U 351 ASN W 149 ASN W 221 ASN W 305 GLN W 321 GLN W 322 ASN W 351 ASN Y 221 ASN Y 322 ASN Y 351 ASN 0 221 ASN 0 305 GLN 0 351 ASN 2 351 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 47670 Z= 0.190 Angle : 0.650 10.164 64860 Z= 0.330 Chirality : 0.041 0.174 7470 Planarity : 0.004 0.028 7980 Dihedral : 9.206 65.851 7283 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.78 % Allowed : 9.96 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.10), residues: 5625 helix: -2.12 (0.08), residues: 3165 sheet: 0.44 (0.29), residues: 375 loop : -0.72 (0.14), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 146 HIS 0.005 0.001 HIS L 287 PHE 0.018 0.002 PHE F 209 TYR 0.014 0.001 TYR N 260 ARG 0.005 0.001 ARG W 213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1372 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1237 time to evaluate : 5.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.8917 (pp) cc_final: 0.8646 (pp) REVERT: B 53 ASP cc_start: 0.8143 (t0) cc_final: 0.7775 (t0) REVERT: B 213 ARG cc_start: 0.7633 (ttp-110) cc_final: 0.6709 (ttp80) REVERT: B 217 ASP cc_start: 0.7343 (m-30) cc_final: 0.6958 (m-30) REVERT: B 239 ASP cc_start: 0.7813 (t0) cc_final: 0.7601 (t0) REVERT: B 252 GLU cc_start: 0.8202 (tt0) cc_final: 0.7986 (tt0) REVERT: B 288 GLU cc_start: 0.7696 (mp0) cc_final: 0.7346 (mp0) REVERT: B 318 ASN cc_start: 0.8422 (t0) cc_final: 0.8118 (t0) REVERT: B 344 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7647 (mm-30) REVERT: A 115 THR cc_start: 0.8718 (p) cc_final: 0.8420 (t) REVERT: A 123 MET cc_start: 0.6276 (mmm) cc_final: 0.5694 (mmm) REVERT: A 213 ARG cc_start: 0.7560 (ttp-110) cc_final: 0.6504 (ttp-110) REVERT: A 217 ASP cc_start: 0.7362 (m-30) cc_final: 0.6821 (m-30) REVERT: A 225 GLU cc_start: 0.7773 (tp30) cc_final: 0.7474 (mm-30) REVERT: A 239 ASP cc_start: 0.7888 (t0) cc_final: 0.7686 (t0) REVERT: A 288 GLU cc_start: 0.7585 (mp0) cc_final: 0.7235 (mp0) REVERT: A 318 ASN cc_start: 0.8376 (t0) cc_final: 0.8089 (t0) REVERT: D 103 GLU cc_start: 0.8041 (mp0) cc_final: 0.7667 (mp0) REVERT: D 217 ASP cc_start: 0.7306 (m-30) cc_final: 0.6829 (m-30) REVERT: D 226 ASP cc_start: 0.7870 (p0) cc_final: 0.7488 (p0) REVERT: D 280 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7725 (mpp) REVERT: D 288 GLU cc_start: 0.7563 (mp0) cc_final: 0.7256 (mp0) REVERT: D 318 ASN cc_start: 0.8424 (t0) cc_final: 0.8216 (t0) REVERT: F 12 LYS cc_start: 0.8482 (mtpp) cc_final: 0.8190 (mttt) REVERT: F 53 ASP cc_start: 0.8098 (t0) cc_final: 0.7777 (t0) REVERT: F 89 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8412 (mm-40) REVERT: F 213 ARG cc_start: 0.7021 (mtm110) cc_final: 0.6821 (ttp-110) REVERT: F 217 ASP cc_start: 0.7464 (m-30) cc_final: 0.6863 (m-30) REVERT: F 239 ASP cc_start: 0.7936 (t0) cc_final: 0.7500 (t0) REVERT: F 263 GLU cc_start: 0.7906 (mp0) cc_final: 0.7323 (mp0) REVERT: F 318 ASN cc_start: 0.8445 (t0) cc_final: 0.8132 (t0) REVERT: H 4 LEU cc_start: 0.8974 (tp) cc_final: 0.8769 (tp) REVERT: H 53 ASP cc_start: 0.8123 (t0) cc_final: 0.7839 (t0) REVERT: H 213 ARG cc_start: 0.7551 (ttm110) cc_final: 0.6973 (ttp-110) REVERT: H 217 ASP cc_start: 0.7392 (m-30) cc_final: 0.7096 (m-30) REVERT: H 239 ASP cc_start: 0.7736 (t0) cc_final: 0.7247 (t0) REVERT: H 318 ASN cc_start: 0.8438 (t0) cc_final: 0.8151 (t0) REVERT: J 53 ASP cc_start: 0.8102 (t0) cc_final: 0.7813 (t0) REVERT: J 103 GLU cc_start: 0.7858 (mp0) cc_final: 0.7614 (mp0) REVERT: J 213 ARG cc_start: 0.7622 (ttp-110) cc_final: 0.7372 (ttp-110) REVERT: J 217 ASP cc_start: 0.7425 (m-30) cc_final: 0.7178 (m-30) REVERT: J 239 ASP cc_start: 0.7757 (t0) cc_final: 0.7513 (t0) REVERT: J 263 GLU cc_start: 0.7716 (mp0) cc_final: 0.7266 (mp0) REVERT: J 288 GLU cc_start: 0.7631 (mp0) cc_final: 0.7358 (mp0) REVERT: J 318 ASN cc_start: 0.8360 (t0) cc_final: 0.8010 (t0) REVERT: J 371 ARG cc_start: 0.8222 (mmt90) cc_final: 0.7995 (mmt90) REVERT: J 375 LYS cc_start: 0.8024 (ttmp) cc_final: 0.7683 (mptt) REVERT: L 12 LYS cc_start: 0.8383 (mtpp) cc_final: 0.8063 (mttt) REVERT: L 29 ARG cc_start: 0.7941 (mtm-85) cc_final: 0.7125 (mtm110) REVERT: L 213 ARG cc_start: 0.7707 (ttp-110) cc_final: 0.6835 (ttp-110) REVERT: L 217 ASP cc_start: 0.7405 (m-30) cc_final: 0.6870 (m-30) REVERT: L 239 ASP cc_start: 0.8059 (t0) cc_final: 0.7804 (t0) REVERT: L 318 ASN cc_start: 0.8350 (t0) cc_final: 0.8138 (t0) REVERT: N 217 ASP cc_start: 0.7441 (m-30) cc_final: 0.6992 (m-30) REVERT: N 239 ASP cc_start: 0.7923 (t0) cc_final: 0.7641 (t0) REVERT: N 317 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7256 (mm-30) REVERT: P 12 LYS cc_start: 0.8388 (mmmt) cc_final: 0.8087 (mttt) REVERT: P 213 ARG cc_start: 0.7705 (ttp-110) cc_final: 0.7317 (ttp-110) REVERT: P 217 ASP cc_start: 0.7380 (m-30) cc_final: 0.6998 (m-30) REVERT: P 239 ASP cc_start: 0.7843 (t0) cc_final: 0.7390 (t0) REVERT: P 318 ASN cc_start: 0.8262 (t0) cc_final: 0.7946 (t0) REVERT: P 371 ARG cc_start: 0.8205 (mmt90) cc_final: 0.7975 (mmt90) REVERT: S 7 SER cc_start: 0.9116 (t) cc_final: 0.8786 (m) REVERT: S 103 GLU cc_start: 0.7918 (mp0) cc_final: 0.7677 (mp0) REVERT: S 209 PHE cc_start: 0.8758 (m-80) cc_final: 0.8456 (m-10) REVERT: S 213 ARG cc_start: 0.7734 (ttm110) cc_final: 0.6819 (ttp-110) REVERT: S 217 ASP cc_start: 0.7505 (m-30) cc_final: 0.6976 (m-30) REVERT: S 239 ASP cc_start: 0.7759 (t0) cc_final: 0.7555 (t0) REVERT: S 318 ASN cc_start: 0.8350 (t0) cc_final: 0.7991 (t0) REVERT: U 7 SER cc_start: 0.9080 (t) cc_final: 0.8857 (p) REVERT: U 144 PHE cc_start: 0.8175 (m-10) cc_final: 0.7847 (m-10) REVERT: U 213 ARG cc_start: 0.7638 (ttp-110) cc_final: 0.6956 (ttp80) REVERT: U 217 ASP cc_start: 0.7636 (m-30) cc_final: 0.7359 (m-30) REVERT: U 239 ASP cc_start: 0.7928 (t0) cc_final: 0.7706 (t0) REVERT: U 280 MET cc_start: 0.8205 (tpp) cc_final: 0.7882 (tpp) REVERT: U 288 GLU cc_start: 0.7632 (mp0) cc_final: 0.7253 (mp0) REVERT: U 318 ASN cc_start: 0.8295 (t0) cc_final: 0.8035 (t0) REVERT: U 361 TYR cc_start: 0.8884 (m-80) cc_final: 0.8607 (m-80) REVERT: W 150 LYS cc_start: 0.8722 (mppt) cc_final: 0.8449 (mppt) REVERT: W 217 ASP cc_start: 0.7474 (m-30) cc_final: 0.7120 (m-30) REVERT: W 221 ASN cc_start: 0.8412 (m-40) cc_final: 0.8008 (m110) REVERT: W 239 ASP cc_start: 0.7879 (t0) cc_final: 0.7605 (t0) REVERT: W 280 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7653 (mpp) REVERT: W 288 GLU cc_start: 0.7741 (mp0) cc_final: 0.7487 (mp0) REVERT: W 300 MET cc_start: 0.8650 (mtt) cc_final: 0.8434 (mtt) REVERT: Y 53 ASP cc_start: 0.8213 (t0) cc_final: 0.7980 (t0) REVERT: Y 86 GLN cc_start: 0.8478 (mt0) cc_final: 0.8132 (mt0) REVERT: Y 213 ARG cc_start: 0.7531 (ttp-110) cc_final: 0.6797 (ttp-110) REVERT: Y 217 ASP cc_start: 0.7488 (m-30) cc_final: 0.7198 (m-30) REVERT: Y 239 ASP cc_start: 0.7904 (t0) cc_final: 0.7618 (t0) REVERT: Y 288 GLU cc_start: 0.7739 (mp0) cc_final: 0.7319 (mp0) REVERT: Y 292 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7531 (mt-10) REVERT: Y 318 ASN cc_start: 0.8266 (t0) cc_final: 0.8033 (t0) REVERT: 0 7 SER cc_start: 0.9084 (t) cc_final: 0.8840 (m) REVERT: 0 89 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8589 (mm-40) REVERT: 0 148 GLU cc_start: 0.7666 (pt0) cc_final: 0.7456 (mt-10) REVERT: 0 239 ASP cc_start: 0.7677 (t0) cc_final: 0.7402 (t0) REVERT: 0 288 GLU cc_start: 0.7504 (mp0) cc_final: 0.7220 (mp0) REVERT: 0 318 ASN cc_start: 0.8300 (t0) cc_final: 0.7889 (t0) REVERT: 2 82 GLU cc_start: 0.7364 (tt0) cc_final: 0.7084 (tt0) REVERT: 2 115 THR cc_start: 0.8620 (p) cc_final: 0.8336 (t) REVERT: 2 128 ASP cc_start: 0.7721 (t0) cc_final: 0.7499 (t0) REVERT: 2 213 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.6959 (ttp-110) REVERT: 2 217 ASP cc_start: 0.7266 (m-30) cc_final: 0.6969 (m-30) REVERT: 2 239 ASP cc_start: 0.7789 (t0) cc_final: 0.7521 (t0) REVERT: 2 280 MET cc_start: 0.8216 (tpp) cc_final: 0.7950 (mmm) REVERT: 2 288 GLU cc_start: 0.7694 (mp0) cc_final: 0.7290 (mp0) REVERT: 2 318 ASN cc_start: 0.8268 (t0) cc_final: 0.7880 (t0) outliers start: 135 outliers final: 65 residues processed: 1318 average time/residue: 0.5839 time to fit residues: 1265.0914 Evaluate side-chains 1129 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1061 time to evaluate : 5.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 255 CYS Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain H residue 375 LYS Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 380 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 193 LEU Chi-restraints excluded: chain L residue 288 GLU Chi-restraints excluded: chain L residue 297 GLU Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain N residue 44 SER Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 288 GLU Chi-restraints excluded: chain N residue 319 SER Chi-restraints excluded: chain N residue 332 LEU Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 44 SER Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain U residue 42 ASP Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 45 ILE Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 186 ASP Chi-restraints excluded: chain U residue 193 LEU Chi-restraints excluded: chain U residue 332 LEU Chi-restraints excluded: chain W residue 45 ILE Chi-restraints excluded: chain W residue 193 LEU Chi-restraints excluded: chain W residue 280 MET Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain Y residue 45 ILE Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Y residue 193 LEU Chi-restraints excluded: chain Y residue 319 SER Chi-restraints excluded: chain Y residue 375 LYS Chi-restraints excluded: chain 0 residue 42 ASP Chi-restraints excluded: chain 0 residue 45 ILE Chi-restraints excluded: chain 0 residue 94 ASP Chi-restraints excluded: chain 0 residue 102 LEU Chi-restraints excluded: chain 0 residue 297 GLU Chi-restraints excluded: chain 0 residue 304 GLN Chi-restraints excluded: chain 0 residue 332 LEU Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 190 ASP Chi-restraints excluded: chain 2 residue 213 ARG Chi-restraints excluded: chain 2 residue 319 SER Chi-restraints excluded: chain 2 residue 332 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 287 optimal weight: 6.9990 chunk 160 optimal weight: 8.9990 chunk 430 optimal weight: 10.0000 chunk 352 optimal weight: 9.9990 chunk 142 optimal weight: 6.9990 chunk 518 optimal weight: 3.9990 chunk 560 optimal weight: 5.9990 chunk 461 optimal weight: 3.9990 chunk 514 optimal weight: 7.9990 chunk 176 optimal weight: 7.9990 chunk 416 optimal weight: 0.0970 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN F 321 GLN F 322 ASN H 86 GLN ** H 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 321 GLN J 321 GLN J 345 ASN L 321 GLN S 321 GLN U 321 GLN Y 321 GLN 0 321 GLN 0 322 ASN 0 345 ASN 2 221 ASN 2 345 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 47670 Z= 0.362 Angle : 0.633 9.763 64860 Z= 0.326 Chirality : 0.044 0.181 7470 Planarity : 0.005 0.055 7980 Dihedral : 8.537 67.128 7251 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.09 % Allowed : 12.72 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.11), residues: 5625 helix: -1.07 (0.09), residues: 3195 sheet: 0.39 (0.28), residues: 375 loop : -0.62 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 215 HIS 0.003 0.001 HIS B 33 PHE 0.025 0.002 PHE F 209 TYR 0.020 0.002 TYR U 361 ARG 0.008 0.000 ARG D 213 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1265 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1115 time to evaluate : 5.