Starting phenix.real_space_refine (version: dev) on Thu Dec 22 08:58:40 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi3_12918/12_2022/7oi3_12918.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi3_12918/12_2022/7oi3_12918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi3_12918/12_2022/7oi3_12918.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi3_12918/12_2022/7oi3_12918.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi3_12918/12_2022/7oi3_12918.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi3_12918/12_2022/7oi3_12918.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.003 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "E ARG 48": "NH1" <-> "NH2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E ARG 57": "NH1" <-> "NH2" Residue "E ARG 100": "NH1" <-> "NH2" Residue "E GLU 108": "OE1" <-> "OE2" Residue "E ARG 142": "NH1" <-> "NH2" Residue "E ARG 194": "NH1" <-> "NH2" Residue "E ARG 195": "NH1" <-> "NH2" Residue "E ARG 203": "NH1" <-> "NH2" Residue "E ARG 204": "NH1" <-> "NH2" Residue "E ARG 222": "NH1" <-> "NH2" Residue "E GLU 225": "OE1" <-> "OE2" Residue "E ARG 230": "NH1" <-> "NH2" Residue "E GLU 278": "OE1" <-> "OE2" Residue "E ARG 370": "NH1" <-> "NH2" 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 GLU 108": "OE1" <-> "OE2" Residue "A ARG 142": "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 222": "NH1" <-> "NH2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A ARG 370": "NH1" <-> "NH2" 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 GLU 108": "OE1" <-> "OE2" Residue "D ARG 142": "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 222": "NH1" <-> "NH2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D ARG 230": "NH1" <-> "NH2" Residue "D GLU 278": "OE1" <-> "OE2" Residue "D ARG 370": "NH1" <-> "NH2" Residue "G ARG 48": "NH1" <-> "NH2" Residue "G ARG 54": "NH1" <-> "NH2" Residue "G ARG 57": "NH1" <-> "NH2" Residue "G ARG 100": "NH1" <-> "NH2" Residue "G GLU 108": "OE1" <-> "OE2" Residue "G ARG 142": "NH1" <-> "NH2" Residue "G ARG 194": "NH1" <-> "NH2" Residue "G ARG 195": "NH1" <-> "NH2" Residue "G ARG 203": "NH1" <-> "NH2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "G ARG 222": "NH1" <-> "NH2" Residue "G GLU 225": "OE1" <-> "OE2" Residue "G ARG 230": "NH1" <-> "NH2" Residue "G GLU 278": "OE1" <-> "OE2" Residue "G ARG 370": "NH1" <-> "NH2" Residue "I ARG 48": "NH1" <-> "NH2" Residue "I ARG 54": "NH1" <-> "NH2" Residue "I ARG 57": "NH1" <-> "NH2" Residue "I ARG 100": "NH1" <-> "NH2" Residue "I GLU 108": "OE1" <-> "OE2" Residue "I ARG 142": "NH1" <-> "NH2" Residue "I ARG 194": "NH1" <-> "NH2" Residue "I ARG 195": "NH1" <-> "NH2" Residue "I ARG 203": "NH1" <-> "NH2" Residue "I ARG 204": "NH1" <-> "NH2" Residue "I ARG 222": "NH1" <-> "NH2" Residue "I GLU 225": "OE1" <-> "OE2" Residue "I ARG 230": "NH1" <-> "NH2" Residue "I GLU 278": "OE1" <-> "OE2" Residue "I ARG 370": "NH1" <-> "NH2" Residue "K ARG 48": "NH1" <-> "NH2" Residue "K ARG 54": "NH1" <-> "NH2" Residue "K ARG 57": "NH1" <-> "NH2" Residue "K ARG 100": "NH1" <-> "NH2" Residue "K GLU 108": "OE1" <-> "OE2" Residue "K ARG 142": "NH1" <-> "NH2" Residue "K ARG 194": "NH1" <-> "NH2" Residue "K ARG 195": "NH1" <-> "NH2" Residue "K ARG 203": "NH1" <-> "NH2" Residue "K ARG 204": "NH1" <-> "NH2" Residue "K ARG 222": "NH1" <-> "NH2" Residue "K GLU 225": "OE1" <-> "OE2" Residue "K ARG 230": "NH1" <-> "NH2" Residue "K GLU 278": "OE1" <-> "OE2" Residue "K ARG 370": "NH1" <-> "NH2" Residue "M ARG 48": "NH1" <-> "NH2" Residue "M ARG 54": "NH1" <-> "NH2" Residue "M ARG 57": "NH1" <-> "NH2" Residue "M ARG 100": "NH1" <-> "NH2" Residue "M GLU 108": "OE1" <-> "OE2" Residue "M ARG 142": "NH1" <-> "NH2" Residue "M ARG 194": "NH1" <-> "NH2" Residue "M ARG 195": "NH1" <-> "NH2" Residue "M ARG 203": "NH1" <-> "NH2" Residue "M ARG 204": "NH1" <-> "NH2" Residue "M ARG 222": "NH1" <-> "NH2" Residue "M GLU 225": "OE1" <-> "OE2" Residue "M ARG 230": "NH1" <-> "NH2" Residue "M GLU 278": "OE1" <-> "OE2" Residue "M ARG 370": "NH1" <-> "NH2" Residue "O ARG 48": "NH1" <-> "NH2" Residue "O ARG 54": "NH1" <-> "NH2" Residue "O ARG 57": "NH1" <-> "NH2" Residue "O ARG 100": "NH1" <-> "NH2" Residue "O GLU 108": "OE1" <-> "OE2" Residue "O ARG 142": "NH1" <-> "NH2" Residue "O ARG 194": "NH1" <-> "NH2" Residue "O ARG 195": "NH1" <-> "NH2" Residue "O ARG 203": "NH1" <-> "NH2" Residue "O ARG 204": "NH1" <-> "NH2" Residue "O ARG 222": "NH1" <-> "NH2" Residue "O GLU 225": "OE1" <-> "OE2" Residue "O ARG 230": "NH1" <-> "NH2" Residue "O GLU 278": "OE1" <-> "OE2" Residue "O ARG 370": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q ARG 54": "NH1" <-> "NH2" Residue "Q ARG 57": "NH1" <-> "NH2" Residue "Q ARG 100": "NH1" <-> "NH2" Residue "Q GLU 108": "OE1" <-> "OE2" Residue "Q ARG 142": "NH1" <-> "NH2" Residue "Q ARG 194": "NH1" <-> "NH2" Residue "Q ARG 195": "NH1" <-> "NH2" Residue "Q ARG 203": "NH1" <-> "NH2" Residue "Q ARG 204": "NH1" <-> "NH2" Residue "Q ARG 222": "NH1" <-> "NH2" Residue "Q GLU 225": "OE1" <-> "OE2" Residue "Q ARG 230": "NH1" <-> "NH2" Residue "Q GLU 278": "OE1" <-> "OE2" Residue "Q ARG 370": "NH1" <-> "NH2" 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 GLU 108": "OE1" <-> "OE2" Residue "S ARG 142": "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 222": "NH1" <-> "NH2" Residue "S GLU 225": "OE1" <-> "OE2" Residue "S ARG 230": "NH1" <-> "NH2" Residue "S GLU 278": "OE1" <-> "OE2" Residue "S ARG 370": "NH1" <-> "NH2" 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 GLU 108": "OE1" <-> "OE2" Residue "U ARG 142": "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 222": "NH1" <-> "NH2" Residue "U GLU 225": "OE1" <-> "OE2" Residue "U ARG 230": "NH1" <-> "NH2" Residue "U GLU 278": "OE1" <-> "OE2" Residue "U ARG 370": "NH1" <-> "NH2" 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 GLU 108": "OE1" <-> "OE2" Residue "W ARG 142": "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 222": "NH1" <-> "NH2" Residue "W GLU 225": "OE1" <-> "OE2" Residue "W ARG 230": "NH1" <-> "NH2" Residue "W GLU 278": "OE1" <-> "OE2" Residue "W ARG 370": "NH1" <-> "NH2" 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 GLU 108": "OE1" <-> "OE2" Residue "Y ARG 142": "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 222": "NH1" <-> "NH2" Residue "Y GLU 225": "OE1" <-> "OE2" Residue "Y ARG 230": "NH1" <-> "NH2" Residue "Y GLU 278": "OE1" <-> "OE2" Residue "Y ARG 370": "NH1" <-> "NH2" 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 GLU 108": "OE1" <-> "OE2" Residue "0 ARG 142": "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 222": "NH1" <-> "NH2" Residue "0 GLU 225": "OE1" <-> "OE2" Residue "0 ARG 230": "NH1" <-> "NH2" Residue "0 GLU 278": "OE1" <-> "OE2" Residue "0 ARG 370": "NH1" <-> "NH2" 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 GLU 108": "OE1" <-> "OE2" Residue "2 ARG 142": "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 222": "NH1" <-> "NH2" Residue "2 GLU 225": "OE1" <-> "OE2" Residue "2 ARG 230": "NH1" <-> "NH2" Residue "2 GLU 278": "OE1" <-> "OE2" Residue "2 ARG 370": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 47955 Number of models: 1 Model: "" Number of chains: 30 Chain: "E" Number of atoms: 3068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3068 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 15, 'TRANS': 378} Chain: "B" 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: 3068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3068 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 15, 'TRANS': 378} 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: 3068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3068 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 15, 'TRANS': 378} Chain: "F" 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: "G" Number of atoms: 3068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3068 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 15, 'TRANS': 378} Chain: "H" 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: "I" Number of atoms: 3068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3068 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 15, 'TRANS': 378} Chain: "J" 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: "K" Number of atoms: 3068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3068 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 15, 'TRANS': 378} Chain: "L" 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: "M" Number of atoms: 3068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3068 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 15, 'TRANS': 378} Chain: "N" 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: "O" Number of atoms: 3068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3068 