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 SER cc_start: 0.9162 (t) cc_final: 0.8892 (m) REVERT: B 34 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8796 (pp) REVERT: B 36 ILE cc_start: 0.8669 (mm) cc_final: 0.8460 (mm) REVERT: B 213 ARG cc_start: 0.7690 (ttp-110) cc_final: 0.6722 (ttp80) REVERT: B 217 ASP cc_start: 0.7395 (m-30) cc_final: 0.6900 (m-30) REVERT: B 226 ASP cc_start: 0.7975 (p0) cc_final: 0.7302 (p0) REVERT: B 239 ASP cc_start: 0.7920 (t0) cc_final: 0.7629 (t0) REVERT: B 318 ASN cc_start: 0.8533 (t0) cc_final: 0.8209 (t0) REVERT: B 361 TYR cc_start: 0.9144 (m-80) cc_final: 0.8834 (m-80) REVERT: A 86 GLN cc_start: 0.8489 (mt0) cc_final: 0.8270 (mt0) REVERT: A 115 THR cc_start: 0.8662 (p) cc_final: 0.8373 (t) REVERT: A 123 MET cc_start: 0.6436 (mmm) cc_final: 0.5695 (mmm) REVERT: A 164 ASN cc_start: 0.8485 (t0) cc_final: 0.8056 (t0) REVERT: A 213 ARG cc_start: 0.7667 (ttp-110) cc_final: 0.6922 (ttp-110) REVERT: A 214 LYS cc_start: 0.8485 (ttpp) cc_final: 0.8077 (tttt) REVERT: A 217 ASP cc_start: 0.7361 (m-30) cc_final: 0.6793 (m-30) REVERT: A 225 GLU cc_start: 0.7828 (tp30) cc_final: 0.7530 (mm-30) REVERT: A 226 ASP cc_start: 0.8263 (p0) cc_final: 0.7817 (p0) REVERT: A 239 ASP cc_start: 0.7989 (t0) cc_final: 0.7697 (t0) REVERT: A 271 LEU cc_start: 0.8488 (mt) cc_final: 0.8287 (mt) REVERT: A 280 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7759 (mpp) REVERT: A 288 GLU cc_start: 0.7731 (mp0) cc_final: 0.7363 (mp0) REVERT: A 318 ASN cc_start: 0.8448 (t0) cc_final: 0.8178 (t0) REVERT: A 342 GLU cc_start: 0.7407 (mp0) cc_final: 0.7127 (mp0) REVERT: D 7 SER cc_start: 0.9114 (t) cc_final: 0.8865 (m) REVERT: D 12 LYS cc_start: 0.8543 (mmtt) cc_final: 0.8235 (mmtt) REVERT: D 103 GLU cc_start: 0.8099 (mp0) cc_final: 0.7709 (mp0) REVERT: D 123 MET cc_start: 0.5375 (mmt) cc_final: 0.4879 (mmm) REVERT: D 213 ARG cc_start: 0.7639 (ttp-110) cc_final: 0.6907 (ttp-110) REVERT: D 217 ASP cc_start: 0.7411 (m-30) cc_final: 0.7010 (m-30) REVERT: D 239 ASP cc_start: 0.8038 (t0) cc_final: 0.7590 (t0) REVERT: D 263 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7665 (mt-10) REVERT: D 288 GLU cc_start: 0.7706 (mp0) cc_final: 0.7295 (mp0) REVERT: D 318 ASN cc_start: 0.8544 (t0) cc_final: 0.8340 (t0) REVERT: F 89 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8428 (mm-40) REVERT: F 213 ARG cc_start: 0.7167 (mtm110) cc_final: 0.6934 (ttp-110) REVERT: F 217 ASP cc_start: 0.7538 (m-30) cc_final: 0.6965 (m-30) REVERT: F 239 ASP cc_start: 0.7920 (t0) cc_final: 0.7439 (t0) REVERT: F 318 ASN cc_start: 0.8528 (t0) cc_final: 0.8209 (t0) REVERT: H 53 ASP cc_start: 0.8219 (t0) cc_final: 0.7810 (t0) REVERT: H 213 ARG cc_start: 0.7645 (ttm110) cc_final: 0.7320 (ttm110) REVERT: H 217 ASP cc_start: 0.7472 (m-30) cc_final: 0.7069 (m-30) REVERT: H 239 ASP cc_start: 0.7849 (t0) cc_final: 0.7403 (t0) REVERT: H 318 ASN cc_start: 0.8553 (t0) cc_final: 0.8350 (t0) REVERT: J 53 ASP cc_start: 0.8071 (t0) cc_final: 0.7867 (t0) REVERT: J 103 GLU cc_start: 0.7907 (mp0) cc_final: 0.7653 (mp0) REVERT: J 239 ASP cc_start: 0.7752 (t0) cc_final: 0.7501 (t0) REVERT: J 255 CYS cc_start: 0.8504 (t) cc_final: 0.8013 (t) REVERT: J 263 GLU cc_start: 0.7792 (mp0) cc_final: 0.7339 (mp0) REVERT: J 288 GLU cc_start: 0.7774 (mp0) cc_final: 0.7427 (mp0) REVERT: J 318 ASN cc_start: 0.8476 (t0) cc_final: 0.8132 (t0) REVERT: J 375 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7669 (mptt) REVERT: J 394 VAL cc_start: 0.8470 (t) cc_final: 0.8217 (t) REVERT: L 213 ARG cc_start: 0.7776 (ttp-110) cc_final: 0.7008 (ttp-110) REVERT: L 217 ASP cc_start: 0.7496 (m-30) cc_final: 0.6987 (m-30) REVERT: L 225 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7370 (mm-30) REVERT: L 239 ASP cc_start: 0.8106 (t0) cc_final: 0.7821 (t0) REVERT: N 103 GLU cc_start: 0.8023 (mp0) cc_final: 0.7817 (mp0) REVERT: N 217 ASP cc_start: 0.7535 (m-30) cc_final: 0.7072 (m-30) REVERT: N 225 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7678 (mm-30) REVERT: N 239 ASP cc_start: 0.7980 (t0) cc_final: 0.7699 (t0) REVERT: N 317 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7435 (mm-30) REVERT: P 213 ARG cc_start: 0.7751 (ttp-110) cc_final: 0.7354 (ttp-110) REVERT: P 217 ASP cc_start: 0.7366 (m-30) cc_final: 0.6978 (m-30) REVERT: P 233 MET cc_start: 0.8840 (mtm) cc_final: 0.8472 (mtp) REVERT: P 239 ASP cc_start: 0.7811 (t0) cc_final: 0.7360 (t0) REVERT: P 288 GLU cc_start: 0.7849 (mp0) cc_final: 0.7304 (mp0) REVERT: P 308 GLU cc_start: 0.7555 (pm20) cc_final: 0.7167 (pm20) REVERT: P 318 ASN cc_start: 0.8435 (t0) cc_final: 0.8206 (t0) REVERT: S 12 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8102 (mttp) REVERT: S 103 GLU cc_start: 0.7940 (mp0) cc_final: 0.7667 (mp0) REVERT: S 209 PHE cc_start: 0.9013 (m-80) cc_final: 0.8758 (m-10) REVERT: S 213 ARG cc_start: 0.7811 (ttm110) cc_final: 0.7021 (ttp-110) REVERT: S 217 ASP cc_start: 0.7461 (m-30) cc_final: 0.7095 (m-30) REVERT: S 239 ASP cc_start: 0.7874 (t0) cc_final: 0.7615 (t0) REVERT: S 318 ASN cc_start: 0.8474 (t0) cc_final: 0.8097 (t0) REVERT: U 213 ARG cc_start: 0.7689 (ttp-110) cc_final: 0.6882 (ttp80) REVERT: U 217 ASP cc_start: 0.7622 (m-30) cc_final: 0.7198 (m-30) REVERT: U 225 GLU cc_start: 0.7844 (tp30) cc_final: 0.7551 (tp30) REVERT: U 239 ASP cc_start: 0.7910 (t0) cc_final: 0.7669 (t0) REVERT: U 280 MET cc_start: 0.8222 (tpp) cc_final: 0.7930 (tpp) REVERT: U 318 ASN cc_start: 0.8362 (t0) cc_final: 0.8139 (t0) REVERT: U 361 TYR cc_start: 0.9119 (m-80) cc_final: 0.8817 (m-80) REVERT: W 129 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7713 (mp10) REVERT: W 217 ASP cc_start: 0.7444 (m-30) cc_final: 0.6731 (m-30) REVERT: W 221 ASN cc_start: 0.8442 (m-40) cc_final: 0.8083 (m110) REVERT: W 239 ASP cc_start: 0.7970 (t0) cc_final: 0.7628 (t0) REVERT: W 271 LEU cc_start: 0.8440 (mt) cc_final: 0.8220 (mt) REVERT: W 280 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7628 (mpp) REVERT: W 288 GLU cc_start: 0.7865 (mp0) cc_final: 0.7495 (mp0) REVERT: Y 7 SER cc_start: 0.9188 (t) cc_final: 0.8934 (m) REVERT: Y 53 ASP cc_start: 0.8353 (t0) cc_final: 0.8006 (t0) REVERT: Y 86 GLN cc_start: 0.8559 (mt0) cc_final: 0.8275 (mt0) REVERT: Y 89 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8542 (mm-40) REVERT: Y 99 ILE cc_start: 0.9259 (mm) cc_final: 0.9012 (tp) REVERT: Y 213 ARG cc_start: 0.7635 (ttp-110) cc_final: 0.7098 (ttp-110) REVERT: Y 217 ASP cc_start: 0.7592 (m-30) cc_final: 0.7301 (m-30) REVERT: Y 239 ASP cc_start: 0.7945 (t0) cc_final: 0.7601 (t0) REVERT: Y 288 GLU cc_start: 0.7833 (mp0) cc_final: 0.7380 (mp0) REVERT: Y 318 ASN cc_start: 0.8339 (t0) cc_final: 0.8016 (t0) REVERT: 0 86 GLN cc_start: 0.8444 (mt0) cc_final: 0.8119 (mt0) REVERT: 0 148 GLU cc_start: 0.7746 (pt0) cc_final: 0.7524 (mt-10) REVERT: 0 239 ASP cc_start: 0.7717 (t0) cc_final: 0.7414 (t0) REVERT: 0 288 GLU cc_start: 0.7674 (mp0) cc_final: 0.7287 (mp0) REVERT: 0 318 ASN cc_start: 0.8464 (t0) cc_final: 0.8038 (t0) REVERT: 2 82 GLU cc_start: 0.7378 (tt0) cc_final: 0.7152 (tt0) REVERT: 2 164 ASN cc_start: 0.8668 (t0) cc_final: 0.8070 (t0) REVERT: 2 213 ARG cc_start: 0.7662 (mtp-110) cc_final: 0.7098 (ttp-110) REVERT: 2 217 ASP cc_start: 0.7335 (m-30) cc_final: 0.7017 (m-30) REVERT: 2 239 ASP cc_start: 0.7839 (t0) cc_final: 0.7408 (t0) REVERT: 2 280 MET cc_start: 0.8316 (tpp) cc_final: 0.7936 (mmt) REVERT: 2 288 GLU cc_start: 0.7787 (mp0) cc_final: 0.7307 (mp0) REVERT: 2 318 ASN cc_start: 0.8354 (t0) cc_final: 0.8013 (t0) REVERT: 2 371 ARG cc_start: 0.8245 (mmt90) cc_final: 0.7984 (mmt90) outliers start: 150 outliers final: 86 residues processed: 1198 average time/residue: 0.5787 time to fit residues: 1135.1629 Evaluate side-chains 1108 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1016 time to evaluate : 5.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 255 CYS Chi-restraints excluded: chain H residue 297 GLU Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 297 GLU Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain J residue 380 LEU Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 49 SER Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 193 LEU Chi-restraints excluded: chain L residue 297 GLU Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 159 ASP Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 319 SER Chi-restraints excluded: chain N residue 332 LEU Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 94 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 297 GLU Chi-restraints excluded: chain P residue 304 GLN Chi-restraints excluded: chain P residue 332 LEU Chi-restraints excluded: chain P residue 376 VAL Chi-restraints excluded: chain S residue 12 LYS Chi-restraints excluded: chain S residue 49 SER Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain U residue 42 ASP Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 49 SER Chi-restraints excluded: chain U residue 94 ASP Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 186 ASP Chi-restraints excluded: chain U residue 193 LEU Chi-restraints excluded: chain U residue 321 GLN Chi-restraints excluded: chain U residue 332 LEU Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 44 SER Chi-restraints excluded: chain W residue 129 GLN Chi-restraints excluded: chain W residue 166 ILE Chi-restraints excluded: chain W residue 280 MET Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain Y residue 45 ILE Chi-restraints excluded: chain Y residue 49 SER Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Y residue 304 GLN Chi-restraints excluded: chain Y residue 319 SER Chi-restraints excluded: chain Y residue 375 LYS Chi-restraints excluded: chain 0 residue 42 ASP Chi-restraints excluded: chain 0 residue 45 ILE Chi-restraints excluded: chain 0 residue 49 SER Chi-restraints excluded: chain 0 residue 94 ASP Chi-restraints excluded: chain 0 residue 159 ASP Chi-restraints excluded: chain 0 residue 297 GLU Chi-restraints excluded: chain 0 residue 304 GLN Chi-restraints excluded: chain 0 residue 332 LEU Chi-restraints excluded: chain 0 residue 355 SER Chi-restraints excluded: chain 2 residue 45 ILE Chi-restraints excluded: chain 2 residue 49 SER Chi-restraints excluded: chain 2 residue 94 ASP Chi-restraints excluded: chain 2 residue 111 GLN Chi-restraints excluded: chain 2 residue 149 ASN Chi-restraints excluded: chain 2 residue 297 GLU Chi-restraints excluded: chain 2 residue 319 SER Chi-restraints excluded: chain 2 residue 332 LEU Chi-restraints excluded: chain 2 residue 369 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 512 optimal weight: 3.9990 chunk 389 optimal weight: 5.9990 chunk 269 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 247 optimal weight: 1.9990 chunk 348 optimal weight: 0.5980 chunk 520 optimal weight: 1.9990 chunk 550 optimal weight: 4.9990 chunk 271 optimal weight: 5.9990 chunk 493 optimal weight: 0.2980 chunk 148 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 86 GLN H 164 ASN ** H 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 321 GLN W 86 GLN 2 221 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 47670 Z= 0.198 Angle : 0.553 9.197 64860 Z= 0.283 Chirality : 0.041 0.160 7470 Planarity : 0.004 0.058 7980 Dihedral : 8.433 69.449 7249 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.72 % Allowed : 13.31 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.11), residues: 5625 helix: -0.46 (0.09), residues: 3195 sheet: 0.26 (0.28), residues: 375 loop : -0.37 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 215 HIS 0.003 0.001 HIS W 287 PHE 0.017 0.002 PHE Y 209 TYR 0.013 0.001 TYR 2 361 ARG 0.006 0.000 ARG N 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1217 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1085 time to evaluate : 5.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8757 (pp) REVERT: B 213 ARG cc_start: 0.7658 (ttp-110) cc_final: 0.6721 (ttp80) REVERT: B 217 ASP cc_start: 0.7353 (m-30) cc_final: 0.6843 (m-30) REVERT: B 239 ASP cc_start: 0.7885 (t0) cc_final: 0.7674 (t0) REVERT: B 318 ASN cc_start: 0.8484 (t0) cc_final: 0.8161 (t0) REVERT: B 361 TYR cc_start: 0.9094 (m-80) cc_final: 0.8732 (m-80) REVERT: A 28 ILE cc_start: 0.8802 (mt) cc_final: 0.8491 (mp) REVERT: A 86 GLN cc_start: 0.8413 (mt0) cc_final: 0.8195 (mt0) REVERT: A 115 THR cc_start: 0.8701 (p) cc_final: 0.8408 (t) REVERT: A 123 MET cc_start: 0.6460 (mmm) cc_final: 0.5656 (mmm) REVERT: A 164 ASN cc_start: 0.8450 (t0) cc_final: 0.7990 (t0) REVERT: A 213 ARG cc_start: 0.7681 (ttp-110) cc_final: 0.6885 (ttp-110) REVERT: A 217 ASP cc_start: 0.7392 (m-30) cc_final: 0.6746 (m-30) REVERT: A 225 GLU cc_start: 0.7820 (tp30) cc_final: 0.7555 (mm-30) REVERT: A 226 ASP cc_start: 0.8065 (p0) cc_final: 0.7796 (p0) REVERT: A 239 ASP cc_start: 0.7979 (t0) cc_final: 0.7711 (t0) REVERT: A 252 GLU cc_start: 0.8275 (tt0) cc_final: 0.8055 (mt-10) REVERT: A 280 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7713 (mpp) REVERT: A 288 GLU cc_start: 0.7800 (mp0) cc_final: 0.7416 (mp0) REVERT: A 318 ASN cc_start: 0.8365 (t0) cc_final: 0.8117 (t0) REVERT: A 342 GLU cc_start: 0.7274 (mp0) cc_final: 0.6979 (mp0) REVERT: D 103 GLU cc_start: 0.8114 (mp0) cc_final: 0.7675 (mp0) REVERT: D 123 MET cc_start: 0.5483 (mmt) cc_final: 0.4973 (mmm) REVERT: D 213 ARG cc_start: 0.7623 (ttp-110) cc_final: 0.6858 (ttp-110) REVERT: D 217 ASP cc_start: 0.7436 (m-30) cc_final: 0.6984 (m-30) REVERT: D 225 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7378 (mm-30) REVERT: D 239 ASP cc_start: 0.7971 (t0) cc_final: 0.7448 (t0) REVERT: D 263 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7634 (mt-10) REVERT: D 288 GLU cc_start: 0.7718 (mp0) cc_final: 0.7473 (mp0) REVERT: D 318 ASN cc_start: 0.8511 (t0) cc_final: 0.8309 (t0) REVERT: F 57 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7758 (mtp180) REVERT: F 89 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8402 (mm-40) REVERT: F 217 ASP cc_start: 0.7473 (m-30) cc_final: 0.6907 (m-30) REVERT: F 225 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7409 (mm-30) REVERT: F 239 ASP cc_start: 0.7851 (t0) cc_final: 0.7399 (t0) REVERT: F 318 ASN cc_start: 0.8480 (t0) cc_final: 0.8198 (t0) REVERT: H 53 ASP cc_start: 0.8169 (t0) cc_final: 0.7804 (t0) REVERT: H 213 ARG cc_start: 0.7633 (ttm110) cc_final: 0.7305 (ttm110) REVERT: H 217 ASP cc_start: 0.7441 (m-30) cc_final: 0.7023 (m-30) REVERT: H 239 ASP cc_start: 0.7741 (t0) cc_final: 0.7288 (t0) REVERT: J 103 GLU cc_start: 0.7925 (mp0) cc_final: 0.7695 (mp0) REVERT: J 164 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8094 (t0) REVERT: J 213 ARG cc_start: 0.7707 (ttp-110) cc_final: 0.7048 (ttp-110) REVERT: J 217 ASP cc_start: 0.7374 (m-30) cc_final: 0.6798 (m-30) REVERT: J 239 ASP cc_start: 0.7773 (t0) cc_final: 0.7546 (t0) REVERT: J 255 CYS cc_start: 0.8450 (t) cc_final: 0.7960 (t) REVERT: J 263 GLU cc_start: 0.7696 (mp0) cc_final: 0.7342 (mp0) REVERT: J 318 ASN cc_start: 0.8383 (t0) cc_final: 0.8060 (t0) REVERT: J 344 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7723 (mm-30) REVERT: J 375 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7581 (mptt) REVERT: L 213 ARG cc_start: 0.7783 (ttp-110) cc_final: 0.7058 (ttp-110) REVERT: L 217 ASP cc_start: 0.7420 (m-30) cc_final: 0.6918 (m-30) REVERT: L 225 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7419 (mm-30) REVERT: L 239 ASP cc_start: 0.8053 (t0) cc_final: 0.7794 (t0) REVERT: L 393 LEU cc_start: 0.8318 (tt) cc_final: 0.7403 (mp) REVERT: N 103 GLU cc_start: 0.8017 (mp0) cc_final: 0.7816 (mp0) REVERT: N 239 ASP cc_start: 0.7970 (t0) cc_final: 0.7715 (t0) REVERT: N 317 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7437 (mm-30) REVERT: P 36 ILE cc_start: 0.8703 (mm) cc_final: 0.8366 (mm) REVERT: P 186 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7768 (p0) REVERT: P 213 ARG cc_start: 0.7740 (ttp-110) cc_final: 0.7309 (ttp-110) REVERT: P 217 ASP cc_start: 0.7309 (m-30) cc_final: 0.6889 (m-30) REVERT: P 239 ASP cc_start: 0.7801 (t0) cc_final: 0.7356 (t0) REVERT: P 288 GLU cc_start: 0.7782 (mp0) cc_final: 0.7376 (mp0) REVERT: P 308 GLU cc_start: 0.7558 (pm20) cc_final: 0.7167 (pm20) REVERT: P 318 ASN cc_start: 0.8300 (t0) cc_final: 0.8006 (t0) REVERT: S 103 GLU cc_start: 0.7924 (mp0) cc_final: 0.7662 (mp0) REVERT: S 209 PHE cc_start: 0.8883 (m-80) cc_final: 0.8554 (m-10) REVERT: S 213 ARG cc_start: 0.7864 (ttm110) cc_final: 0.7053 (ttp-110) REVERT: S 217 ASP cc_start: 0.7443 (m-30) cc_final: 0.7125 (m-30) REVERT: S 239 ASP cc_start: 0.7769 (t0) cc_final: 0.7502 (t0) REVERT: S 318 ASN cc_start: 0.8412 (t0) cc_final: 0.8047 (t0) REVERT: U 213 ARG cc_start: 0.7684 (ttp-110) cc_final: 0.6831 (ttp80) REVERT: U 217 ASP cc_start: 0.7621 (m-30) cc_final: 0.7192 (m-30) REVERT: U 225 GLU cc_start: 0.7864 (tp30) cc_final: 0.7606 (tp30) REVERT: U 280 MET cc_start: 0.8218 (tpp) cc_final: 0.7953 (tpp) REVERT: U 318 ASN cc_start: 0.8174 (t0) cc_final: 0.7887 (t0) REVERT: U 361 TYR cc_start: 0.9086 (m-80) cc_final: 0.8773 (m-80) REVERT: W 217 ASP cc_start: 0.7410 (m-30) cc_final: 0.6876 (m-30) REVERT: W 225 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7679 (mm-30) REVERT: W 280 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7611 (mpp) REVERT: W 317 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7514 (mm-30) REVERT: Y 7 SER cc_start: 0.9133 (t) cc_final: 0.8901 (m) REVERT: Y 28 ILE cc_start: 0.8841 (mt) cc_final: 0.8602 (mt) REVERT: Y 53 ASP cc_start: 0.8264 (t0) cc_final: 0.7909 (t0) REVERT: Y 86 GLN cc_start: 0.8500 (mt0) cc_final: 0.8133 (mt0) REVERT: Y 89 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8518 (mm-40) REVERT: Y 115 THR cc_start: 0.8585 (p) cc_final: 0.8248 (t) REVERT: Y 213 ARG cc_start: 0.7602 (ttp-110) cc_final: 0.7135 (ttp-110) REVERT: Y 217 ASP cc_start: 0.7438 (m-30) cc_final: 0.7229 (m-30) REVERT: Y 239 ASP cc_start: 0.7885 (t0) cc_final: 0.7554 (t0) REVERT: Y 288 GLU cc_start: 0.7783 (mp0) cc_final: 0.7311 (mp0) REVERT: Y 292 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7504 (mt-10) REVERT: Y 318 ASN cc_start: 0.8315 (t0) cc_final: 0.8014 (t0) REVERT: 0 28 ILE cc_start: 0.8835 (mt) cc_final: 0.8576 (mt) REVERT: 0 86 GLN cc_start: 0.8416 (mt0) cc_final: 0.8190 (mt0) REVERT: 0 115 THR cc_start: 0.8648 (p) cc_final: 0.8325 (t) REVERT: 0 239 ASP cc_start: 0.7719 (t0) cc_final: 0.7452 (t0) REVERT: 0 246 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.8177 (p0) REVERT: 0 288 GLU cc_start: 0.7660 (mp0) cc_final: 0.7304 (mp0) REVERT: 0 318 ASN cc_start: 0.8376 (t0) cc_final: 0.8007 (t0) REVERT: 2 213 ARG cc_start: 0.7707 (mtp-110) cc_final: 0.7165 (ttp-110) REVERT: 2 217 ASP cc_start: 0.7245 (m-30) cc_final: 0.6979 (m-30) REVERT: 2 239 ASP cc_start: 0.7776 (t0) cc_final: 0.7433 (t0) REVERT: 2 280 MET cc_start: 0.8285 (tpp) cc_final: 0.8024 (mmm) REVERT: 2 288 GLU cc_start: 0.7783 (mp0) cc_final: 0.7449 (mp0) REVERT: 2 318 ASN cc_start: 0.8291 (t0) cc_final: 0.7972 (t0) REVERT: 2 371 ARG cc_start: 0.8170 (mmt90) cc_final: 0.7904 (mmt90) outliers start: 132 outliers final: 78 residues processed: 1160 average time/residue: 0.5913 time to fit residues: 1118.2968 Evaluate side-chains 1073 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 986 time to evaluate : 5.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 297 GLU Chi-restraints excluded: chain H residue 304 GLN Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain H residue 375 LYS Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 164 ASN Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain J residue 246 ASN Chi-restraints excluded: chain J residue 297 GLU Chi-restraints excluded: chain J residue 321 GLN Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain J residue 380 LEU Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 297 GLU Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 159 ASP Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 288 GLU Chi-restraints excluded: chain N residue 319 SER Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 57 ARG Chi-restraints excluded: chain P residue 94 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 186 ASP Chi-restraints excluded: chain P residue 246 ASN Chi-restraints excluded: chain P residue 252 GLU Chi-restraints excluded: chain P residue 297 GLU Chi-restraints excluded: chain P residue 375 LYS Chi-restraints excluded: chain S residue 49 SER Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain U residue 42 ASP Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 94 ASP Chi-restraints excluded: chain U residue 186 ASP Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 49 SER Chi-restraints excluded: chain W residue 102 LEU Chi-restraints excluded: chain W residue 129 GLN Chi-restraints excluded: chain W residue 166 ILE Chi-restraints excluded: chain W residue 280 MET Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Y residue 159 ASP Chi-restraints excluded: chain Y residue 252 GLU Chi-restraints excluded: chain Y residue 304 GLN Chi-restraints excluded: chain Y residue 319 SER Chi-restraints excluded: chain Y residue 375 LYS Chi-restraints excluded: chain 0 residue 42 ASP Chi-restraints excluded: chain 0 residue 94 ASP Chi-restraints excluded: chain 0 residue 102 LEU Chi-restraints excluded: chain 0 residue 159 ASP Chi-restraints excluded: chain 0 residue 246 ASN Chi-restraints excluded: chain 0 residue 297 GLU Chi-restraints excluded: chain 0 residue 332 LEU Chi-restraints excluded: chain 2 residue 94 ASP Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 111 GLN Chi-restraints excluded: chain 2 residue 149 ASN Chi-restraints excluded: chain 2 residue 304 GLN Chi-restraints excluded: chain 2 residue 319 SER Chi-restraints excluded: chain 2 residue 332 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 458 optimal weight: 20.0000 chunk 312 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 410 optimal weight: 8.9990 chunk 227 optimal weight: 20.0000 chunk 470 optimal weight: 7.9990 chunk 380 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 281 optimal weight: 2.9990 chunk 494 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 86 GLN H 164 ASN W 86 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 47670 Z= 0.479 Angle : 0.669 8.988 64860 Z= 0.338 Chirality : 0.046 0.207 7470 Planarity : 0.005 0.066 7980 Dihedral : 8.357 69.061 7247 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.49 % Allowed : 12.65 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.11), residues: 5625 helix: -0.35 (0.09), residues: 3210 sheet: 0.16 (0.29), residues: 375 loop : -0.58 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 215 HIS 0.004 0.002 HIS B 33 PHE 0.029 0.002 PHE L 209 TYR 0.019 0.002 TYR 0 361 ARG 0.012 0.001 ARG F 213 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1262 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 1044 time to evaluate : 5.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8855 (pp) REVERT: B 213 ARG cc_start: 0.7771 (ttp-110) cc_final: 0.6885 (ttp80) REVERT: B 217 ASP cc_start: 0.7430 (m-30) cc_final: 0.6922 (m-30) REVERT: B 226 ASP cc_start: 0.8035 (p0) cc_final: 0.7424 (p0) REVERT: B 239 ASP cc_start: 0.8008 (t0) cc_final: 0.7664 (t0) REVERT: B 361 TYR cc_start: 0.9120 (m-80) cc_final: 0.8798 (m-80) REVERT: A 92 THR cc_start: 0.8667 (t) cc_final: 0.8464 (t) REVERT: A 123 MET cc_start: 0.6373 (mmm) cc_final: 0.5436 (mmm) REVERT: A 164 ASN cc_start: 0.8513 (t0) cc_final: 0.8036 (t0) REVERT: A 213 ARG cc_start: 0.7768 (ttp-110) cc_final: 0.6976 (ttp-110) REVERT: A 217 ASP cc_start: 0.7475 (m-30) cc_final: 0.6874 (m-30) REVERT: A 225 GLU cc_start: 0.7875 (tp30) cc_final: 0.7583 (mm-30) REVERT: A 239 ASP cc_start: 0.8055 (t0) cc_final: 0.7749 (t0) REVERT: A 280 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7761 (mpp) REVERT: A 288 GLU cc_start: 0.7886 (mp0) cc_final: 0.7328 (mp0) REVERT: A 318 ASN cc_start: 0.8495 (t0) cc_final: 0.8278 (t0) REVERT: D 103 GLU cc_start: 0.8139 (mp0) cc_final: 0.7742 (mp0) REVERT: D 213 ARG cc_start: 0.7672 (ttp-110) cc_final: 0.6833 (ttp-110) REVERT: D 217 ASP cc_start: 0.7401 (m-30) cc_final: 0.6910 (m-30) REVERT: D 225 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7436 (mm-30) REVERT: D 239 ASP cc_start: 0.8108 (t0) cc_final: 0.7613 (t0) REVERT: D 263 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7678 (mt-10) REVERT: D 288 GLU cc_start: 0.7732 (mp0) cc_final: 0.7382 (mp0) REVERT: F 213 ARG cc_start: 0.7737 (ttp-110) cc_final: 0.7076 (ttp-110) REVERT: F 217 ASP cc_start: 0.7607 (m-30) cc_final: 0.7078 (m-30) REVERT: F 225 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7446 (mm-30) REVERT: F 239 ASP cc_start: 0.7886 (t0) cc_final: 0.7391 (t0) REVERT: F 300 MET cc_start: 0.8666 (mtm) cc_final: 0.8433 (mtt) REVERT: F 318 ASN cc_start: 0.8611 (t0) cc_final: 0.8306 (t0) REVERT: F 332 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8949 (tm) REVERT: H 53 ASP cc_start: 0.8232 (t0) cc_final: 0.7843 (t0) REVERT: H 213 ARG cc_start: 0.7726 (ttm110) cc_final: 0.7355 (ttm110) REVERT: H 217 ASP cc_start: 0.7478 (m-30) cc_final: 0.6907 (m-30) REVERT: H 221 ASN cc_start: 0.8520 (m-40) cc_final: 0.8306 (m110) REVERT: H 239 ASP cc_start: 0.7842 (t0) cc_final: 0.7449 (t0) REVERT: H 271 LEU cc_start: 0.8675 (mt) cc_final: 0.8432 (mt) REVERT: H 280 MET cc_start: 0.8137 (mmm) cc_final: 0.7865 (mmt) REVERT: H 318 ASN cc_start: 0.8566 (t0) cc_final: 0.8334 (t0) REVERT: J 36 ILE cc_start: 0.8661 (mm) cc_final: 0.8444 (mm) REVERT: J 103 GLU cc_start: 0.7962 (mp0) cc_final: 0.7726 (mp0) REVERT: J 239 ASP cc_start: 0.7814 (t0) cc_final: 0.7552 (t0) REVERT: J 263 GLU cc_start: 0.7834 (mp0) cc_final: 0.7453 (mp0) REVERT: J 280 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7470 (mpp) REVERT: J 318 ASN cc_start: 0.8461 (t0) cc_final: 0.8136 (t0) REVERT: J 347 MET cc_start: 0.8525 (ttt) cc_final: 0.8175 (ttt) REVERT: J 375 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7579 (mptt) REVERT: L 213 ARG cc_start: 0.7848 (ttp-110) cc_final: 0.7240 (ttp-110) REVERT: L 217 ASP cc_start: 0.7516 (m-30) cc_final: 0.7057 (m-30) REVERT: L 225 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7633 (mm-30) REVERT: L 239 ASP cc_start: 0.8078 (t0) cc_final: 0.7814 (t0) REVERT: L 380 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7903 (tt) REVERT: N 63 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7794 (m-30) REVERT: N 148 GLU cc_start: 0.7763 (pt0) cc_final: 0.7469 (mt-10) REVERT: N 225 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7714 (mm-30) REVERT: N 239 ASP cc_start: 0.7993 (t0) cc_final: 0.7764 (t0) REVERT: N 317 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7619 (mm-30) REVERT: P 36 ILE cc_start: 0.8906 (mm) cc_final: 0.8582 (mm) REVERT: P 213 ARG cc_start: 0.7791 (ttp-110) cc_final: 0.7257 (ttp-110) REVERT: P 217 ASP cc_start: 0.7408 (m-30) cc_final: 0.6968 (m-30) REVERT: P 233 MET cc_start: 0.8794 (mtm) cc_final: 0.8426 (mtp) REVERT: P 239 ASP cc_start: 0.7861 (t0) cc_final: 0.7408 (t0) REVERT: P 308 GLU cc_start: 0.7578 (pm20) cc_final: 0.7170 (pm20) REVERT: P 318 ASN cc_start: 0.8509 (t0) cc_final: 0.8206 (t0) REVERT: S 28 ILE cc_start: 0.8910 (mt) cc_final: 0.8690 (mp) REVERT: S 103 GLU cc_start: 0.7956 (mp0) cc_final: 0.7694 (mp0) REVERT: S 209 PHE cc_start: 0.9048 (m-80) cc_final: 0.8648 (m-10) REVERT: S 213 ARG cc_start: 0.7933 (ttm110) cc_final: 0.7278 (ttp-110) REVERT: S 217 ASP cc_start: 0.7451 (m-30) cc_final: 0.7110 (m-30) REVERT: S 239 ASP cc_start: 0.7943 (t0) cc_final: 0.7663 (t0) REVERT: S 318 ASN cc_start: 0.8525 (t0) cc_final: 0.8190 (t0) REVERT: U 213 ARG cc_start: 0.7728 (ttp-110) cc_final: 0.6768 (ttp80) REVERT: U 217 ASP cc_start: 0.7626 (m-30) cc_final: 0.7124 (m-30) REVERT: U 225 GLU cc_start: 0.7916 (tp30) cc_final: 0.7589 (tp30) REVERT: U 239 ASP cc_start: 0.8206 (t0) cc_final: 0.7759 (t0) REVERT: U 280 MET cc_start: 0.8297 (tpp) cc_final: 0.7976 (tpp) REVERT: U 318 ASN cc_start: 0.8399 (t0) cc_final: 0.8170 (t0) REVERT: W 129 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7682 (mp10) REVERT: W 239 ASP cc_start: 0.8190 (t0) cc_final: 0.7811 (t0) REVERT: W 317 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7665 (mm-30) REVERT: W 380 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7934 (tt) REVERT: Y 7 SER cc_start: 0.9218 (t) cc_final: 0.8912 (m) REVERT: Y 28 ILE cc_start: 0.8938 (mt) cc_final: 0.8620 (mt) REVERT: Y 86 GLN cc_start: 0.8610 (mt0) cc_final: 0.8283 (mt0) REVERT: Y 115 THR cc_start: 0.8625 (p) cc_final: 0.8279 (t) REVERT: Y 213 ARG cc_start: 0.7618 (ttp-110) cc_final: 0.7225 (ttp-110) REVERT: Y 239 ASP cc_start: 0.7956 (t0) cc_final: 0.7582 (t0) REVERT: Y 288 GLU cc_start: 0.7904 (mp0) cc_final: 0.7421 (mp0) REVERT: Y 318 ASN cc_start: 0.8465 (t0) cc_final: 0.7990 (t0) REVERT: Y 323 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8692 (ttmm) REVERT: 0 28 ILE cc_start: 0.8950 (mt) cc_final: 0.8567 (mt) REVERT: 0 36 ILE cc_start: 0.8723 (mm) cc_final: 0.8434 (mm) REVERT: 0 115 THR cc_start: 0.8622 (p) cc_final: 0.8269 (t) REVERT: 0 164 ASN cc_start: 0.8103 (t0) cc_final: 0.7902 (t0) REVERT: 0 239 ASP cc_start: 0.7849 (t0) cc_final: 0.7613 (t0) REVERT: 0 246 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8388 (p0) REVERT: 0 288 GLU cc_start: 0.7785 (mp0) cc_final: 0.7250 (mp0) REVERT: 0 318 ASN cc_start: 0.8462 (t0) cc_final: 0.8063 (t0) REVERT: 0 337 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8432 (mmp) REVERT: 2 164 ASN cc_start: 0.8681 (t0) cc_final: 0.8039 (t0) REVERT: 2 213 ARG cc_start: 0.7733 (mtp-110) cc_final: 0.7222 (ttp-110) REVERT: 2 217 ASP cc_start: 0.7289 (m-30) cc_final: 0.7038 (m-30) REVERT: 2 239 ASP cc_start: 0.7912 (t0) cc_final: 0.7542 (t0) REVERT: 2 280 MET cc_start: 0.8363 (tpp) cc_final: 0.7958 (mmm) REVERT: 2 318 ASN cc_start: 0.8432 (t0) cc_final: 0.8131 (t0) outliers start: 218 outliers final: 136 residues processed: 1179 average time/residue: 0.5732 time to fit residues: 1104.3905 Evaluate side-chains 1156 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1007 time to evaluate : 5.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 304 GLN Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 246 ASN Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 255 CYS Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 355 SER Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 255 CYS Chi-restraints excluded: chain H residue 297 GLU Chi-restraints excluded: chain H residue 304 GLN Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain H residue 367 GLU Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain J residue 258 ASP Chi-restraints excluded: chain J residue 280 MET Chi-restraints excluded: chain J residue 297 GLU Chi-restraints excluded: chain J residue 320 ILE Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 355 SER Chi-restraints excluded: chain J residue 367 GLU Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain J residue 380 LEU Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 49 SER Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 193 LEU Chi-restraints excluded: chain L residue 246 ASN Chi-restraints excluded: chain L residue 258 ASP Chi-restraints excluded: chain L residue 297 GLU Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain L residue 367 GLU Chi-restraints excluded: chain L residue 380 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 44 SER Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 63 ASP Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 159 ASP Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 304 GLN Chi-restraints excluded: chain N residue 319 SER Chi-restraints excluded: chain N residue 332 LEU Chi-restraints excluded: chain N residue 367 GLU Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 57 ARG Chi-restraints excluded: chain P residue 94 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 186 ASP Chi-restraints excluded: chain P residue 252 GLU Chi-restraints excluded: chain P residue 297 GLU Chi-restraints excluded: chain P residue 369 VAL Chi-restraints excluded: chain P residue 375 LYS Chi-restraints excluded: chain S residue 49 SER Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain S residue 246 ASN Chi-restraints excluded: chain S residue 332 LEU Chi-restraints excluded: chain S residue 367 GLU Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 42 ASP Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain U residue 49 SER Chi-restraints excluded: chain U residue 94 ASP Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 186 ASP Chi-restraints excluded: chain U residue 193 LEU Chi-restraints excluded: chain U residue 246 ASN Chi-restraints excluded: chain U residue 332 LEU Chi-restraints excluded: chain U residue 367 GLU Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 44 SER Chi-restraints excluded: chain W residue 45 ILE Chi-restraints excluded: chain W residue 49 SER Chi-restraints excluded: chain W residue 129 GLN Chi-restraints excluded: chain W residue 166 ILE Chi-restraints excluded: chain W residue 252 GLU Chi-restraints excluded: chain W residue 258 ASP Chi-restraints excluded: chain W residue 367 GLU Chi-restraints excluded: chain W residue 380 LEU Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain Y residue 45 ILE Chi-restraints excluded: chain Y residue 49 SER Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Y residue 148 GLU Chi-restraints excluded: chain Y residue 159 ASP Chi-restraints excluded: chain Y residue 193 LEU Chi-restraints excluded: chain Y residue 252 GLU Chi-restraints excluded: chain Y residue 258 ASP Chi-restraints excluded: chain Y residue 304 GLN Chi-restraints excluded: chain Y residue 319 SER Chi-restraints excluded: chain Y residue 323 LYS Chi-restraints excluded: chain Y residue 375 LYS Chi-restraints excluded: chain 0 residue 42 ASP Chi-restraints excluded: chain 0 residue 45 ILE Chi-restraints excluded: chain 0 residue 49 SER Chi-restraints excluded: chain 0 residue 94 ASP Chi-restraints excluded: chain 0 residue 159 ASP Chi-restraints excluded: chain 0 residue 246 ASN Chi-restraints excluded: chain 0 residue 297 GLU Chi-restraints excluded: chain 0 residue 332 LEU Chi-restraints excluded: chain 0 residue 337 MET Chi-restraints excluded: chain 0 residue 367 GLU Chi-restraints excluded: chain 2 residue 42 ASP Chi-restraints excluded: chain 2 residue 45 ILE Chi-restraints excluded: chain 2 residue 49 SER Chi-restraints excluded: chain 2 residue 94 ASP Chi-restraints excluded: chain 2 residue 111 GLN Chi-restraints excluded: chain 2 residue 297 GLU Chi-restraints excluded: chain 2 residue 304 GLN Chi-restraints excluded: chain 2 residue 319 SER Chi-restraints excluded: chain 2 residue 332 LEU Chi-restraints excluded: chain 2 residue 367 GLU Chi-restraints excluded: chain 2 residue 369 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 185 optimal weight: 1.9990 chunk 496 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 323 optimal weight: 6.9990 chunk 136 optimal weight: 0.9990 chunk 551 optimal weight: 5.9990 chunk 457 optimal weight: 20.0000 chunk 255 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 182 optimal weight: 0.8980 chunk 289 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 305 GLN H 86 GLN H 321 GLN W 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 47670 Z= 0.184 Angle : 0.550 9.533 64860 Z= 0.278 Chirality : 0.040 0.149 7470 Planarity : 0.004 0.060 7980 Dihedral : 8.343 71.206 7247 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.33 % Allowed : 14.28 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.12), residues: 5625 helix: 0.01 (0.09), residues: 3225 sheet: 0.16 (0.29), residues: 375 loop : -0.28 (0.15), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 215 HIS 0.003 0.001 HIS J 287 PHE 0.019 0.001 PHE L 209 TYR 0.013 0.001 TYR 0 361 ARG 0.011 0.000 ARG N 392 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1243 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1081 time to evaluate : 5.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8792 (pp) REVERT: B 213 ARG cc_start: 0.7675 (ttp-110) cc_final: 0.6770 (ttp80) REVERT: B 217 ASP cc_start: 0.7343 (m-30) cc_final: 0.6831 (m-30) REVERT: B 239 ASP cc_start: 0.7880 (t0) cc_final: 0.7543 (t0) REVERT: B 249 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8267 (ptm160) REVERT: B 361 TYR cc_start: 0.9091 (m-80) cc_final: 0.8754 (m-80) REVERT: A 123 MET cc_start: 0.6258 (mmm) cc_final: 0.5320 (mmm) REVERT: A 213 ARG cc_start: 0.7710 (ttp-110) cc_final: 0.7502 (ttp-110) REVERT: A 225 GLU cc_start: 0.7847 (tp30) cc_final: 0.7569 (mm-30) REVERT: A 239 ASP cc_start: 0.7943 (t0) cc_final: 0.7665 (t0) REVERT: A 280 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7677 (mpp) REVERT: A 288 GLU cc_start: 0.7839 (mp0) cc_final: 0.7453 (mp0) REVERT: D 103 GLU cc_start: 0.8122 (mp0) cc_final: 0.7649 (mp0) REVERT: D 213 ARG cc_start: 0.7631 (ttp-110) cc_final: 0.6829 (ttp-110) REVERT: D 217 ASP cc_start: 0.7428 (m-30) cc_final: 0.6899 (m-30) REVERT: D 225 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7426 (mm-30) REVERT: D 239 ASP cc_start: 0.7969 (t0) cc_final: 0.7384 (t0) REVERT: D 263 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7616 (mt-10) REVERT: F 53 ASP cc_start: 0.8146 (t0) cc_final: 0.7814 (t0) REVERT: F 57 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7660 (mtp180) REVERT: F 89 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8448 (mm-40) REVERT: F 225 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7475 (mm-30) REVERT: F 239 ASP cc_start: 0.7777 (t0) cc_final: 0.7553 (t0) REVERT: F 318 ASN cc_start: 0.8477 (t0) cc_final: 0.8174 (t0) REVERT: H 12 LYS cc_start: 0.8261 (mmtt) cc_final: 0.8045 (mmtt) REVERT: H 213 ARG cc_start: 0.7664 (ttm110) cc_final: 0.7055 (ttp-110) REVERT: H 217 ASP cc_start: 0.7421 (m-30) cc_final: 0.6971 (m-30) REVERT: H 239 ASP cc_start: 0.7715 (t0) cc_final: 0.7320 (t0) REVERT: H 280 MET cc_start: 0.8084 (mmm) cc_final: 0.7778 (mmt) REVERT: H 300 MET cc_start: 0.8482 (mtm) cc_final: 0.8271 (mtt) REVERT: H 318 ASN cc_start: 0.8359 (t0) cc_final: 0.8116 (t0) REVERT: J 103 GLU cc_start: 0.7967 (mp0) cc_final: 0.7747 (mp0) REVERT: J 217 ASP cc_start: 0.7425 (m-30) cc_final: 0.6789 (m-30) REVERT: J 225 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7631 (mm-30) REVERT: J 255 CYS cc_start: 0.8504 (t) cc_final: 0.7990 (t) REVERT: J 263 GLU cc_start: 0.7699 (mp0) cc_final: 0.7341 (mp0) REVERT: J 280 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7405 (mpp) REVERT: J 318 ASN cc_start: 0.8367 (t0) cc_final: 0.8084 (t0) REVERT: J 347 MET cc_start: 0.8425 (ttt) cc_final: 0.8151 (ttt) REVERT: J 375 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7492 (mptt) REVERT: L 213 ARG cc_start: 0.7853 (ttp-110) cc_final: 0.7161 (ttp-110) REVERT: L 217 ASP cc_start: 0.7370 (m-30) cc_final: 0.6861 (m-30) REVERT: L 225 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7584 (mm-30) REVERT: L 239 ASP cc_start: 0.7981 (t0) cc_final: 0.7736 (t0) REVERT: L 393 LEU cc_start: 0.8327 (tt) cc_final: 0.7332 (mp) REVERT: N 217 ASP cc_start: 0.7493 (m-30) cc_final: 0.6972 (m-30) REVERT: N 225 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7714 (mm-30) REVERT: N 239 ASP cc_start: 0.7917 (t0) cc_final: 0.7700 (t0) REVERT: N 314 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8828 (t) REVERT: N 317 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7533 (mm-30) REVERT: P 36 ILE cc_start: 0.8898 (mm) cc_final: 0.8571 (mm) REVERT: P 86 GLN cc_start: 0.8531 (mt0) cc_final: 0.8251 (mt0) REVERT: P 192 GLU cc_start: 0.7581 (mp0) cc_final: 0.7375 (mt-10) REVERT: P 213 ARG cc_start: 0.7738 (ttp-110) cc_final: 0.7206 (ttp-110) REVERT: P 217 ASP cc_start: 0.7385 (m-30) cc_final: 0.6887 (m-30) REVERT: P 239 ASP cc_start: 0.7769 (t0) cc_final: 0.7325 (t0) REVERT: P 288 GLU cc_start: 0.7846 (mp0) cc_final: 0.7552 (mp0) REVERT: P 308 GLU cc_start: 0.7541 (pm20) cc_final: 0.7120 (pm20) REVERT: P 318 ASN cc_start: 0.8307 (t0) cc_final: 0.7995 (t0) REVERT: S 103 GLU cc_start: 0.7958 (mp0) cc_final: 0.7699 (mp0) REVERT: S 209 PHE cc_start: 0.8906 (m-80) cc_final: 0.8570 (m-10) REVERT: S 213 ARG cc_start: 0.7855 (ttm110) cc_final: 0.7203 (ttp-110) REVERT: S 217 ASP cc_start: 0.7403 (m-30) cc_final: 0.7098 (m-30) REVERT: S 239 ASP cc_start: 0.7837 (t0) cc_final: 0.7545 (t0) REVERT: S 318 ASN cc_start: 0.8408 (t0) cc_final: 0.8067 (t0) REVERT: U 32 LYS cc_start: 0.8279 (mttp) cc_final: 0.7848 (mmtt) REVERT: U 213 ARG cc_start: 0.7643 (ttp-110) cc_final: 0.6727 (ttp80) REVERT: U 217 ASP cc_start: 0.7632 (m-30) cc_final: 0.7178 (m-30) REVERT: U 225 GLU cc_start: 0.7865 (tp30) cc_final: 0.7587 (tp30) REVERT: U 239 ASP cc_start: 0.8047 (t0) cc_final: 0.7785 (t0) REVERT: U 280 MET cc_start: 0.8225 (tpp) cc_final: 0.7940 (tpp) REVERT: U 318 ASN cc_start: 0.8270 (t0) cc_final: 0.8062 (t0) REVERT: U 361 TYR cc_start: 0.9090 (m-80) cc_final: 0.8727 (m-80) REVERT: W 28 ILE cc_start: 0.9060 (mt) cc_final: 0.8747 (mt) REVERT: W 225 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7581 (mm-30) REVERT: W 239 ASP cc_start: 0.8155 (t0) cc_final: 0.7790 (t0) REVERT: W 317 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7648 (mm-30) REVERT: W 380 LEU cc_start: 0.8035 (tt) cc_final: 0.7815 (tt) REVERT: Y 86 GLN cc_start: 0.8552 (mt0) cc_final: 0.8236 (mt0) REVERT: Y 213 ARG cc_start: 0.7517 (ttp-110) cc_final: 0.7200 (ttp-110) REVERT: Y 239 ASP cc_start: 0.7857 (t0) cc_final: 0.7578 (t0) REVERT: Y 288 GLU cc_start: 0.7859 (mp0) cc_final: 0.7501 (mp0) REVERT: Y 318 ASN cc_start: 0.8315 (t0) cc_final: 0.7888 (t0) REVERT: Y 323 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8521 (ttmm) REVERT: 0 28 ILE cc_start: 0.8868 (mt) cc_final: 0.8544 (mt) REVERT: 0 225 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7501 (mm-30) REVERT: 0 288 GLU cc_start: 0.7720 (mp0) cc_final: 0.7346 (mp0) REVERT: 0 318 ASN cc_start: 0.8309 (t0) cc_final: 0.7965 (t0) REVERT: 2 213 ARG cc_start: 0.7721 (mtp-110) cc_final: 0.7166 (ttp-110) REVERT: 2 217 ASP cc_start: 0.7254 (m-30) cc_final: 0.6987 (m-30) REVERT: 2 239 ASP cc_start: 0.7777 (t0) cc_final: 0.7411 (t0) REVERT: 2 280 MET cc_start: 0.8301 (tpp) cc_final: 0.7940 (mmm) REVERT: 2 288 GLU cc_start: 0.7836 (mp0) cc_final: 0.7543 (mp0) REVERT: 2 318 ASN cc_start: 0.8262 (t0) cc_final: 0.7984 (t0) REVERT: 2 371 ARG cc_start: 0.8113 (mmt90) cc_final: 0.7898 (mmt90) outliers start: 162 outliers final: 104 residues processed: 1179 average time/residue: 0.6224 time to fit residues: 1198.1012 Evaluate side-chains 1131 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1018 time to evaluate : 5.