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 15, 'TRANS': 378} Chain: "P" 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: "Q" Number of atoms: 3068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3068 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 15, 'TRANS': 378} 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: "S" Number of atoms: 3068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3068 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 15, 'TRANS': 378} 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: 3068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3068 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 15, 'TRANS': 378} 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: 3068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3068 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 15, 'TRANS': 378} 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: 3068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3068 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 15, 'TRANS': 378} 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: 3068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3068 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 15, 'TRANS': 378} 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: 3068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3068 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 15, 'TRANS': 378} 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: 25.42, per 1000 atoms: 0.53 Number of scatterers: 47955 At special positions: 0 Unit cell: (216.91, 215.82, 154.78, 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 9270 8.00 N 8310 7.00 C 30120 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: 19.25 Conformation dependent library (CDL) restraints added in 6.3 seconds 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10920 Finding SS restraints... Secondary structure from input PDB file: 330 helices and 15 sheets defined 64.2% alpha, 4.6% beta 0 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 12.69 Creating SS restraints... Processing helix chain 'E' and resid 2 through 16 removed outlier: 4.155A pdb=" N ARG E 6 " --> pdb=" O ALA E 2 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP E 16 " --> pdb=" O LYS E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 60 Processing helix chain 'E' and resid 65 through 78 Processing helix chain 'E' and resid 83 through 92 removed outlier: 3.795A pdb=" N LEU E 87 " --> pdb=" O SER E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 132 Processing helix chain 'E' and resid 140 through 144 removed outlier: 3.838A pdb=" N THR E 144 " --> pdb=" O THR E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 176 Processing helix chain 'E' and resid 177 through 180 Processing helix chain 'E' and resid 188 through 201 removed outlier: 3.787A pdb=" N GLU E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN E 201 " --> pdb=" O ILE E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 210 Processing helix chain 'E' and resid 212 through 226 Processing helix chain 'E' and resid 227 through 242 Processing helix chain 'E' and resid 248 through 262 removed outlier: 4.489A pdb=" N THR E 259 " --> pdb=" O CYS E 255 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR E 260 " --> pdb=" O ASP E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 277 removed outlier: 3.964A pdb=" N THR E 272 " --> pdb=" O SER E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 286 Processing helix chain 'E' and resid 289 through 307 removed outlier: 3.875A pdb=" N GLY E 307 " --> pdb=" O TYR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 314 removed outlier: 4.355A pdb=" N VAL E 314 " --> pdb=" O PRO E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 328 removed outlier: 3.735A pdb=" N GLN E 321 " --> pdb=" O ASN E 318 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN E 322 " --> pdb=" O SER E 319 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ALA E 326 " --> pdb=" O LYS E 323 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLY E 327 " --> pdb=" O PHE E 324 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER E 328 " --> pdb=" O SER E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 344 removed outlier: 3.661A pdb=" N GLU E 342 " --> pdb=" O GLY E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 372 Processing helix chain 'E' and resid 378 through 385 Processing helix chain 'E' and resid 387 through 391 removed outlier: 3.825A pdb=" N ASP E 390 " --> pdb=" O THR E 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 16 removed outlier: 4.155A pdb=" N ARG A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 60 Processing helix chain 'A' and resid 65 through 78 Processing helix chain 'A' and resid 83 through 92 removed outlier: 3.794A pdb=" N LEU A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 144 removed outlier: 3.838A pdb=" N THR A 144 " --> pdb=" O THR A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 176 Processing helix chain 'A' and resid 177 through 180 Processing helix chain 'A' and resid 188 through 201 removed outlier: 3.787A pdb=" N GLU A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A 201 " --> pdb=" O ILE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 227 through 242 Processing helix chain 'A' and resid 248 through 262 removed outlier: 4.489A pdb=" N THR A 259 " --> pdb=" O CYS A 255 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 removed outlier: 3.964A pdb=" N THR A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 289 through 307 removed outlier: 3.875A pdb=" N GLY A 307 " --> pdb=" O TYR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 314 removed outlier: 4.355A pdb=" N VAL A 314 " --> pdb=" O PRO A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 328 removed outlier: 3.735A pdb=" N GLN A 321 " --> pdb=" O ASN A 318 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN A 322 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ALA A 326 " --> pdb=" O LYS A 323 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLY A 327 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER A 328 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 344 removed outlier: 3.662A pdb=" N GLU A 342 " --> pdb=" O GLY A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 372 Processing helix chain 'A' and resid 378 through 385 Processing helix chain 'A' and resid 387 through 391 removed outlier: 3.824A pdb=" N ASP A 390 " --> pdb=" O THR A 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 16 removed outlier: 4.154A pdb=" N ARG D 6 " --> pdb=" O ALA D 2 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP D 16 " --> pdb=" O LYS D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 60 Processing helix chain 'D' and resid 65 through 78 Processing helix chain 'D' and resid 83 through 92 removed outlier: 3.795A pdb=" N LEU D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 132 Processing helix chain 'D' and resid 140 through 144 removed outlier: 3.838A pdb=" N THR D 144 " --> pdb=" O THR D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 176 Processing helix chain 'D' and resid 177 through 180 Processing helix chain 'D' and resid 188 through 201 removed outlier: 3.787A pdb=" N GLU D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN D 201 " --> pdb=" O ILE D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 210 Processing helix chain 'D' and resid 212 through 226 Processing helix chain 'D' and resid 227 through 242 Processing helix chain 'D' and resid 248 through 262 removed outlier: 4.489A pdb=" N THR D 259 " --> pdb=" O CYS D 255 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR D 260 " --> pdb=" O ASP D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 277 removed outlier: 3.965A pdb=" N THR D 272 " --> pdb=" O SER D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 286 Processing helix chain 'D' and resid 289 through 307 removed outlier: 3.875A pdb=" N GLY D 307 " --> pdb=" O TYR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 314 removed outlier: 4.355A pdb=" N VAL D 314 " --> pdb=" O PRO D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 328 removed outlier: 3.735A pdb=" N GLN D 321 " --> pdb=" O ASN D 318 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN D 322 " --> pdb=" O SER D 319 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA D 326 " --> pdb=" O LYS D 323 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLY D 327 " --> pdb=" O PHE D 324 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER D 328 " --> pdb=" O SER D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 344 removed outlier: 3.662A pdb=" N GLU D 342 " --> pdb=" O GLY D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 372 Processing helix chain 'D' and resid 378 through 385 Processing helix chain 'D' and resid 387 through 391 removed outlier: 3.824A pdb=" N ASP D 390 " --> pdb=" O THR D 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 16 removed outlier: 4.154A pdb=" N ARG G 6 " --> pdb=" O ALA G 2 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP G 16 " --> pdb=" O LYS G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 60 Processing helix chain 'G' and resid 65 through 78 Processing helix chain 'G' and resid 83 through 92 removed outlier: 3.794A pdb=" N LEU G 87 " --> pdb=" O SER G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 132 Processing helix chain 'G' and resid 140 through 144 removed outlier: 3.838A pdb=" N THR G 144 " --> pdb=" O THR G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 176 Processing helix chain 'G' and resid 177 through 180 Processing helix chain 'G' and resid 188 through 201 removed outlier: 3.787A pdb=" N GLU G 192 " --> pdb=" O ALA G 188 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN G 201 " --> pdb=" O ILE G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 210 Processing helix chain 'G' and resid 212 through 226 Processing helix chain 'G' and resid 227 through 242 Processing helix chain 'G' and resid 248 through 262 removed outlier: 4.489A pdb=" N THR G 259 " --> pdb=" O CYS G 255 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR G 260 " --> pdb=" O ASP G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 266 through 277 removed outlier: 3.965A pdb=" N THR G 272 " --> pdb=" O SER G 268 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 286 Processing helix chain 'G' and resid 289 through 307 removed outlier: 3.875A pdb=" N GLY G 307 " --> pdb=" O TYR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 314 removed outlier: 4.355A pdb=" N VAL G 314 " --> pdb=" O PRO G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 318 through 328 removed outlier: 3.735A pdb=" N GLN G 321 " --> pdb=" O ASN G 318 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN G 322 " --> pdb=" O SER G 319 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA G 326 " --> pdb=" O LYS G 323 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLY G 327 " --> pdb=" O PHE G 324 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER G 328 " --> pdb=" O SER G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 344 removed outlier: 3.662A pdb=" N GLU G 342 " --> pdb=" O GLY G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 372 Processing helix chain 'G' and resid 378 through 385 Processing helix chain 'G' and resid 387 through 391 removed outlier: 3.824A pdb=" N ASP G 390 " --> pdb=" O THR G 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 16 removed outlier: 4.154A pdb=" N ARG I 6 " --> pdb=" O ALA I 2 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP I 16 " --> pdb=" O LYS I 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 60 Processing helix chain 'I' and resid 65 through 78 Processing helix chain 'I' and resid 83 through 92 removed outlier: 3.794A pdb=" N LEU I 87 " --> pdb=" O SER I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 132 Processing helix chain 'I' and resid 140 through 144 removed outlier: 3.838A pdb=" N THR I 144 " --> pdb=" O THR I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 176 Processing helix chain 'I' and resid 177 through 180 Processing helix chain 'I' and resid 188 through 201 removed outlier: 3.788A pdb=" N GLU I 192 " --> pdb=" O ALA I 188 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN I 201 " --> pdb=" O ILE I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 210 Processing helix chain 'I' and resid 212 through 226 Processing helix chain 'I' and resid 227 through 242 Processing helix chain 'I' and resid 248 through 262 removed outlier: 4.489A pdb=" N THR I 259 " --> pdb=" O CYS I 255 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR I 260 " --> pdb=" O ASP I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 266 through 277 removed outlier: 3.964A pdb=" N THR I 272 " --> pdb=" O SER I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 281 through 286 Processing helix chain 'I' and resid 289 through 307 removed outlier: 3.875A pdb=" N GLY I 307 " --> pdb=" O TYR I 303 " (cutoff:3.500A) Processing helix chain 'I' and resid 310 through 314 removed outlier: 4.355A pdb=" N VAL I 314 " --> pdb=" O PRO I 311 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 328 removed outlier: 3.735A pdb=" N GLN I 321 " --> pdb=" O ASN I 318 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN I 322 " --> pdb=" O SER I 319 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ALA I 326 " --> pdb=" O LYS I 323 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLY I 327 " --> pdb=" O PHE I 324 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER I 328 " --> pdb=" O SER I 325 " (cutoff:3.500A) Processing helix chain 'I' and resid 329 through 344 removed outlier: 3.661A pdb=" N GLU I 342 " --> pdb=" O GLY I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 372 Processing helix chain 'I' and resid 378 through 385 Processing helix chain 'I' and resid 387 through 391 removed outlier: 3.824A pdb=" N ASP I 390 " --> pdb=" O THR I 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 16 removed outlier: 4.155A pdb=" N ARG K 6 " --> pdb=" O ALA K 2 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP K 16 " --> pdb=" O LYS K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 60 Processing helix chain 'K' and resid 65 through 78 Processing helix chain 'K' and resid 83 through 92 removed outlier: 3.795A pdb=" N LEU K 87 " --> pdb=" O SER K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 132 Processing helix chain 'K' and resid 140 through 144 removed outlier: 3.838A pdb=" N THR K 144 " --> pdb=" O THR K 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 176 Processing helix chain 'K' and resid 177 through 180 Processing helix chain 'K' and resid 188 through 201 removed outlier: 3.787A pdb=" N GLU K 192 " --> pdb=" O ALA K 188 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN K 201 " --> pdb=" O ILE K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 210 Processing helix chain 'K' and resid 212 through 226 Processing helix chain 'K' and resid 227 through 242 Processing helix chain 'K' and resid 248 through 262 removed outlier: 4.489A pdb=" N THR K 259 " --> pdb=" O CYS K 255 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR K 260 " --> pdb=" O ASP K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 266 through 277 removed outlier: 3.964A pdb=" N THR K 272 " --> pdb=" O SER K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 281 through 286 Processing helix chain 'K' and resid 289 through 307 removed outlier: 3.875A pdb=" N GLY K 307 " --> pdb=" O TYR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 310 through 314 removed outlier: 4.355A pdb=" N VAL K 314 " --> pdb=" O PRO K 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 318 through 328 removed outlier: 3.735A pdb=" N GLN K 321 " --> pdb=" O ASN K 318 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN K 322 " --> pdb=" O SER K 319 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA K 326 " --> pdb=" O LYS K 323 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLY K 327 " --> pdb=" O PHE K 324 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER K 328 " --> pdb=" O SER K 325 " (cutoff:3.500A) Processing helix chain 'K' and resid 329 through 344 removed outlier: 3.661A pdb=" N GLU K 342 " --> pdb=" O GLY K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 372 Processing helix chain 'K' and resid 378 through 385 Processing helix chain 'K' and resid 387 through 391 removed outlier: 3.825A pdb=" N ASP K 390 " --> pdb=" O THR K 387 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 16 removed outlier: 4.155A pdb=" N ARG M 6 " --> pdb=" O ALA M 2 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP M 16 " --> pdb=" O LYS M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 60 Processing helix chain 'M' and resid 65 through 78 Processing helix chain 'M' and resid 83 through 92 removed outlier: 3.795A pdb=" N LEU M 87 " --> pdb=" O SER M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 124 through 132 Processing helix chain 'M' and resid 140 through 144 removed outlier: 3.838A pdb=" N THR M 144 " --> pdb=" O THR M 141 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 176 Processing helix chain 'M' and resid 177 through 180 Processing helix chain 'M' and resid 188 through 201 removed outlier: 3.788A pdb=" N GLU M 192 " --> pdb=" O ALA M 188 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN M 201 " --> pdb=" O ILE M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 210 Processing helix chain 