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 304 GLN Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 246 ASN Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 255 CYS Chi-restraints excluded: chain H residue 297 GLU Chi-restraints excluded: chain H residue 304 GLN Chi-restraints excluded: chain H residue 321 GLN Chi-restraints excluded: chain H residue 367 GLU Chi-restraints excluded: chain H residue 375 LYS Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 246 ASN Chi-restraints excluded: chain J residue 280 MET Chi-restraints excluded: chain J residue 297 GLU Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 367 GLU Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain J residue 380 LEU Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 246 ASN Chi-restraints excluded: chain L residue 297 GLU Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain L residue 367 GLU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 44 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 159 ASP Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 288 GLU Chi-restraints excluded: chain N residue 314 VAL Chi-restraints excluded: chain N residue 319 SER Chi-restraints excluded: chain N residue 332 LEU Chi-restraints excluded: chain N residue 367 GLU Chi-restraints excluded: chain P residue 57 ARG Chi-restraints excluded: chain P residue 94 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 159 ASP Chi-restraints excluded: chain P residue 246 ASN Chi-restraints excluded: chain P residue 252 GLU Chi-restraints excluded: chain P residue 255 CYS Chi-restraints excluded: chain P residue 297 GLU Chi-restraints excluded: chain P residue 355 SER Chi-restraints excluded: chain P residue 369 VAL Chi-restraints excluded: chain P residue 375 LYS Chi-restraints excluded: chain S residue 34 ILE Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain S residue 246 ASN Chi-restraints excluded: chain S residue 367 GLU Chi-restraints excluded: chain U residue 42 ASP Chi-restraints excluded: chain U residue 94 ASP Chi-restraints excluded: chain U residue 186 ASP Chi-restraints excluded: chain U residue 255 CYS Chi-restraints excluded: chain U residue 332 LEU Chi-restraints excluded: chain U residue 375 LYS Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 44 SER Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain W residue 102 LEU Chi-restraints excluded: chain W residue 129 GLN Chi-restraints excluded: chain W residue 258 ASP Chi-restraints excluded: chain W residue 304 GLN Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Y residue 159 ASP Chi-restraints excluded: chain Y residue 252 GLU Chi-restraints excluded: chain Y residue 304 GLN Chi-restraints excluded: chain Y residue 319 SER Chi-restraints excluded: chain Y residue 323 LYS Chi-restraints excluded: chain Y residue 367 GLU Chi-restraints excluded: chain Y residue 375 LYS Chi-restraints excluded: chain 0 residue 42 ASP Chi-restraints excluded: chain 0 residue 94 ASP Chi-restraints excluded: chain 0 residue 102 LEU Chi-restraints excluded: chain 0 residue 159 ASP Chi-restraints excluded: chain 0 residue 297 GLU Chi-restraints excluded: chain 0 residue 319 SER Chi-restraints excluded: chain 0 residue 332 LEU Chi-restraints excluded: chain 2 residue 42 ASP Chi-restraints excluded: chain 2 residue 94 ASP Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 255 CYS Chi-restraints excluded: chain 2 residue 304 GLN Chi-restraints excluded: chain 2 residue 319 SER Chi-restraints excluded: chain 2 residue 367 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 531 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 314 optimal weight: 0.3980 chunk 402 optimal weight: 5.9990 chunk 312 optimal weight: 1.9990 chunk 464 optimal weight: 2.9990 chunk 307 optimal weight: 0.8980 chunk 549 optimal weight: 9.9990 chunk 343 optimal weight: 7.9990 chunk 334 optimal weight: 6.9990 chunk 253 optimal weight: 0.7980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 ASN H 86 GLN H 202 GLN ** L 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 321 GLN U 86 GLN W 86 GLN 0 305 GLN 2 86 GLN 2 345 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 47670 Z= 0.181 Angle : 0.552 10.137 64860 Z= 0.276 Chirality : 0.040 0.151 7470 Planarity : 0.004 0.056 7980 Dihedral : 8.255 72.089 7247 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.13 % Allowed : 15.19 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.12), residues: 5625 helix: 0.35 (0.09), residues: 3165 sheet: 0.12 (0.29), residues: 375 loop : -0.13 (0.15), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP W 215 HIS 0.003 0.001 HIS A 287 PHE 0.017 0.001 PHE U 209 TYR 0.011 0.001 TYR Y 361 ARG 0.013 0.000 ARG N 392 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1214 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1062 time to evaluate : 4.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8690 (pp) REVERT: B 213 ARG cc_start: 0.7682 (ttp-110) cc_final: 0.6786 (ttp80) REVERT: B 217 ASP cc_start: 0.7306 (m-30) cc_final: 0.6803 (m-30) REVERT: B 239 ASP cc_start: 0.7847 (t0) cc_final: 0.7529 (t0) REVERT: B 361 TYR cc_start: 0.9086 (m-80) cc_final: 0.8759 (m-80) REVERT: A 123 MET cc_start: 0.6288 (mmm) cc_final: 0.5364 (mmm) REVERT: A 225 GLU cc_start: 0.7834 (tp30) cc_final: 0.7572 (mm-30) REVERT: A 239 ASP cc_start: 0.7822 (t0) cc_final: 0.7518 (t0) REVERT: A 280 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7650 (mpp) REVERT: D 103 GLU cc_start: 0.8148 (mp0) cc_final: 0.7637 (mp0) REVERT: D 213 ARG cc_start: 0.7622 (ttp-110) cc_final: 0.6803 (ttp-110) REVERT: D 217 ASP cc_start: 0.7407 (m-30) cc_final: 0.6867 (m-30) REVERT: D 225 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7348 (mm-30) REVERT: D 239 ASP cc_start: 0.7952 (t0) cc_final: 0.7376 (t0) REVERT: D 263 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7541 (mt-10) REVERT: F 57 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7673 (mtp180) REVERT: F 89 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8410 (mm-40) REVERT: F 192 GLU cc_start: 0.7556 (mp0) cc_final: 0.7295 (mt-10) REVERT: F 225 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7506 (mm-30) REVERT: F 239 ASP cc_start: 0.7788 (t0) cc_final: 0.7553 (t0) REVERT: F 318 ASN cc_start: 0.8457 (t0) cc_final: 0.8160 (t0) REVERT: F 342 GLU cc_start: 0.7314 (mp0) cc_final: 0.7003 (mp0) REVERT: H 213 ARG cc_start: 0.7636 (ttm110) cc_final: 0.6974 (ttp-110) REVERT: H 217 ASP cc_start: 0.7415 (m-30) cc_final: 0.6944 (m-30) REVERT: H 239 ASP cc_start: 0.7711 (t0) cc_final: 0.7340 (t0) REVERT: H 308 GLU cc_start: 0.7488 (pm20) cc_final: 0.7282 (pm20) REVERT: J 28 ILE cc_start: 0.9050 (mt) cc_final: 0.8746 (mt) REVERT: J 217 ASP cc_start: 0.7353 (m-30) cc_final: 0.6691 (m-30) REVERT: J 225 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7661 (mm-30) REVERT: J 239 ASP cc_start: 0.7776 (t0) cc_final: 0.7404 (t0) REVERT: J 263 GLU cc_start: 0.7630 (mp0) cc_final: 0.7329 (mp0) REVERT: J 280 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7410 (mpp) REVERT: J 318 ASN cc_start: 0.8316 (t0) cc_final: 0.8025 (t0) REVERT: J 347 MET cc_start: 0.8402 (ttt) cc_final: 0.8142 (ttt) REVERT: J 375 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7437 (mptt) REVERT: L 213 ARG cc_start: 0.7858 (ttp-110) cc_final: 0.7148 (ttp-110) REVERT: L 217 ASP cc_start: 0.7374 (m-30) cc_final: 0.6839 (m-30) REVERT: L 225 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7601 (mm-30) REVERT: L 239 ASP cc_start: 0.7976 (t0) cc_final: 0.7718 (t0) REVERT: L 393 LEU cc_start: 0.8262 (tt) cc_final: 0.7306 (mp) REVERT: N 192 GLU cc_start: 0.7568 (mp0) cc_final: 0.7316 (mt-10) REVERT: N 217 ASP cc_start: 0.7441 (m-30) cc_final: 0.6953 (m-30) REVERT: N 225 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7759 (mm-30) REVERT: N 314 VAL cc_start: 0.9042 (OUTLIER) cc_final: 0.8768 (t) REVERT: N 317 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7351 (mm-30) REVERT: P 12 LYS cc_start: 0.8354 (mmmt) cc_final: 0.7874 (mttt) REVERT: P 36 ILE cc_start: 0.8792 (mm) cc_final: 0.8432 (mm) REVERT: P 103 GLU cc_start: 0.7946 (mp0) cc_final: 0.7735 (mp0) REVERT: P 192 GLU cc_start: 0.7572 (mp0) cc_final: 0.7350 (mt-10) REVERT: P 213 ARG cc_start: 0.7717 (ttp-110) cc_final: 0.7253 (ttp-110) REVERT: P 217 ASP cc_start: 0.7367 (m-30) cc_final: 0.6852 (m-30) REVERT: P 239 ASP cc_start: 0.7762 (t0) cc_final: 0.7512 (t0) REVERT: P 288 GLU cc_start: 0.7955 (mp0) cc_final: 0.7589 (mp0) REVERT: P 308 GLU cc_start: 0.7557 (pm20) cc_final: 0.7129 (pm20) REVERT: P 318 ASN cc_start: 0.8291 (t0) cc_final: 0.7994 (t0) REVERT: P 367 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6484 (pt0) REVERT: S 12 LYS cc_start: 0.8432 (mmtt) cc_final: 0.8129 (mmtt) REVERT: S 103 GLU cc_start: 0.7936 (mp0) cc_final: 0.7677 (mp0) REVERT: S 209 PHE cc_start: 0.8873 (m-80) cc_final: 0.8526 (m-10) REVERT: S 213 ARG cc_start: 0.7880 (ttm110) cc_final: 0.7298 (ttp-110) REVERT: S 217 ASP cc_start: 0.7409 (m-30) cc_final: 0.7099 (m-30) REVERT: S 225 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7811 (mm-30) REVERT: S 318 ASN cc_start: 0.8379 (t0) cc_final: 0.8051 (t0) REVERT: U 32 LYS cc_start: 0.8219 (mttp) cc_final: 0.7817 (mmtt) REVERT: U 213 ARG cc_start: 0.7661 (ttp-110) cc_final: 0.6731 (ttp80) REVERT: U 217 ASP cc_start: 0.7583 (m-30) cc_final: 0.7126 (m-30) REVERT: U 225 GLU cc_start: 0.7884 (tp30) cc_final: 0.7607 (tp30) REVERT: U 239 ASP cc_start: 0.8053 (t0) cc_final: 0.7781 (t0) REVERT: U 280 MET cc_start: 0.8187 (tpp) cc_final: 0.7916 (tpp) REVERT: U 361 TYR cc_start: 0.9076 (m-80) cc_final: 0.8750 (m-80) REVERT: W 28 ILE cc_start: 0.9059 (mt) cc_final: 0.8733 (mt) REVERT: W 239 ASP cc_start: 0.8058 (t0) cc_final: 0.7702 (t0) REVERT: W 317 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7649 (mm-30) REVERT: Y 213 ARG cc_start: 0.7471 (ttp-110) cc_final: 0.7232 (ttp-110) REVERT: Y 239 ASP cc_start: 0.7809 (t0) cc_final: 0.7513 (t0) REVERT: Y 288 GLU cc_start: 0.7861 (mp0) cc_final: 0.7546 (mp0) REVERT: Y 318 ASN cc_start: 0.8266 (t0) cc_final: 0.7999 (t0) REVERT: Y 323 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8485 (ttmm) REVERT: 0 28 ILE cc_start: 0.8864 (mt) cc_final: 0.8648 (mt) REVERT: 0 164 ASN cc_start: 0.8120 (t0) cc_final: 0.7912 (t0) REVERT: 0 225 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7620 (mm-30) REVERT: 0 239 ASP cc_start: 0.7960 (t0) cc_final: 0.7688 (t0) REVERT: 0 246 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.8258 (p0) REVERT: 0 288 GLU cc_start: 0.7729 (mp0) cc_final: 0.7381 (mp0) REVERT: 0 318 ASN cc_start: 0.8271 (t0) cc_final: 0.7960 (t0) REVERT: 2 213 ARG cc_start: 0.7726 (mtp-110) cc_final: 0.7128 (ttp-110) REVERT: 2 217 ASP cc_start: 0.7184 (m-30) cc_final: 0.6899 (m-30) REVERT: 2 239 ASP cc_start: 0.7733 (t0) cc_final: 0.7532 (t0) REVERT: 2 280 MET cc_start: 0.8292 (tpp) cc_final: 0.7930 (mmm) REVERT: 2 288 GLU cc_start: 0.7822 (mp0) cc_final: 0.7523 (mp0) REVERT: 2 318 ASN cc_start: 0.8220 (t0) cc_final: 0.7970 (t0) outliers start: 152 outliers final: 106 residues processed: 1160 average time/residue: 0.6211 time to fit residues: 1181.5950 Evaluate side-chains 1109 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 993 time to evaluate : 5.