'M' and resid 212 through 226 Processing helix chain 'M' and resid 227 through 242 Processing helix chain 'M' and resid 248 through 262 removed outlier: 4.489A pdb=" N THR M 259 " --> pdb=" O CYS M 255 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR M 260 " --> pdb=" O ASP M 256 " (cutoff:3.500A) Processing helix chain 'M' and resid 266 through 277 removed outlier: 3.965A pdb=" N THR M 272 " --> pdb=" O SER M 268 " (cutoff:3.500A) Processing helix chain 'M' and resid 281 through 286 Processing helix chain 'M' and resid 289 through 307 removed outlier: 3.875A pdb=" N GLY M 307 " --> pdb=" O TYR M 303 " (cutoff:3.500A) Processing helix chain 'M' and resid 310 through 314 removed outlier: 4.355A pdb=" N VAL M 314 " --> pdb=" O PRO M 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 318 through 328 removed outlier: 3.735A pdb=" N GLN M 321 " --> pdb=" O ASN M 318 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN M 322 " --> pdb=" O SER M 319 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA M 326 " --> pdb=" O LYS M 323 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLY M 327 " --> pdb=" O PHE M 324 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER M 328 " --> pdb=" O SER M 325 " (cutoff:3.500A) Processing helix chain 'M' and resid 329 through 344 removed outlier: 3.661A pdb=" N GLU M 342 " --> pdb=" O GLY M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 358 through 372 Processing helix chain 'M' and resid 378 through 385 Processing helix chain 'M' and resid 387 through 391 removed outlier: 3.824A pdb=" N ASP M 390 " --> pdb=" O THR M 387 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 16 removed outlier: 4.155A pdb=" N ARG O 6 " --> pdb=" O ALA O 2 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP O 16 " --> pdb=" O LYS O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 60 Processing helix chain 'O' and resid 65 through 78 Processing helix chain 'O' and resid 83 through 92 removed outlier: 3.796A pdb=" N LEU O 87 " --> pdb=" O SER O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 124 through 132 Processing helix chain 'O' and resid 140 through 144 removed outlier: 3.838A pdb=" N THR O 144 " --> pdb=" O THR O 141 " (cutoff:3.500A) Processing helix chain 'O' and resid 159 through 176 Processing helix chain 'O' and resid 177 through 180 Processing helix chain 'O' and resid 188 through 201 removed outlier: 3.787A pdb=" N GLU O 192 " --> pdb=" O ALA O 188 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN O 201 " --> pdb=" O ILE O 197 " (cutoff:3.500A) Processing helix chain 'O' and resid 206 through 210 Processing helix chain 'O' and resid 212 through 226 Processing helix chain 'O' and resid 227 through 242 Processing helix chain 'O' and resid 248 through 262 removed outlier: 4.489A pdb=" N THR O 259 " --> pdb=" O CYS O 255 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR O 260 " --> pdb=" O ASP O 256 " (cutoff:3.500A) Processing helix chain 'O' and resid 266 through 277 removed outlier: 3.965A pdb=" N THR O 272 " --> pdb=" O SER O 268 " (cutoff:3.500A) Processing helix chain 'O' and resid 281 through 286 Processing helix chain 'O' and resid 289 through 307 removed outlier: 3.875A pdb=" N GLY O 307 " --> pdb=" O TYR O 303 " (cutoff:3.500A) Processing helix chain 'O' and resid 310 through 314 removed outlier: 4.355A pdb=" N VAL O 314 " --> pdb=" O PRO O 311 " (cutoff:3.500A) Processing helix chain 'O' and resid 318 through 328 removed outlier: 3.735A pdb=" N GLN O 321 " --> pdb=" O ASN O 318 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN O 322 " --> pdb=" O SER O 319 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ALA O 326 " --> pdb=" O LYS O 323 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLY O 327 " --> pdb=" O PHE O 324 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER O 328 " --> pdb=" O SER O 325 " (cutoff:3.500A) Processing helix chain 'O' and resid 329 through 344 removed outlier: 3.661A pdb=" N GLU O 342 " --> pdb=" O GLY O 338 " (cutoff:3.500A) Processing helix chain 'O' and resid 358 through 372 Processing helix chain 'O' and resid 378 through 385 Processing helix chain 'O' and resid 387 through 391 removed outlier: 3.825A pdb=" N ASP O 390 " --> pdb=" O THR O 387 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 16 removed outlier: 4.154A pdb=" N ARG Q 6 " --> pdb=" O ALA Q 2 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP Q 16 " --> pdb=" O LYS Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 60 Processing helix chain 'Q' and resid 65 through 78 Processing helix chain 'Q' and resid 83 through 92 removed outlier: 3.794A pdb=" N LEU Q 87 " --> pdb=" O SER Q 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 124 through 132 Processing helix chain 'Q' and resid 140 through 144 removed outlier: 3.838A pdb=" N THR Q 144 " --> pdb=" O THR Q 141 " (cutoff:3.500A) Processing helix chain 'Q' and resid 159 through 176 Processing helix chain 'Q' and resid 177 through 180 Processing helix chain 'Q' and resid 188 through 201 removed outlier: 3.788A pdb=" N GLU Q 192 " --> pdb=" O ALA Q 188 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN Q 201 " --> pdb=" O ILE Q 197 " (cutoff:3.500A) Processing helix chain 'Q' and resid 206 through 210 Processing helix chain 'Q' and resid 212 through 226 Processing helix chain 'Q' and resid 227 through 242 Processing helix chain 'Q' and resid 248 through 262 removed outlier: 4.489A pdb=" N THR Q 259 " --> pdb=" O CYS Q 255 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR Q 260 " --> pdb=" O ASP Q 256 " (cutoff:3.500A) Processing helix chain 'Q' and resid 266 through 277 removed outlier: 3.964A pdb=" N THR Q 272 " --> pdb=" O SER Q 268 " (cutoff:3.500A) Processing helix chain 'Q' and resid 281 through 286 Processing helix chain 'Q' and resid 289 through 307 removed outlier: 3.875A pdb=" N GLY Q 307 " --> pdb=" O TYR Q 303 " (cutoff:3.500A) Processing helix chain 'Q' and resid 310 through 314 removed outlier: 4.354A pdb=" N VAL Q 314 " --> pdb=" O PRO Q 311 " (cutoff:3.500A) Processing helix chain 'Q' and resid 318 through 328 removed outlier: 3.735A pdb=" N GLN Q 321 " --> pdb=" O ASN Q 318 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN Q 322 " --> pdb=" O SER Q 319 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA Q 326 " --> pdb=" O LYS Q 323 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLY Q 327 " --> pdb=" O PHE Q 324 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER Q 328 " --> pdb=" O SER Q 325 " (cutoff:3.500A) Processing helix chain 'Q' and resid 329 through 344 removed outlier: 3.662A pdb=" N GLU Q 342 " --> pdb=" O GLY Q 338 " (cutoff:3.500A) Processing helix chain 'Q' and resid 358 through 372 Processing helix chain 'Q' and resid 378 through 385 Processing helix chain 'Q' and resid 387 through 391 removed outlier: 3.825A pdb=" N ASP Q 390 " --> pdb=" O THR Q 387 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 16 removed outlier: 4.155A pdb=" N ARG S 6 " --> pdb=" O ALA S 2 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP S 16 " --> pdb=" O LYS S 12 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 60 Processing helix chain 'S' and resid 65 through 78 Processing helix chain 'S' and resid 83 through 92 removed outlier: 3.795A pdb=" N LEU S 87 " --> pdb=" O SER S 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 124 through 132 Processing helix chain 'S' and resid 140 through 144 removed outlier: 3.837A pdb=" N THR S 144 " --> pdb=" O THR S 141 " (cutoff:3.500A) Processing helix chain 'S' and resid 159 through 176 Processing helix chain 'S' and resid 177 through 180 Processing helix chain 'S' and resid 188 through 201 removed outlier: 3.788A pdb=" N GLU S 192 " --> pdb=" O ALA S 188 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN S 201 " --> pdb=" O ILE S 197 " (cutoff:3.500A) Processing helix chain 'S' and resid 206 through 210 Processing helix chain 'S' and resid 212 through 226 Processing helix chain 'S' and resid 227 through 242 Processing helix chain 'S' and resid 248 through 262 removed outlier: 4.489A pdb=" N THR S 259 " --> pdb=" O CYS S 255 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR S 260 " --> pdb=" O ASP S 256 " (cutoff:3.500A) Processing helix chain 'S' and resid 266 through 277 removed outlier: 3.964A pdb=" N THR S 272 " --> pdb=" O SER S 268 " (cutoff:3.500A) Processing helix chain 'S' and resid 281 through 286 Processing helix chain 'S' and resid 289 through 307 removed outlier: 3.875A pdb=" N GLY S 307 " --> pdb=" O TYR S 303 " (cutoff:3.500A) Processing helix chain 'S' and resid 310 through 314 removed outlier: 4.355A pdb=" N VAL S 314 " --> pdb=" O PRO S 311 " (cutoff:3.500A) Processing helix chain 'S' and resid 318 through 328 removed outlier: 3.735A pdb=" N GLN S 321 " --> pdb=" O ASN S 318 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN S 322 " --> pdb=" O SER S 319 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA S 326 " --> pdb=" O LYS S 323 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLY S 327 " --> pdb=" O PHE S 324 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER S 328 " --> pdb=" O SER S 325 " (cutoff:3.500A) Processing helix chain 'S' and resid 329 through 344 removed outlier: 3.661A pdb=" N GLU S 342 " --> pdb=" O GLY S 338 " (cutoff:3.500A) Processing helix chain 'S' and resid 358 through 372 Processing helix chain 'S' and resid 378 through 385 Processing helix chain 'S' and resid 387 through 391 removed outlier: 3.825A pdb=" N ASP S 390 " --> pdb=" O THR S 387 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 16 removed outlier: 4.155A pdb=" N ARG U 6 " --> pdb=" O ALA U 2 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP U 16 " --> pdb=" O LYS U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 60 Processing helix chain 'U' and resid 65 through 78 Processing helix chain 'U' and resid 83 through 92 removed outlier: 3.795A pdb=" N LEU U 87 " --> pdb=" O SER U 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 124 through 132 Processing helix chain 'U' and resid 140 through 144 removed outlier: 3.838A pdb=" N THR U 144 " --> pdb=" O THR U 141 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 176 Processing helix chain 'U' and resid 177 through 180 Processing helix chain 'U' and resid 188 through 201 removed outlier: 3.788A pdb=" N GLU U 192 " --> pdb=" O ALA U 188 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN U 201 " --> pdb=" O ILE U 197 " (cutoff:3.500A) Processing helix chain 'U' and resid 206 through 210 Processing helix chain 'U' and resid 212 through 226 Processing helix chain 'U' and resid 227 through 242 Processing helix chain 'U' and resid 248 through 262 removed outlier: 4.489A pdb=" N THR U 259 " --> pdb=" O CYS U 255 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR U 260 " --> pdb=" O ASP U 256 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 277 removed outlier: 3.965A pdb=" N THR U 272 " --> pdb=" O SER U 268 " (cutoff:3.500A) Processing helix chain 'U' and resid 281 through 286 Processing helix chain 'U' and resid 289 through 307 removed outlier: 3.875A pdb=" N GLY U 307 " --> pdb=" O TYR U 303 " (cutoff:3.500A) Processing helix chain 'U' and resid 310 through 314 removed outlier: 4.355A pdb=" N VAL U 314 " --> pdb=" O PRO U 311 " (cutoff:3.500A) Processing helix chain 'U' and resid 318 through 328 removed outlier: 3.735A pdb=" N GLN U 321 " --> pdb=" O ASN U 318 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN U 322 " --> pdb=" O SER U 319 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ALA U 326 " --> pdb=" O LYS U 323 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLY U 327 " --> pdb=" O PHE U 324 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER U 328 " --> pdb=" O SER U 325 " (cutoff:3.500A) Processing helix chain 'U' and resid 329 through 344 removed outlier: 3.661A pdb=" N GLU U 342 " --> pdb=" O GLY U 338 " (cutoff:3.500A) Processing helix chain 'U' and resid 358 through 372 Processing helix chain 'U' and resid 378 through 385 Processing helix chain 'U' and resid 387 through 391 removed outlier: 3.824A pdb=" N ASP U 390 " --> pdb=" O THR U 387 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 16 removed outlier: 4.155A pdb=" N ARG W 6 " --> pdb=" O ALA W 2 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP W 16 " --> pdb=" O LYS W 12 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 60 Processing helix chain 'W' and resid 65 through 78 Processing helix chain 'W' and resid 83 through 92 removed outlier: 3.795A pdb=" N LEU W 87 " --> pdb=" O SER W 83 " (cutoff:3.500A) Processing helix chain 'W' and resid 124 through 132 Processing helix chain 'W' and resid 140 through 144 removed outlier: 3.838A pdb=" N THR W 144 " --> pdb=" O THR W 141 " (cutoff:3.500A) Processing helix chain 'W' and resid 159 through 176 Processing helix chain 'W' and resid 177 through 180 Processing helix chain 'W' and resid 188 through 201 removed outlier: 3.787A pdb=" N GLU W 192 " --> pdb=" O ALA W 188 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN W 201 " --> pdb=" O ILE W 197 " (cutoff:3.500A) Processing helix chain 'W' and resid 206 through 210 Processing helix chain 'W' and resid 212 through 226 Processing helix chain 'W' and resid 227 through 242 Processing helix chain 'W' and resid 248 through 262 removed outlier: 4.489A pdb=" N THR W 259 " --> pdb=" O CYS W 255 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR W 260 " --> pdb=" O ASP W 256 " (cutoff:3.500A) Processing helix chain 'W' and resid 266 through 277 removed outlier: 3.964A pdb=" N THR W 272 " --> pdb=" O SER W 268 " (cutoff:3.500A) Processing helix chain 'W' and resid 281 through 286 Processing helix chain 'W' and resid 289 through 307 removed outlier: 3.875A pdb=" N GLY W 307 " --> pdb=" O TYR W 303 " (cutoff:3.500A) Processing helix chain 'W' and resid 310 through 314 removed outlier: 4.355A pdb=" N VAL W 314 " --> pdb=" O PRO W 311 " (cutoff:3.500A) Processing helix chain 'W' and resid 318 through 328 removed outlier: 3.735A pdb=" N GLN W 321 " --> pdb=" O ASN W 318 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN W 322 " --> pdb=" O SER W 319 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA W 326 " --> pdb=" O LYS W 323 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLY W 327 " --> pdb=" O PHE W 324 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER W 328 " --> pdb=" O SER W 325 " (cutoff:3.500A) Processing helix chain 'W' and resid 329 through 344 removed outlier: 3.662A pdb=" N GLU W 342 " --> pdb=" O GLY W 338 " (cutoff:3.500A) Processing helix chain 'W' and resid 358 through 372 Processing helix chain 'W' and resid 378 through 385 Processing helix chain 'W' and resid 387 through 391 removed outlier: 3.824A pdb=" N ASP W 390 " --> pdb=" O THR W 387 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 16 removed outlier: 4.155A pdb=" N ARG Y 6 " --> pdb=" O ALA Y 2 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP Y 16 " --> pdb=" O LYS Y 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 60 Processing helix chain 'Y' and resid 65 through 78 Processing helix chain 'Y' and resid 83 through 92 removed outlier: 3.794A pdb=" N LEU Y 87 " --> pdb=" O SER Y 83 " (cutoff:3.500A) Processing helix chain 'Y' and resid 124 through 132 Processing helix chain 'Y' and resid 140 through 144 removed outlier: 3.837A pdb=" N THR Y 144 " --> pdb=" O THR Y 141 " (cutoff:3.500A) Processing helix chain 'Y' and resid 159 through 176 Processing helix chain 'Y' and resid 177 through 180 Processing helix chain 'Y' and resid 188 through 201 removed outlier: 3.788A pdb=" N GLU Y 192 " --> pdb=" O ALA Y 188 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN Y 201 " --> pdb=" O ILE Y 197 " (cutoff:3.500A) Processing helix chain 'Y' and resid 206 through 210 Processing helix chain 'Y' and resid 212 through 226 Processing helix chain 'Y' and resid 227 through 242 Processing helix chain 'Y' and resid 248 through 262 removed outlier: 4.489A pdb=" N THR Y 259 " --> pdb=" O CYS Y 255 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR Y 260 " --> pdb=" O ASP Y 256 " (cutoff:3.500A) Processing helix chain 'Y' and resid 266 through 277 removed outlier: 3.965A pdb=" N THR Y 272 " --> pdb=" O SER Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 281 through 286 Processing helix chain 'Y' and resid 289 through 307 removed outlier: 3.875A pdb=" N GLY Y 307 " --> pdb=" O TYR Y 303 " (cutoff:3.500A) Processing helix chain 'Y' and resid 310 through 314 removed outlier: 4.355A pdb=" N VAL Y 314 " --> pdb=" O PRO Y 311 " (cutoff:3.500A) Processing helix chain 'Y' and resid 318 through 328 removed outlier: 3.735A pdb=" N GLN Y 321 " --> pdb=" O ASN Y 318 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN Y 322 " --> pdb=" O SER Y 319 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA Y 326 " --> pdb=" O LYS Y 323 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLY Y 327 " --> pdb=" O PHE Y 324 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER Y 328 " --> pdb=" O SER Y 325 " (cutoff:3.500A) Processing helix chain 'Y' and resid 329 through 344 removed outlier: 3.661A pdb=" N GLU Y 342 " --> pdb=" O GLY Y 338 " (cutoff:3.500A) Processing helix chain 'Y' and resid 358 through 372 Processing helix chain 'Y' and resid 378 through 385 Processing helix chain 'Y' and resid 387 through 391 removed outlier: 3.825A pdb=" N ASP Y 390 " --> pdb=" O THR Y 387 " (cutoff:3.500A) Processing helix chain '0' and resid 2 through 16 removed outlier: 4.154A pdb=" N