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 304 GLN Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 246 ASN Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 355 SER Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 255 CYS Chi-restraints excluded: chain H residue 297 GLU Chi-restraints excluded: chain H residue 304 GLN Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain H residue 367 GLU Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 246 ASN Chi-restraints excluded: chain J residue 280 MET Chi-restraints excluded: chain J residue 297 GLU Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 367 GLU Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 246 ASN Chi-restraints excluded: chain L residue 297 GLU Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain L residue 367 GLU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 31 ILE Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 159 ASP Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 314 VAL Chi-restraints excluded: chain N residue 321 GLN Chi-restraints excluded: chain N residue 332 LEU Chi-restraints excluded: chain N residue 367 GLU Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 57 ARG Chi-restraints excluded: chain P residue 94 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 186 ASP Chi-restraints excluded: chain P residue 246 ASN Chi-restraints excluded: chain P residue 252 GLU Chi-restraints excluded: chain P residue 297 GLU Chi-restraints excluded: chain P residue 355 SER Chi-restraints excluded: chain P residue 367 GLU Chi-restraints excluded: chain P residue 375 LYS Chi-restraints excluded: chain S residue 42 ASP Chi-restraints excluded: chain S residue 49 SER Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain S residue 304 GLN Chi-restraints excluded: chain S residue 332 LEU Chi-restraints excluded: chain S residue 367 GLU Chi-restraints excluded: chain U residue 42 ASP Chi-restraints excluded: chain U residue 94 ASP Chi-restraints excluded: chain U residue 186 ASP Chi-restraints excluded: chain U residue 246 ASN Chi-restraints excluded: chain U residue 332 LEU Chi-restraints excluded: chain U residue 367 GLU Chi-restraints excluded: chain U residue 375 LYS Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 49 SER Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain W residue 102 LEU Chi-restraints excluded: chain W residue 129 GLN Chi-restraints excluded: chain W residue 252 GLU Chi-restraints excluded: chain W residue 258 ASP Chi-restraints excluded: chain W residue 367 GLU Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Y residue 159 ASP Chi-restraints excluded: chain Y residue 252 GLU Chi-restraints excluded: chain Y residue 258 ASP Chi-restraints excluded: chain Y residue 304 GLN Chi-restraints excluded: chain Y residue 319 SER Chi-restraints excluded: chain Y residue 323 LYS Chi-restraints excluded: chain Y residue 367 GLU Chi-restraints excluded: chain Y residue 375 LYS Chi-restraints excluded: chain 0 residue 42 ASP Chi-restraints excluded: chain 0 residue 94 ASP Chi-restraints excluded: chain 0 residue 102 LEU Chi-restraints excluded: chain 0 residue 159 ASP Chi-restraints excluded: chain 0 residue 246 ASN Chi-restraints excluded: chain 0 residue 297 GLU Chi-restraints excluded: chain 0 residue 332 LEU Chi-restraints excluded: chain 2 residue 42 ASP Chi-restraints excluded: chain 2 residue 94 ASP Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 255 CYS Chi-restraints excluded: chain 2 residue 319 SER Chi-restraints excluded: chain 2 residue 345 ASN Chi-restraints excluded: chain 2 residue 367 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 339 optimal weight: 4.9990 chunk 219 optimal weight: 0.8980 chunk 328 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 349 optimal weight: 6.9990 chunk 374 optimal weight: 0.9990 chunk 271 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 431 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 86 GLN H 202 GLN ** L 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 86 GLN U 86 GLN W 86 GLN Y 86 GLN 2 86 GLN 2 345 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 47670 Z= 0.284 Angle : 0.584 10.531 64860 Z= 0.292 Chirality : 0.042 0.127 7470 Planarity : 0.004 0.058 7980 Dihedral : 8.210 71.375 7247 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.27 % Allowed : 15.39 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.12), residues: 5625 helix: 0.51 (0.10), residues: 3120 sheet: 0.07 (0.29), residues: 375 loop : -0.20 (0.14), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 215 HIS 0.003 0.001 HIS A 287 PHE 0.020 0.001 PHE H 209 TYR 0.013 0.001 TYR 0 361 ARG 0.013 0.000 ARG N 392 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1187 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1028 time to evaluate : 5.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8747 (pp) REVERT: B 213 ARG cc_start: 0.7693 (ttp-110) cc_final: 0.6815 (ttp80) REVERT: B 217 ASP cc_start: 0.7389 (m-30) cc_final: 0.6854 (m-30) REVERT: B 361 TYR cc_start: 0.9099 (m-80) cc_final: 0.8743 (m-80) REVERT: A 103 GLU cc_start: 0.8106 (mp0) cc_final: 0.7639 (mp0) REVERT: A 123 MET cc_start: 0.6259 (mmm) cc_final: 0.5318 (mmm) REVERT: A 164 ASN cc_start: 0.8453 (t0) cc_final: 0.7959 (t0) REVERT: A 192 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7358 (mt-10) REVERT: A 225 GLU cc_start: 0.7881 (tp30) cc_final: 0.7605 (mm-30) REVERT: A 239 ASP cc_start: 0.7775 (t0) cc_final: 0.7491 (t0) REVERT: A 280 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7680 (mpp) REVERT: D 103 GLU cc_start: 0.8169 (mp0) cc_final: 0.7679 (mp0) REVERT: D 213 ARG cc_start: 0.7655 (ttp-110) cc_final: 0.6818 (ttp-110) REVERT: D 217 ASP cc_start: 0.7404 (m-30) cc_final: 0.6865 (m-30) REVERT: D 225 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7300 (mm-30) REVERT: D 239 ASP cc_start: 0.7961 (t0) cc_final: 0.7420 (t0) REVERT: F 12 LYS cc_start: 0.8388 (mtpt) cc_final: 0.8138 (mttt) REVERT: F 53 ASP cc_start: 0.8164 (t0) cc_final: 0.7929 (t0) REVERT: F 89 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8397 (mm-40) REVERT: F 225 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7479 (mm-30) REVERT: F 239 ASP cc_start: 0.7779 (t0) cc_final: 0.7555 (t0) REVERT: F 300 MET cc_start: 0.8406 (mtm) cc_final: 0.8139 (mtt) REVERT: F 318 ASN cc_start: 0.8521 (t0) cc_final: 0.8220 (t0) REVERT: F 323 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8657 (ttmm) REVERT: F 342 GLU cc_start: 0.7467 (mp0) cc_final: 0.7201 (mp0) REVERT: H 12 LYS cc_start: 0.8159 (mmtt) cc_final: 0.7922 (mmtt) REVERT: H 213 ARG cc_start: 0.7749 (ttm110) cc_final: 0.7123 (ttp-110) REVERT: H 217 ASP cc_start: 0.7434 (m-30) cc_final: 0.7029 (m-30) REVERT: H 239 ASP cc_start: 0.7716 (t0) cc_final: 0.7342 (t0) REVERT: H 280 MET cc_start: 0.8089 (mmm) cc_final: 0.7856 (mmt) REVERT: H 308 GLU cc_start: 0.7523 (pm20) cc_final: 0.7305 (pm20) REVERT: H 318 ASN cc_start: 0.8444 (t0) cc_final: 0.8178 (t0) REVERT: J 28 ILE cc_start: 0.9088 (mt) cc_final: 0.8747 (mt) REVERT: J 217 ASP cc_start: 0.7422 (m-30) cc_final: 0.6765 (m-30) REVERT: J 225 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7640 (mm-30) REVERT: J 239 ASP cc_start: 0.7773 (t0) cc_final: 0.7407 (t0) REVERT: J 263 GLU cc_start: 0.7742 (mp0) cc_final: 0.7421 (mp0) REVERT: J 318 ASN cc_start: 0.8378 (t0) cc_final: 0.8126 (t0) REVERT: J 347 MET cc_start: 0.8468 (ttt) cc_final: 0.8204 (ttt) REVERT: J 375 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7404 (mptt) REVERT: L 213 ARG cc_start: 0.7871 (ttp-110) cc_final: 0.7189 (ttp-110) REVERT: L 217 ASP cc_start: 0.7428 (m-30) cc_final: 0.6903 (m-30) REVERT: L 225 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7687 (mm-30) REVERT: L 239 ASP cc_start: 0.7997 (t0) cc_final: 0.7728 (t0) REVERT: L 393 LEU cc_start: 0.8268 (tt) cc_final: 0.7370 (mp) REVERT: N 217 ASP cc_start: 0.7468 (m-30) cc_final: 0.6952 (m-30) REVERT: N 225 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7849 (mm-30) REVERT: N 239 ASP cc_start: 0.8036 (t0) cc_final: 0.7646 (t0) REVERT: N 314 VAL cc_start: 0.9058 (OUTLIER) cc_final: 0.8837 (t) REVERT: N 317 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7572 (mm-30) REVERT: N 342 GLU cc_start: 0.7407 (mp0) cc_final: 0.6998 (mp0) REVERT: P 36 ILE cc_start: 0.8844 (mm) cc_final: 0.8481 (mm) REVERT: P 103 GLU cc_start: 0.7963 (mp0) cc_final: 0.7749 (mp0) REVERT: P 192 GLU cc_start: 0.7616 (mp0) cc_final: 0.7345 (mt-10) REVERT: P 213 ARG cc_start: 0.7723 (ttp-110) cc_final: 0.7240 (ttp-110) REVERT: P 217 ASP cc_start: 0.7390 (m-30) cc_final: 0.6842 (m-30) REVERT: P 239 ASP cc_start: 0.7789 (t0) cc_final: 0.7558 (t0) REVERT: P 306 MET cc_start: 0.7920 (mtp) cc_final: 0.7632 (mtp) REVERT: P 308 GLU cc_start: 0.7585 (pm20) cc_final: 0.7172 (pm20) REVERT: P 318 ASN cc_start: 0.8367 (t0) cc_final: 0.8061 (t0) REVERT: P 367 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.6522 (pt0) REVERT: S 12 LYS cc_start: 0.8423 (mmtt) cc_final: 0.8197 (mmmt) REVERT: S 103 GLU cc_start: 0.7935 (mp0) cc_final: 0.7679 (mp0) REVERT: S 129 GLN cc_start: 0.8033 (mp10) cc_final: 0.7816 (mp10) REVERT: S 209 PHE cc_start: 0.8936 (m-80) cc_final: 0.8592 (m-10) REVERT: S 213 ARG cc_start: 0.7885 (ttm110) cc_final: 0.7339 (ttp-110) REVERT: S 217 ASP cc_start: 0.7430 (m-30) cc_final: 0.7122 (m-30) REVERT: S 225 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7788 (mm-30) REVERT: S 318 ASN cc_start: 0.8413 (t0) cc_final: 0.8091 (t0) REVERT: U 213 ARG cc_start: 0.7677 (ttp-110) cc_final: 0.6748 (ttp80) REVERT: U 217 ASP cc_start: 0.7583 (m-30) cc_final: 0.7129 (m-30) REVERT: U 225 GLU cc_start: 0.7899 (tp30) cc_final: 0.7614 (tp30) REVERT: U 239 ASP cc_start: 0.8102 (t0) cc_final: 0.7806 (t0) REVERT: U 280 MET cc_start: 0.8204 (tpp) cc_final: 0.7916 (tpp) REVERT: W 28 ILE cc_start: 0.9086 (mt) cc_final: 0.8742 (mt) REVERT: W 129 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7637 (mp-120) REVERT: W 239 ASP cc_start: 0.8052 (t0) cc_final: 0.7717 (t0) REVERT: W 317 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7712 (mm-30) REVERT: Y 32 LYS cc_start: 0.8209 (mttp) cc_final: 0.7987 (mttp) REVERT: Y 239 ASP cc_start: 0.7842 (t0) cc_final: 0.7539 (t0) REVERT: Y 288 GLU cc_start: 0.7889 (mp0) cc_final: 0.7443 (mp0) REVERT: Y 318 ASN cc_start: 0.8312 (t0) cc_final: 0.8022 (t0) REVERT: Y 323 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8498 (ttmm) REVERT: 0 28 ILE cc_start: 0.8903 (mt) cc_final: 0.8650 (mt) REVERT: 0 36 ILE cc_start: 0.8863 (mm) cc_final: 0.8595 (mm) REVERT: 0 164 ASN cc_start: 0.8129 (t0) cc_final: 0.7923 (t0) REVERT: 0 225 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7578 (mm-30) REVERT: 0 226 ASP cc_start: 0.8263 (p0) cc_final: 0.8000 (p0) REVERT: 0 239 ASP cc_start: 0.7962 (t0) cc_final: 0.7695 (t0) REVERT: 0 246 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.8218 (p0) REVERT: 0 288 GLU cc_start: 0.7731 (mp0) cc_final: 0.7366 (mp0) REVERT: 0 318 ASN cc_start: 0.8320 (t0) cc_final: 0.7992 (t0) REVERT: 2 164 ASN cc_start: 0.8682 (t0) cc_final: 0.8249 (t0) REVERT: 2 213 ARG cc_start: 0.7734 (mtp-110) cc_final: 0.7147 (ttp-110) REVERT: 2 217 ASP cc_start: 0.7236 (m-30) cc_final: 0.6967 (m-30) REVERT: 2 280 MET cc_start: 0.8336 (tpp) cc_final: 0.7967 (mmm) REVERT: 2 288 GLU cc_start: 0.7832 (mp0) cc_final: 0.7478 (mp0) REVERT: 2 318 ASN cc_start: 0.8261 (t0) cc_final: 0.8026 (t0) outliers start: 159 outliers final: 122 residues processed: 1129 average time/residue: 0.5798 time to fit residues: 1071.0344 Evaluate side-chains 1127 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 994 time to evaluate : 5.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 304 GLN Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 246 ASN Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 323 LYS Chi-restraints excluded: chain F residue 355 SER Chi-restraints excluded: chain F residue 367 GLU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 255 CYS Chi-restraints excluded: chain H residue 297 GLU Chi-restraints excluded: chain H residue 304 GLN Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain H residue 355 SER Chi-restraints excluded: chain H residue 367 GLU Chi-restraints excluded: chain H residue 375 LYS Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 246 ASN Chi-restraints excluded: chain J residue 297 GLU Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain J residue 380 LEU Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 246 ASN Chi-restraints excluded: chain L residue 252 GLU Chi-restraints excluded: chain L residue 297 GLU Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain L residue 367 GLU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 31 ILE Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 159 ASP Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 314 VAL Chi-restraints excluded: chain N residue 319 SER Chi-restraints excluded: chain N residue 332 LEU Chi-restraints excluded: chain N residue 367 GLU Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 57 ARG Chi-restraints excluded: chain P residue 94 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 159 ASP Chi-restraints excluded: chain P residue 246 ASN Chi-restraints excluded: chain P residue 252 GLU Chi-restraints excluded: chain P residue 255 CYS Chi-restraints excluded: chain P residue 297 GLU Chi-restraints excluded: chain P residue 355 SER Chi-restraints excluded: chain P residue 367 GLU Chi-restraints excluded: chain P residue 375 LYS Chi-restraints excluded: chain S residue 42 ASP Chi-restraints excluded: chain S residue 49 SER Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain S residue 246 ASN Chi-restraints excluded: chain S residue 304 GLN Chi-restraints excluded: chain S residue 332 LEU Chi-restraints excluded: chain S residue 367 GLU Chi-restraints excluded: chain U residue 42 ASP Chi-restraints excluded: chain U residue 94 ASP Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 186 ASP Chi-restraints excluded: chain U residue 246 ASN Chi-restraints excluded: chain U residue 332 LEU Chi-restraints excluded: chain U residue 367 