ARG 0 6 " --> pdb=" O ALA 0 2 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP 0 16 " --> pdb=" O LYS 0 12 " (cutoff:3.500A) Processing helix chain '0' and resid 45 through 60 Processing helix chain '0' and resid 65 through 78 Processing helix chain '0' and resid 83 through 92 removed outlier: 3.796A pdb=" N LEU 0 87 " --> pdb=" O SER 0 83 " (cutoff:3.500A) Processing helix chain '0' and resid 124 through 132 Processing helix chain '0' and resid 140 through 144 removed outlier: 3.838A pdb=" N THR 0 144 " --> pdb=" O THR 0 141 " (cutoff:3.500A) Processing helix chain '0' and resid 159 through 176 Processing helix chain '0' and resid 177 through 180 Processing helix chain '0' and resid 188 through 201 removed outlier: 3.787A pdb=" N GLU 0 192 " --> pdb=" O ALA 0 188 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN 0 201 " --> pdb=" O ILE 0 197 " (cutoff:3.500A) Processing helix chain '0' and resid 206 through 210 Processing helix chain '0' and resid 212 through 226 Processing helix chain '0' and resid 227 through 242 Processing helix chain '0' and resid 248 through 262 removed outlier: 4.489A pdb=" N THR 0 259 " --> pdb=" O CYS 0 255 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR 0 260 " --> pdb=" O ASP 0 256 " (cutoff:3.500A) Processing helix chain '0' and resid 266 through 277 removed outlier: 3.964A pdb=" N THR 0 272 " --> pdb=" O SER 0 268 " (cutoff:3.500A) Processing helix chain '0' and resid 281 through 286 Processing helix chain '0' and resid 289 through 307 removed outlier: 3.875A pdb=" N GLY 0 307 " --> pdb=" O TYR 0 303 " (cutoff:3.500A) Processing helix chain '0' and resid 310 through 314 removed outlier: 4.354A pdb=" N VAL 0 314 " --> pdb=" O PRO 0 311 " (cutoff:3.500A) Processing helix chain '0' and resid 318 through 328 removed outlier: 3.734A pdb=" N GLN 0 321 " --> pdb=" O ASN 0 318 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN 0 322 " --> pdb=" O SER 0 319 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA 0 326 " --> pdb=" O LYS 0 323 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLY 0 327 " --> pdb=" O PHE 0 324 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER 0 328 " --> pdb=" O SER 0 325 " (cutoff:3.500A) Processing helix chain '0' and resid 329 through 344 removed outlier: 3.661A pdb=" N GLU 0 342 " --> pdb=" O GLY 0 338 " (cutoff:3.500A) Processing helix chain '0' and resid 358 through 372 Processing helix chain '0' and resid 378 through 385 Processing helix chain '0' and resid 387 through 391 removed outlier: 3.825A pdb=" N ASP 0 390 " --> pdb=" O THR 0 387 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 16 removed outlier: 4.154A pdb=" N ARG 2 6 " --> pdb=" O ALA 2 2 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP 2 16 " --> pdb=" O LYS 2 12 " (cutoff:3.500A) Processing helix chain '2' and resid 45 through 60 Processing helix chain '2' and resid 65 through 78 Processing helix chain '2' and resid 83 through 92 removed outlier: 3.794A pdb=" N LEU 2 87 " --> pdb=" O SER 2 83 " (cutoff:3.500A) Processing helix chain '2' and resid 124 through 132 Processing helix chain '2' and resid 140 through 144 removed outlier: 3.838A pdb=" N THR 2 144 " --> pdb=" O THR 2 141 " (cutoff:3.500A) Processing helix chain '2' and resid 159 through 176 Processing helix chain '2' and resid 177 through 180 Processing helix chain '2' and resid 188 through 201 removed outlier: 3.787A pdb=" N GLU 2 192 " --> pdb=" O ALA 2 188 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN 2 201 " --> pdb=" O ILE 2 197 " (cutoff:3.500A) Processing helix chain '2' and resid 206 through 210 Processing helix chain '2' and resid 212 through 226 Processing helix chain '2' and resid 227 through 242 Processing helix chain '2' and resid 248 through 262 removed outlier: 4.488A pdb=" N THR 2 259 " --> pdb=" O CYS 2 255 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR 2 260 " --> pdb=" O ASP 2 256 " (cutoff:3.500A) Processing helix chain '2' and resid 266 through 277 removed outlier: 3.964A pdb=" N THR 2 272 " --> pdb=" O SER 2 268 " (cutoff:3.500A) Processing helix chain '2' and resid 281 through 286 Processing helix chain '2' and resid 289 through 307 removed outlier: 3.875A pdb=" N GLY 2 307 " --> pdb=" O TYR 2 303 " (cutoff:3.500A) Processing helix chain '2' and resid 310 through 314 removed outlier: 4.355A pdb=" N VAL 2 314 " --> pdb=" O PRO 2 311 " (cutoff:3.500A) Processing helix chain '2' and resid 318 through 328 removed outlier: 3.735A pdb=" N GLN 2 321 " --> pdb=" O ASN 2 318 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN 2 322 " --> pdb=" O SER 2 319 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ALA 2 326 " --> pdb=" O LYS 2 323 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLY 2 327 " --> pdb=" O PHE 2 324 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER 2 328 " --> pdb=" O SER 2 325 " (cutoff:3.500A) Processing helix chain '2' and resid 329 through 344 removed outlier: 3.660A pdb=" N GLU 2 342 " --> pdb=" O GLY 2 338 " (cutoff:3.500A) Processing helix chain '2' and resid 358 through 372 Processing helix chain '2' and resid 378 through 385 Processing helix chain '2' and resid 387 through 391 removed outlier: 3.825A pdb=" N ASP 2 390 " --> pdb=" O THR 2 387 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'E' and resid 33 through 40 removed outlier: 6.052A pdb=" N HIS E 33 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG E 100 " --> pdb=" O HIS E 33 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE E 35 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL E 102 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL E 37 " --> pdb=" O VAL E 102 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL E 104 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL E 39 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N GLN E 106 " --> pdb=" O VAL E 39 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 33 through 40 removed outlier: 6.051A pdb=" N HIS A 33 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG A 100 " --> pdb=" O HIS A 33 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE A 35 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL A 102 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL A 37 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL A 104 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A 39 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N GLN A 106 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'D' and resid 33 through 40 removed outlier: 6.051A pdb=" N HIS D 33 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG D 100 " --> pdb=" O HIS D 33 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE D 35 " --> pdb=" O ARG D 100 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL D 102 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL D 37 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL D 104 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL D 39 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N GLN D 106 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'G' and resid 33 through 40 removed outlier: 6.052A pdb=" N HIS G 33 " --> pdb=" O SER G 98 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ARG G 100 " --> pdb=" O HIS G 33 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE G 35 " --> pdb=" O ARG G 100 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL G 102 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL G 37 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL G 104 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL G 39 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N GLN G 106 " --> pdb=" O VAL G 39 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'I' and resid 33 through 40 removed outlier: 6.052A pdb=" N HIS I 33 " --> pdb=" O SER I 98 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ARG I 100 " --> pdb=" O HIS I 33 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE I 35 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL I 102 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL I 37 " --> pdb=" O VAL I 102 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL I 104 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL I 39 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N GLN I 106 " --> pdb=" O VAL I 39 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'K' and resid 33 through 40 removed outlier: 6.051A pdb=" N HIS K 33 " --> pdb=" O SER K 98 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG K 100 " --> pdb=" O HIS K 33 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE K 35 " --> pdb=" O ARG K 100 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL K 102 " --> pdb=" O ILE K 35 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL K 37 " --> pdb=" O VAL K 102 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL K 104 " --> pdb=" O VAL K 37 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL K 39 " --> pdb=" O VAL K 104 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N GLN K 106 " --> pdb=" O VAL K 39 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'M' and resid 33 through 40 removed outlier: 6.052A pdb=" N HIS M 33 " --> pdb=" O SER M 98 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG M 100 " --> pdb=" O HIS M 33 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE M 35 " --> pdb=" O ARG M 100 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL M 102 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL M 37 " --> pdb=" O VAL M 102 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL M 104 " --> pdb=" O VAL M 37 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL M 39 " --> pdb=" O VAL M 104 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N GLN M 106 " --> pdb=" O VAL M 39 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'O' and resid 33 through 40 removed outlier: 6.051A pdb=" N HIS O 33 " --> pdb=" O SER O 98 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG O 100 " --> pdb=" O HIS O 33 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE O 35 " --> pdb=" O ARG O 100 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL O 102 " --> pdb=" O ILE O 35 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL O 37 " --> pdb=" O VAL O 102 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL O 104 " --> pdb=" O VAL O 37 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL O 39 " --> pdb=" O VAL O 104 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N GLN O 106 " --> pdb=" O VAL O 39 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'Q' and resid 33 through 40 removed outlier: 6.051A pdb=" N HIS Q 33 " --> pdb=" O SER Q 98 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ARG Q 100 " --> pdb=" O HIS Q 33 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE Q 35 " --> pdb=" O ARG Q 100 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL Q 102 " --> pdb=" O ILE Q 35 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL Q 37 " --> pdb=" O VAL Q 102 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL Q 104 " --> pdb=" O VAL Q 37 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL Q 39 " --> pdb=" O VAL Q 104 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N GLN Q 106 " --> pdb=" O VAL Q 39 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'S' and resid 33 through 40 removed outlier: 6.051A pdb=" N HIS S 33 " --> pdb=" O SER S 98 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG S 100 " --> pdb=" O HIS S 33 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE S 35 " --> pdb=" O ARG S 100 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL S 102 " --> pdb=" O ILE S 35 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL S 37 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL S 104 " --> pdb=" O VAL S 37 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL S 39 " --> pdb=" O VAL S 104 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N GLN S 106 " --> pdb=" O VAL S 39 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'U' and resid 33 through 40 removed outlier: 6.052A pdb=" N HIS U 33 " --> pdb=" O SER U 98 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG U 100 " --> pdb=" O HIS U 33 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE U 35 " --> pdb=" O ARG U 100 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL U 102 " --> pdb=" O ILE U 35 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL U 37 " --> pdb=" O VAL U 102 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL U 104 " --> pdb=" O VAL U 37 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL U 39 " --> pdb=" O VAL U 104 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N GLN U 106 " --> pdb=" O VAL U 39 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'W' and resid 33 through 40 removed outlier: 6.052A pdb=" N HIS W 33 " --> pdb=" O SER W 98 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG W 100 " --> pdb=" O HIS W 33 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE W 35 " --> pdb=" O ARG W 100 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL W 102 " --> pdb=" O ILE W 35 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL W 37 " --> pdb=" O VAL W 102 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL W 104 " --> pdb=" O VAL W 37 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL W 39 " --> pdb=" O VAL W 104 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N GLN W 106 " --> pdb=" O VAL W 39 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'Y' and resid 33 through 40 removed outlier: 6.051A pdb=" N HIS Y 33 " --> pdb=" O SER Y 98 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG Y 100 " --> pdb=" O HIS Y 33 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE Y 35 " --> pdb=" O ARG Y 100 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL Y 102 " --> pdb=" O ILE Y 35 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL Y 37 " --> pdb=" O VAL Y 102 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL Y 104 " --> pdb=" O VAL Y 37 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL Y 39 " --> pdb=" O VAL Y 104 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N GLN Y 106 " --> pdb=" O VAL Y 39 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '0' and resid 33 through 40 removed outlier: 6.052A pdb=" N HIS 0 33 " --> pdb=" O SER 0 98 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG 0 100 " --> pdb=" O HIS 0 33 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE 0 35 " --> pdb=" O ARG 0 100 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL 0 102 " --> pdb=" O ILE 0 35 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL 0 37 " --> pdb=" O VAL 0 102 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL 0 104 " --> pdb=" O VAL 0 37 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL 0 39 " --> pdb=" O VAL 0 104 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N GLN 0 106 " --> pdb=" O VAL 0 39 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain '2' and resid 33 through 40 removed outlier: 6.052A pdb=" N HIS 2 33 " --> pdb=" O SER 2 98 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG 2 100 " --> pdb=" O HIS 2 33 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE 2 35 " --> pdb=" O ARG 2 100 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL 2 102 " --> pdb=" O ILE 2 35 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL 2 37 " --> pdb=" O VAL 2 102 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL 2 104 " --> pdb=" O VAL 2 37 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL 2 39 " --> pdb=" O VAL 2 104 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N GLN 2 106 " --> pdb=" O VAL 2 39 " (cutoff:3.500A) 2340 hydrogen bonds defined for protein. 6480 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: 16.44 Time building geometry restraints manager: 20.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 15735 1.34 - 1.46: 10911 1.46 - 1.57: 21864 1.57 - 1.69: 150 1.69 - 1.81: 345 Bond restraints: 49005 Sorted by residual: bond pdb=" CB MET 2 306 " pdb=" CG MET 2 306 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.83e+00 bond pdb=" CB MET W 306 " pdb=" CG MET W 306 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.81e+00 bond pdb=" CB MET M 306 " pdb=" CG MET M 306 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.79e+00 bond pdb=" CB MET S 306 " pdb=" CG MET S 306 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.78e+00 bond pdb=" CB MET A 306 " pdb=" CG MET A 306 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.78e+00 ... (remaining 49000 not shown) Histogram of bond angle deviations from ideal: 98.29 - 105.44: 1251 105.44 - 112.60: 26364 112.60 - 119.75: 15701 119.75 - 126.91: 22540 126.91 - 134.06: 894 Bond angle restraints: 66750 Sorted by residual: angle pdb=" N VAL K 394 " pdb=" CA VAL K 394 " pdb=" C VAL K 394 " ideal model delta sigma weight residual 112.96 109.61 3.35 1.00e+00 1.00e+00 1.12e+01 angle pdb=" N VAL A 394 " pdb=" CA VAL A 394 " pdb=" C VAL A 394 " ideal model delta sigma weight residual 112.96 109.62 3.34 1.00e+00 1.00e+00 1.11e+01 angle pdb=" N VAL D 394 " pdb=" CA VAL D 394 " pdb=" C VAL D 394 " ideal model delta sigma weight residual 112.96 109.63 3.33 1.00e+00 1.00e+00 1.11e+01 angle pdb=" N VAL O 394 " pdb=" CA VAL O 394 " pdb=" C VAL O 394 " ideal model delta sigma weight residual 112.96 109.63 3.33 1.00e+00 1.00e+00 1.11e+01 angle pdb=" N VAL Q 394 " pdb=" CA VAL Q 394 " pdb=" C VAL Q 394 " ideal model delta sigma weight residual 112.96 109.64 3.32 1.00e+00 1.00e+00 1.10e+01 ... (remaining 