GLU Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 49 SER Chi-restraints excluded: chain W residue 129 GLN Chi-restraints excluded: chain W residue 252 GLU Chi-restraints excluded: chain W residue 258 ASP Chi-restraints excluded: chain W residue 367 GLU Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Y residue 102 LEU Chi-restraints excluded: chain Y residue 159 ASP Chi-restraints excluded: chain Y residue 246 ASN Chi-restraints excluded: chain Y residue 252 GLU Chi-restraints excluded: chain Y residue 258 ASP Chi-restraints excluded: chain Y residue 304 GLN Chi-restraints excluded: chain Y residue 319 SER Chi-restraints excluded: chain Y residue 323 LYS Chi-restraints excluded: chain Y residue 367 GLU Chi-restraints excluded: chain Y residue 375 LYS Chi-restraints excluded: chain 0 residue 45 ILE Chi-restraints excluded: chain 0 residue 94 ASP Chi-restraints excluded: chain 0 residue 105 VAL Chi-restraints excluded: chain 0 residue 159 ASP Chi-restraints excluded: chain 0 residue 246 ASN Chi-restraints excluded: chain 0 residue 297 GLU Chi-restraints excluded: chain 0 residue 319 SER Chi-restraints excluded: chain 0 residue 332 LEU Chi-restraints excluded: chain 0 residue 355 SER Chi-restraints excluded: chain 0 residue 367 GLU Chi-restraints excluded: chain 2 residue 42 ASP Chi-restraints excluded: chain 2 residue 49 SER Chi-restraints excluded: chain 2 residue 94 ASP Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 255 CYS Chi-restraints excluded: chain 2 residue 297 GLU Chi-restraints excluded: chain 2 residue 319 SER Chi-restraints excluded: chain 2 residue 332 LEU Chi-restraints excluded: chain 2 residue 345 ASN Chi-restraints excluded: chain 2 residue 367 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 499 optimal weight: 2.9990 chunk 526 optimal weight: 4.9990 chunk 480 optimal weight: 0.1980 chunk 511 optimal weight: 10.0000 chunk 308 optimal weight: 10.0000 chunk 223 optimal weight: 8.9990 chunk 402 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 462 optimal weight: 0.0980 chunk 484 optimal weight: 0.7980 chunk 510 optimal weight: 0.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 321 GLN H 86 GLN H 202 GLN ** L 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 86 GLN U 321 GLN W 86 GLN Y 86 GLN 2 86 GLN 2 301 ASN 2 345 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 47670 Z= 0.149 Angle : 0.544 11.377 64860 Z= 0.271 Chirality : 0.040 0.128 7470 Planarity : 0.004 0.057 7980 Dihedral : 8.245 73.071 7247 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.70 % Allowed : 16.30 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.12), residues: 5625 helix: 0.80 (0.10), residues: 3045 sheet: 0.00 (0.28), residues: 375 loop : -0.07 (0.15), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP W 215 HIS 0.003 0.001 HIS Y 287 PHE 0.012 0.001 PHE U 209 TYR 0.008 0.001 TYR 2 361 ARG 0.012 0.000 ARG N 392 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1222 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1091 time to evaluate : 5.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8691 (pp) REVERT: B 213 ARG cc_start: 0.7683 (ttp-110) cc_final: 0.6808 (ttp80) REVERT: B 217 ASP cc_start: 0.7287 (m-30) cc_final: 0.6771 (m-30) REVERT: B 239 ASP cc_start: 0.7945 (t0) cc_final: 0.7737 (t0) REVERT: B 361 TYR cc_start: 0.9059 (m-80) cc_final: 0.8770 (m-80) REVERT: A 103 GLU cc_start: 0.8053 (mp0) cc_final: 0.7571 (mp0) REVERT: A 123 MET cc_start: 0.6212 (mmm) cc_final: 0.5215 (mmm) REVERT: A 164 ASN cc_start: 0.8447 (t0) cc_final: 0.7940 (t0) REVERT: A 192 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7245 (mt-10) REVERT: A 225 GLU cc_start: 0.7795 (tp30) cc_final: 0.7578 (mm-30) REVERT: A 280 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7553 (mpp) REVERT: A 342 GLU cc_start: 0.7553 (pm20) cc_final: 0.7287 (pm20) REVERT: D 192 GLU cc_start: 0.7619 (mp0) cc_final: 0.7206 (mt-10) REVERT: D 213 ARG cc_start: 0.7681 (ttp-110) cc_final: 0.6782 (ttp-110) REVERT: D 217 ASP cc_start: 0.7348 (m-30) cc_final: 0.6756 (m-30) REVERT: D 225 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7282 (mm-30) REVERT: D 263 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7562 (mt-10) REVERT: F 89 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8406 (mm-40) REVERT: F 103 GLU cc_start: 0.8117 (mp0) cc_final: 0.7653 (mp0) REVERT: F 192 GLU cc_start: 0.7565 (mp0) cc_final: 0.7288 (mt-10) REVERT: F 225 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7450 (mm-30) REVERT: F 239 ASP cc_start: 0.7747 (t0) cc_final: 0.7529 (t0) REVERT: F 300 MET cc_start: 0.8286 (mtm) cc_final: 0.8050 (mtt) REVERT: F 318 ASN cc_start: 0.8350 (t0) cc_final: 0.8091 (t0) REVERT: F 323 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8606 (ttmm) REVERT: F 342 GLU cc_start: 0.7394 (mp0) cc_final: 0.7101 (mp0) REVERT: H 213 ARG cc_start: 0.7617 (ttm110) cc_final: 0.6961 (ttp-110) REVERT: H 217 ASP cc_start: 0.7404 (m-30) cc_final: 0.6894 (m-30) REVERT: H 239 ASP cc_start: 0.7626 (t0) cc_final: 0.7232 (t0) REVERT: H 308 GLU cc_start: 0.7496 (pm20) cc_final: 0.7266 (pm20) REVERT: H 318 ASN cc_start: 0.8323 (t0) cc_final: 0.8037 (t0) REVERT: J 28 ILE cc_start: 0.9034 (mt) cc_final: 0.8684 (mt) REVERT: J 217 ASP cc_start: 0.7277 (m-30) cc_final: 0.6595 (m-30) REVERT: J 225 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7574 (mm-30) REVERT: J 239 ASP cc_start: 0.7720 (t0) cc_final: 0.7373 (t0) REVERT: J 263 GLU cc_start: 0.7591 (mp0) cc_final: 0.7290 (mp0) REVERT: J 288 GLU cc_start: 0.7809 (mp0) cc_final: 0.7588 (mp0) REVERT: J 318 ASN cc_start: 0.8211 (t0) cc_final: 0.7965 (t0) REVERT: J 347 MET cc_start: 0.8321 (ttt) cc_final: 0.8113 (ttt) REVERT: J 375 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7344 (mptt) REVERT: L 192 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7176 (mt-10) REVERT: L 213 ARG cc_start: 0.7865 (ttp-110) cc_final: 0.7153 (ttp-110) REVERT: L 217 ASP cc_start: 0.7337 (m-30) cc_final: 0.6816 (m-30) REVERT: L 225 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7769 (mm-30) REVERT: L 239 ASP cc_start: 0.7896 (t0) cc_final: 0.7651 (t0) REVERT: L 393 LEU cc_start: 0.8222 (tt) cc_final: 0.7401 (mp) REVERT: N 192 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7323 (mt-10) REVERT: N 209 PHE cc_start: 0.8857 (m-80) cc_final: 0.8626 (m-10) REVERT: N 217 ASP cc_start: 0.7382 (m-30) cc_final: 0.6816 (m-30) REVERT: N 225 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7751 (mm-30) REVERT: N 239 ASP cc_start: 0.7943 (t0) cc_final: 0.7528 (t0) REVERT: N 260 TYR cc_start: 0.9108 (m-10) cc_final: 0.8855 (m-10) REVERT: N 314 VAL cc_start: 0.8958 (OUTLIER) cc_final: 0.8652 (t) REVERT: N 317 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7362 (mm-30) REVERT: N 342 GLU cc_start: 0.7377 (mp0) cc_final: 0.7056 (mp0) REVERT: P 192 GLU cc_start: 0.7503 (mp0) cc_final: 0.7267 (mt-10) REVERT: P 213 ARG cc_start: 0.7699 (ttp-110) cc_final: 0.7220 (ttp-110) REVERT: P 217 ASP cc_start: 0.7323 (m-30) cc_final: 0.6810 (m-30) REVERT: P 239 ASP cc_start: 0.7735 (t0) cc_final: 0.7516 (t0) REVERT: P 288 GLU cc_start: 0.7954 (mp0) cc_final: 0.7608 (mp0) REVERT: P 306 MET cc_start: 0.7876 (mtp) cc_final: 0.7548 (mtt) REVERT: P 308 GLU cc_start: 0.7544 (pm20) cc_final: 0.7114 (pm20) REVERT: P 318 ASN cc_start: 0.8198 (t0) cc_final: 0.7887 (t0) REVERT: P 342 GLU cc_start: 0.7656 (mp0) cc_final: 0.7359 (mp0) REVERT: S 103 GLU cc_start: 0.7901 (mp0) cc_final: 0.7609 (mp0) REVERT: S 213 ARG cc_start: 0.7845 (ttm110) cc_final: 0.7460 (ttm110) REVERT: S 217 ASP cc_start: 0.7402 (m-30) cc_final: 0.7077 (m-30) REVERT: S 318 ASN cc_start: 0.8308 (t0) cc_final: 0.7969 (t0) REVERT: U 32 LYS cc_start: 0.8190 (mttp) cc_final: 0.7822 (mmtt) REVERT: U 213 ARG cc_start: 0.7631 (ttp-110) cc_final: 0.6739 (ttp80) REVERT: U 217 ASP cc_start: 0.7540 (m-30) cc_final: 0.7071 (m-30) REVERT: U 225 GLU cc_start: 0.7894 (tp30) cc_final: 0.7637 (tp30) REVERT: U 239 ASP cc_start: 0.8035 (t0) cc_final: 0.7769 (t0) REVERT: U 280 MET cc_start: 0.8143 (tpp) cc_final: 0.7889 (tpp) REVERT: U 288 GLU cc_start: 0.7563 (mp0) cc_final: 0.7219 (mp0) REVERT: U 361 TYR cc_start: 0.9071 (m-80) cc_final: 0.8812 (m-80) REVERT: U 367 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.5968 (mt-10) REVERT: W 28 ILE cc_start: 0.9045 (mt) cc_final: 0.8706 (mt) REVERT: W 126 GLU cc_start: 0.7268 (tt0) cc_final: 0.7061 (tt0) REVERT: W 225 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7488 (mm-30) REVERT: W 239 ASP cc_start: 0.7957 (t0) cc_final: 0.7734 (t0) REVERT: W 317 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7615 (mm-30) REVERT: Y 164 ASN cc_start: 0.8586 (t0) cc_final: 0.8020 (t0) REVERT: Y 239 ASP cc_start: 0.7782 (t0) cc_final: 0.7464 (t0) REVERT: Y 288 GLU cc_start: 0.7795 (mp0) cc_final: 0.7390 (mp0) REVERT: Y 318 ASN cc_start: 0.8244 (t0) cc_final: 0.7955 (t0) REVERT: Y 323 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8434 (ttmm) REVERT: 0 164 ASN cc_start: 0.8179 (t0) cc_final: 0.7964 (t0) REVERT: 0 246 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8161 (p0) REVERT: 0 288 GLU cc_start: 0.7687 (mp0) cc_final: 0.7356 (mp0) REVERT: 0 306 MET cc_start: 0.7791 (mtp) cc_final: 0.7583 (mtp) REVERT: 0 318 ASN cc_start: 0.8197 (t0) cc_final: 0.7917 (t0) REVERT: 2 164 ASN cc_start: 0.8650 (t0) cc_final: 0.8222 (t0) REVERT: 2 213 ARG cc_start: 0.7715 (mtp-110) cc_final: 0.7113 (ttp-110) REVERT: 2 217 ASP cc_start: 0.7173 (m-30) cc_final: 0.6946 (m-30) REVERT: 2 280 MET cc_start: 0.8265 (tpp) cc_final: 0.7954 (mmm) REVERT: 2 288 GLU cc_start: 0.7757 (mp0) cc_final: 0.7503 (mp0) REVERT: 2 317 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7766 (mm-30) REVERT: 2 318 ASN cc_start: 0.8109 (t0) cc_final: 0.7895 (t0) REVERT: 2 371 ARG cc_start: 0.8037 (mmt90) cc_final: 0.7336 (ptm160) outliers start: 131 outliers final: 94 residues processed: 1170 average time/residue: 0.5778 time to fit residues: 1106.5798 Evaluate side-chains 1122 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1016 time to evaluate : 5.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 280 MET Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 246 ASN Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 323 LYS Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 255 CYS Chi-restraints excluded: chain H residue 297 GLU Chi-restraints excluded: chain H residue 304 GLN Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain H residue 367 GLU Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 246 ASN Chi-restraints excluded: chain J residue 297 GLU Chi-restraints excluded: chain J residue 304 GLN Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain J residue 380 LEU Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 192 GLU Chi-restraints excluded: chain L residue 252 GLU Chi-restraints excluded: chain L residue 297 GLU Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain L residue 367 GLU Chi-restraints excluded: chain N residue 31 ILE Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain N residue 159 ASP Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 192 GLU Chi-restraints excluded: chain N residue 314 VAL Chi-restraints excluded: chain N residue 332 LEU Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 57 ARG Chi-restraints excluded: chain P residue 94 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 149 ASN Chi-restraints excluded: chain P residue 159 ASP Chi-restraints excluded: chain P residue 246 ASN Chi-restraints excluded: chain P residue 252 GLU Chi-restraints excluded: chain P residue 297 GLU Chi-restraints excluded: chain P residue 375 LYS Chi-restraints excluded: chain S residue 42 ASP Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain S residue 246 ASN Chi-restraints excluded: chain U residue 42 ASP Chi-restraints excluded: chain U residue 94 ASP Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 186 ASP Chi-restraints excluded: chain U residue 246 ASN Chi-restraints excluded: chain U residue 252 GLU Chi-restraints excluded: chain U residue 332 LEU Chi-restraints excluded: chain U residue 367 GLU Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 49 SER Chi-restraints excluded: chain W residue 102 LEU Chi-restraints excluded: chain W residue 258 ASP Chi-restraints excluded: chain W residue 367 GLU Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Y residue 159 ASP Chi-restraints excluded: chain Y residue 246 ASN Chi-restraints excluded: chain Y residue 252 GLU Chi-restraints excluded: chain Y residue 319 SER Chi-restraints excluded: chain Y residue 323 LYS Chi-restraints excluded: chain Y residue 367 GLU Chi-restraints excluded: chain Y residue 375 LYS Chi-restraints excluded: chain 0 residue 42 ASP Chi-restraints excluded: chain 0 residue 94 ASP Chi-restraints excluded: chain 0 residue 159 ASP Chi-restraints excluded: chain 0 residue 246 ASN Chi-restraints excluded: chain 0 residue 297 GLU Chi-restraints excluded: chain 0 residue 367 GLU Chi-restraints excluded: chain 2 residue 49 SER Chi-restraints excluded: chain 2 residue 94 ASP Chi-restraints excluded: chain 2 residue 101 LEU Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 255 CYS Chi-restraints excluded: chain 2 residue 319 SER Chi-restraints excluded: chain 2 residue 345 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 336 optimal weight: 0.9990 chunk 541 optimal weight: 0.0070 chunk 330 optimal weight: 4.9990 chunk 256 optimal weight: 0.9990 chunk 376 optimal weight: 9.9990 chunk 567 optimal weight: 6.9990 chunk 522 optimal weight: 6.9990 chunk 452 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 349 optimal weight: 0.0050 chunk 277 optimal weight: 7.9990 overall best weight: 1.2018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 ASN H 202 GLN ** L 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 86 GLN W 86 GLN 2 86 GLN 2 345 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 47670 Z= 0.171 Angle : 0.554 10.806 64860 Z= 0.276 Chirality : 0.040 0.139 7470 Planarity : 0.004 0.057 7980 Dihedral : 8.191 73.061 7247 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.28 % Allowed : 16.89 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.12), residues: 5625 helix: 0.87 (0.10), residues: 3090 sheet: -0.07 (0.28), residues: 375 loop : 0.03 (0.15), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 215 HIS 0.005 0.001 HIS A 287 PHE 0.018 0.001 PHE U 209 TYR 0.015 0.001 TYR N 281 ARG 0.012 0.000 ARG N 392 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1143 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1032 time to evaluate : 5.814 Fit side-chains revert: symmetry clash REVERT: B 34 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8721 (pp) REVERT: B 213 ARG cc_start: 0.7674 (ttp-110) cc_final: 0.6835 (ttp80) REVERT: B 217 ASP cc_start: 0.7319 (m-30) cc_final: 0.6830 (m-30) REVERT: B 342 GLU cc_start: 0.7408 (mp0) cc_final: 0.7102 (mp0) REVERT: B 361 TYR cc_start: 0.9082 (m-80) cc_final: 0.8771 (m-80) REVERT: A 103 GLU cc_start: 0.8040 (mp0) cc_final: 0.7624 (mp0) REVERT: A 123 MET cc_start: 0.6222 (mmm) cc_final: 0.5209 (mmm) REVERT: A 164 ASN cc_start: 0.8447 (t0) cc_final: 0.7952 (t0) REVERT: A 192 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7195 (mt-10) REVERT: A 201 GLN cc_start: 0.8591 (mm110) cc_final: 0.8335 (mm110) REVERT: A 225 GLU cc_start: 0.7804 (tp30) cc_final: 0.7562 (mm-30) REVERT: A 342 GLU cc_start: 0.7544 (pm20) cc_final: 0.6337 (mt-10) REVERT: D 164 ASN cc_start: 0.8652 (t0) cc_final: 0.8376 (t0) REVERT: D 197 ILE cc_start: 0.8742 (mm) cc_final: 0.8523 (mp) REVERT: D 213 ARG cc_start: 0.7702 (ttp-110) cc_final: 0.6836 (ttp-110) REVERT: D 217 ASP cc_start: 0.7297 (m-30) cc_final: 0.6730 (m-30) REVERT: D 225 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7220 (mm-30) REVERT: D 263 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7546 (mt-10) REVERT: D 280 MET cc_start: 0.8326 (tpp) cc_final: 0.8091 (mmt) REVERT: F 89 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8421 (mm-40) REVERT: F 103 GLU cc_start: 0.8079 (mp0) cc_final: 0.7682 (mp0) REVERT: F 192 GLU cc_start: 0.7564 (mp0) cc_final: 0.7280 (mt-10) REVERT: F 225 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7441 (mm-30) REVERT: F 239 ASP cc_start: 0.7739 (t0) cc_final: 0.7534 (t0) REVERT: F 280 MET cc_start: 0.8145 (mmm) cc_final: 0.7858 (mmt) REVERT: F 300 MET cc_start: 0.8336 (mtm) cc_final: 0.8101 (mtt) REVERT: F 318 ASN cc_start: 0.8338 (t0) cc_final: 0.8089 (t0) REVERT: F 323 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8592 (ttmm) REVERT: F 342 GLU cc_start: 0.7541 (mp0) cc_final: 0.7223 (mp0) REVERT: F 371 ARG cc_start: 0.8073 (mmt90) cc_final: 0.7820 (mmt90) REVERT: H 213 ARG cc_start: 0.7689 (ttm110) cc_final: 0.7038 (ttp-110) REVERT: H 217 ASP cc_start: 0.7407 (m-30) cc_final: 0.6884 (m-30) REVERT: H 239 ASP cc_start: 0.7623 (t0) cc_final: 0.7285 (t0) REVERT: H 308 GLU cc_start: 0.7499 (pm20) cc_final: 0.7271 (pm20) REVERT: H 318 ASN cc_start: 0.8317 (t0) cc_final: 0.8025 (t0) REVERT: J 28 ILE cc_start: 0.9043 (mt) cc_final: 0.8682 (mt) REVERT: J 217 ASP cc_start: 0.7279 (m-30) cc_final: 0.6620 (m-30) REVERT: J 225 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7596 (mm-30) REVERT: J 239 ASP cc_start: 0.7663 (t0) cc_final: 0.7301 (t0) REVERT: J 263 GLU cc_start: 0.7610 (mp0) cc_final: 0.7305 (mp0) REVERT: J 288 GLU cc_start: 0.7810 (mp0) cc_final: 0.7594 (mp0) REVERT: J 318 ASN cc_start: 0.8166 (t0) cc_final: 0.7961 (t0) REVERT: J 347 MET cc_start: 0.8365 (ttt) cc_final: 0.8143 (ttt) REVERT: J 375 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.7302 (mptt) REVERT: L 192 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7205 (mt-10) REVERT: L 213 ARG cc_start: 0.7882 (ttp-110) cc_final: 0.7113 (ttp-110) REVERT: L 217 ASP cc_start: 0.7300 (m-30) cc_final: 0.6747 (m-30) REVERT: L 239 ASP cc_start: 0.7880 (t0) cc_final: 0.7639 (t0) REVERT: L 393 LEU cc_start: 0.8233 (tt) cc_final: 0.7385 (mp) REVERT: N 192 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7349 (mt-10) REVERT: N 209 PHE cc_start: 0.8858 (m-80) cc_final: 0.8645 (m-10) REVERT: N 217 ASP cc_start: 0.7389 (m-30) cc_final: 0.6845 (m-30) REVERT: N 225 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7708 (mm-30) REVERT: N 239 ASP cc_start: 0.7930 (t0) cc_final: 0.7564 (t0) REVERT: N 260 TYR cc_start: 0.9107 (m-10) cc_final: 0.8854 (m-10) REVERT: N 314 VAL cc_start: 0.8951 (OUTLIER) cc_final: 0.8658 (t) REVERT: N 317 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7371 (mm-30) REVERT: N 342 GLU cc_start: 0.7415 (mp0) cc_final: 0.7092 (mp0) REVERT: N 371 ARG cc_start: 0.8093 (mmt90) cc_final: 0.7811 (mmt90) REVERT: P 192 GLU cc_start: 0.7541 (mp0) cc_final: 0.7293 (mt-10) REVERT: P 213 ARG cc_start: 0.7714 (ttp-110) cc_final: 0.7210 (ttp-110) REVERT: P 217 ASP cc_start: 0.7311 (m-30) cc_final: 0.6766 (m-30) REVERT: P 239 ASP cc_start: 0.7751 (t0) cc_final: 0.7515 (t0) REVERT: P 288 GLU cc_start: 0.7965 (mp0) cc_final: 0.7593 (mp0) REVERT: P 306 MET cc_start: 0.7886 (mtp) cc_final: 0.7536 (mtt) REVERT: P 308 GLU cc_start: 0.7550 (pm20) cc_final: 0.7121 (pm20) REVERT: P 318 ASN cc_start: 0.8221 (t0) cc_final: 0.7917 (t0) REVERT: P 342 GLU cc_start: 0.7693 (mp0) cc_final: 0.7228 (mp0) REVERT: P 367 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.5981 (mt-10) REVERT: S 103 GLU cc_start: 0.7891 (mp0) cc_final: 0.7621 (mp0) REVERT: S 213 ARG cc_start: 0.7859 (ttm110) cc_final: 0.7449 (ttm110) REVERT: S 217 ASP cc_start: 0.7424 (m-30) cc_final: 0.7062 (m-30) REVERT: S 318 ASN cc_start: 0.8325 (t0) cc_final: 0.7997 (t0) REVERT: U 32 LYS cc_start: 0.8195 (mttp) cc_final: 0.7869 (mmtt) REVERT: U 213 ARG cc_start: 0.7684 (ttp-110) cc_final: 0.6782 (ttp80) REVERT: U 217 ASP cc_start: 0.7513 (m-30) cc_final: 0.7047 (m-30) REVERT: U 225 GLU cc_start: 0.7911 (tp30) cc_final: 0.7650 (tp30) REVERT: U 239 ASP cc_start: 0.8039 (t0) cc_final: 0.7775 (t0) REVERT: U 280 MET cc_start: 0.8134 (tpp) cc_final: 0.7881 (tpp) REVERT: U 288 GLU cc_start: 0.7564 (mp0) cc_final: 0.7161 (mp0) REVERT: U 361 TYR cc_start: 0.9073 (m-80) cc_final: 0.8828 (m-80) REVERT: U 367 GLU cc_start: 0.6592 (OUTLIER) cc_final: 0.5988 (mt-10) REVERT: W 28 ILE cc_start: 0.9052 (mt) cc_final: 0.8720 (mt) REVERT: W 129 GLN cc_start: 0.7644 (mp-120) cc_final: 0.7435 (mp10) REVERT: W 239 ASP cc_start: 0.7963 (t0) cc_final: 0.7680 (t0) REVERT: W 317 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7659 (mm-30) REVERT: Y 53 ASP cc_start: 0.8210 (t0) cc_final: 0.7816 (t0) REVERT: Y 164 ASN cc_start: 0.8579 (t0) cc_final: 0.8016 (t0) REVERT: Y 239 ASP cc_start: 0.7769 (t0) cc_final: 0.7475 (t0) REVERT: Y 288 GLU cc_start: 0.7851 (mp0) cc_final: 0.7409 (mp0) REVERT: Y 318 ASN cc_start: 0.8253 (t0) cc_final: 0.7970 (t0) REVERT: 0 164 ASN cc_start: 0.8211 (t0) cc_final: 0.7990 (t0) REVERT: 0 217 ASP cc_start: 0.7427 (m-30) cc_final: 0.7200 (m-30) REVERT: 0 246 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8170 (p0) REVERT: 0 288 GLU cc_start: 0.7661 (mp0) cc_final: 0.7366 (mp0) REVERT: 0 318 ASN cc_start: 0.8185 (t0) cc_final: 0.7915 (t0) REVERT: 2 164 ASN cc_start: 0.8636 (t0) cc_final: 0.8221 (t0) REVERT: 2 213 ARG cc_start: 0.7718 (mtp-110) cc_final: 0.7096 (ttp-110) REVERT: 2 217 ASP cc_start: 0.7258 (m-30) cc_final: 0.6958 (m-30) REVERT: 2 280 MET cc_start: 0.8275 (tpp) cc_final: 0.7965 (mmm) REVERT: 2 288 GLU cc_start: 0.7735 (mp0) cc_final: 0.7504 (mp0) REVERT: 2 318 ASN cc_start: 0.8105 (t0) cc_final: 0.7904 (t0) REVERT: 2 371 ARG cc_start: 0.8022 (mmt90) cc_final: 0.7244 (ptm160) outliers start: 111 outliers final: 90 residues processed: 1101 average time/residue: 0.5812 time to fit residues: 1048.3588 Evaluate side-chains 1081 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 980 time to evaluate : 5.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 246 ASN Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 323 LYS Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 255 CYS Chi-restraints excluded: chain H residue 297 GLU Chi-restraints excluded: chain H residue 304 GLN Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain H residue 367 GLU Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 246 ASN Chi-restraints excluded: chain J residue 297 GLU Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain J residue 380 LEU Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 192 GLU Chi-restraints excluded: chain L residue 246 ASN Chi-restraints excluded: chain L residue 252 GLU Chi-restraints excluded: chain L residue 297 GLU Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain L residue 367 GLU Chi-restraints excluded: chain N residue 31 ILE Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain N residue 159 ASP Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 192 GLU Chi-restraints excluded: chain N residue 314 VAL Chi-restraints excluded: chain N residue 332 LEU Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 57 ARG Chi-restraints excluded: chain P residue 94 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 159 ASP Chi-restraints excluded: chain P residue 246 ASN Chi-restraints excluded: chain P residue 252 GLU Chi-restraints excluded: chain P residue 255 CYS Chi-restraints excluded: chain P residue 297 GLU Chi-restraints excluded: chain P residue 367 GLU Chi-restraints excluded: chain P residue 375 LYS Chi-restraints excluded: chain S residue 42 ASP Chi-restraints excluded: chain S residue 49 SER Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain S residue 246 ASN Chi-restraints excluded: chain S residue 332 LEU Chi-restraints excluded: chain U residue 42 ASP Chi-restraints excluded: chain U residue 94 ASP Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 186 ASP Chi-restraints excluded: chain U residue 246 ASN Chi-restraints excluded: chain U residue 252 GLU Chi-restraints excluded: chain U residue 332 LEU Chi-restraints excluded: chain U residue 367 GLU Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain W residue 49 SER Chi-restraints excluded: chain W residue 252 GLU Chi-restraints excluded: chain W residue 258 ASP Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Y residue 159 ASP Chi-restraints excluded: chain Y residue 252 GLU Chi-restraints excluded: chain Y residue 319 SER Chi-restraints excluded: chain Y residue 367 GLU Chi-restraints excluded: chain Y residue 375 LYS Chi-restraints excluded: chain 0 residue 94 ASP Chi-restraints excluded: chain 0 residue 159 ASP Chi-restraints excluded: chain 0 residue 246 ASN Chi-restraints excluded: chain 0 residue 297 GLU Chi-restraints excluded: chain 0 residue 367 GLU Chi-restraints excluded: chain 2 residue 42 ASP Chi-restraints excluded: chain 2 residue 49 SER Chi-restraints excluded: chain 2 residue 94 ASP Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 255 CYS Chi-restraints excluded: chain 2 residue 297 GLU Chi-restraints excluded: chain 2 residue 319 SER Chi-restraints excluded: chain 2 residue 345 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 359 optimal weight: 1.9990 chunk 481 optimal weight: 0.9980 chunk 138 optimal weight: 10.0000 chunk 416 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 452 optimal weight: 0.0570 chunk 189 optimal weight: 10.0000 chunk 465 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 chunk 83 optimal weight: 0.3980 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 ASN ** L 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 366 GLN W 86 GLN W 149 ASN 2 345 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.119478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.099423 restraints weight = 63942.880| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.93 r_work: 0.2901 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 47670 Z= 0.153 Angle : 0.545 10.977 64860 Z= 0.271 Chirality : 0.040 0.126 7470 Planarity : 0.004 0.057 7980 Dihedral : 8.189 73.251 7247 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.22 % Allowed : 17.02 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.12), residues: 5625 helix: 0.86 (0.10), residues: 3165 sheet: -0.12 (0.28), residues: 375 loop : -0.02 (0.15), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP W 215 HIS 0.004 0.001 HIS A 287 PHE 0.019 0.001 PHE Y 357 TYR 0.013 0.001 TYR H 312 ARG 0.012 0.000 ARG N 392 =============================================================================== Job complete usr+sys time: 17026.56 seconds wall clock time: 300 minutes 52.30 seconds (18052.30 seconds total)