66745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 27077 17.29 - 34.59: 1873 34.59 - 51.88: 270 51.88 - 69.18: 105 69.18 - 86.47: 90 Dihedral angle restraints: 29415 sinusoidal: 12435 harmonic: 16980 Sorted by residual: dihedral pdb=" CA ASP D 140 " pdb=" CB ASP D 140 " pdb=" CG ASP D 140 " pdb=" OD1 ASP D 140 " ideal model delta sinusoidal sigma weight residual -30.00 -88.97 58.97 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ASP A 140 " pdb=" CB ASP A 140 " pdb=" CG ASP A 140 " pdb=" OD1 ASP A 140 " ideal model delta sinusoidal sigma weight residual -30.00 -88.96 58.96 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ASP Q 140 " pdb=" CB ASP Q 140 " pdb=" CG ASP Q 140 " pdb=" OD1 ASP Q 140 " ideal model delta sinusoidal sigma weight residual -30.00 -88.95 58.95 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 29412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 5449 0.040 - 0.079: 1595 0.079 - 0.119: 561 0.119 - 0.159: 90 0.159 - 0.198: 30 Chirality restraints: 7725 Sorted by residual: chirality pdb=" C2' A C 1 " pdb=" C3' A C 1 " pdb=" O2' A C 1 " pdb=" C1' A C 1 " both_signs ideal model delta sigma weight residual False -2.75 -2.56 -0.20 2.00e-01 2.50e+01 9.83e-01 chirality pdb=" C2' A P 1 " pdb=" C3' A P 1 " pdb=" O2' A P 1 " pdb=" C1' A P 1 " both_signs ideal model delta sigma weight residual False -2.75 -2.56 -0.20 2.00e-01 2.50e+01 9.83e-01 chirality pdb=" C2' A F 1 " pdb=" C3' A F 1 " pdb=" O2' A F 1 " pdb=" C1' A F 1 " both_signs ideal model delta sigma weight residual False -2.75 -2.56 -0.20 2.00e-01 2.50e+01 9.82e-01 ... (remaining 7722 not shown) Planarity restraints: 8235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG W 142 " 0.050 9.50e-02 1.11e+02 2.63e-02 2.79e+00 pdb=" NE ARG W 142 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG W 142 " 0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG W 142 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG W 142 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 142 " -0.049 9.50e-02 1.11e+02 2.60e-02 2.78e+00 pdb=" NE ARG K 142 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG K 142 " -0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG K 142 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG K 142 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG O 142 " 0.050 9.50e-02 1.11e+02 2.64e-02 2.74e+00 pdb=" NE ARG O 142 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG O 142 " 0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG O 142 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG O 142 " -0.007 2.00e-02 2.50e+03 ... (remaining 8232 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.31: 245 2.31 - 2.96: 25919 2.96 - 3.61: 72494 3.61 - 4.25: 109082 4.25 - 4.90: 184676 Nonbonded interactions: 392416 Sorted by model distance: nonbonded pdb=" CD PRO A 244 " pdb=" O SER D 24 " model vdw 1.666 3.440 nonbonded pdb=" CD PRO I 244 " pdb=" O SER K 24 " model vdw 1.666 3.440 nonbonded pdb=" CD PRO K 244 " pdb=" O SER M 24 " model vdw 1.666 3.440 nonbonded pdb=" CD PRO E 244 " pdb=" O SER A 24 " model vdw 1.666 3.440 nonbonded pdb=" CD PRO G 244 " pdb=" O SER I 24 " model vdw 1.666 3.440 ... (remaining 392411 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 'D' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain '1' selection = chain '3' selection = chain 'B' selection = chain 'C' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' 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 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 30120 2.51 5 N 8310 2.21 5 O 9270 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue 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: 1.130 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: 0.100 Extract box with map and model: 8.620 Check model and map are aligned: 0.650 Convert atoms to be neutral: 0.390 Process input model: 122.410 Find NCS groups from input model: 3.370 Set up NCS constraints: 0.480 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5073 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 : 0.009 0.053 49005 Z= 0.600 Angle : 0.714 6.829 66750 Z= 0.430 Chirality : 0.044 0.198 7725 Planarity : 0.004 0.037 8235 Dihedral : 12.950 86.472 18495 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer Outliers : 0.30 % 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: -2.28 (0.10), residues: 5880 helix: -0.52 (0.08), residues: 3300 sheet: -4.25 (0.14), residues: 150 loop : -2.72 (0.11), residues: 2430 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1196 residues out of total 4980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1181 time to evaluate : 5.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 1196 average time/residue: 0.6273 time to fit residues: 1233.9209 Evaluate side-chains 716 residues out of total 4980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 711 time to evaluate : 5.011 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4134 time to fit residues: 11.3090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 493 optimal weight: 0.9990 chunk 443 optimal weight: 7.9990 chunk 246 optimal weight: 0.6980 chunk 151 optimal weight: 0.4980 chunk 299 optimal weight: 40.0000 chunk 236 optimal weight: 6.9990 chunk 458 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 278 optimal weight: 10.0000 chunk 341 optimal weight: 0.7980 chunk 531 optimal weight: 50.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 304 GLN E 305 GLN D 202 GLN D 305 GLN G 201 GLN I 201 GLN K 149 ASN K 201 GLN K 305 GLN M 149 ASN M 201 GLN M 321 GLN O 149 ASN O 201 GLN Q 305 GLN U 201 GLN U 304 GLN W 145 HIS W 201 GLN ** Y 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 149 ASN 2 149 ASN 2 201 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5567 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 49005 Z= 0.182 Angle : 0.567 10.178 66750 Z= 0.289 Chirality : 0.040 0.142 7725 Planarity : 0.004 0.050 8235 Dihedral : 5.222 40.379 7485 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.92 (0.11), residues: 5880 helix: 0.81 (0.09), residues: 3360 sheet: -3.41 (0.22), residues: 150 loop : -2.60 (0.11), residues: 2370 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 4980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 816 time to evaluate : 5.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 62 residues processed: 880 average time/residue: 0.5593 time to fit residues: 830.4083 Evaluate side-chains 731 residues out of total 4980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 669 time to evaluate : 5.052 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 0.4291 time to fit residues: 57.5329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 295 optimal weight: 20.0000 chunk 164 optimal weight: 40.0000 chunk 442 optimal weight: 6.9990 chunk 361 optimal weight: 9.9990 chunk 146 optimal weight: 0.9980 chunk 532 optimal weight: 20.0000 chunk 574 optimal weight: 8.9990 chunk 473 optimal weight: 30.0000 chunk 527 optimal weight: 5.9990 chunk 181 optimal weight: 0.9980 chunk 426 optimal weight: 6.9990 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 14 ASN E 33 HIS E 201 GLN D 14 ASN D 33 HIS D 304 GLN D 305 GLN G 14 ASN ** G 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 ASN I 202 GLN K 134 GLN K 305 GLN M 321 GLN O 106 GLN Q 14 ASN ** Q 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 ASN ** S 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 14 ASN ** U 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 201 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6048 moved from start: 0.5880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.079 49005 Z= 0.402 Angle : 0.737 10.129 66750 Z= 0.376 Chirality : 0.045 0.181 7725 Planarity : 0.005 0.098 8235 Dihedral : 6.172 41.690 7485 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 3.03 % 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: -1.20 (0.11), residues: 5880 helix: 0.51 (0.09), residues: 3495 sheet: -3.68 (0.18), residues: 300 loop : -2.64 (0.12), residues: 2085 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1046 residues out of total 4980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 895 time to evaluate : 5.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 151 outliers final: 63 residues processed: 985 average time/residue: 0.5617 time to fit residues: 926.3915 Evaluate side-chains 795 residues out of total 4980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 732 time to evaluate : 5.102 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.4290 time to fit residues: 57.5249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 525 optimal weight: 30.0000 chunk 400 optimal weight: 50.0000 chunk 276 optimal weight: 30.0000 chunk 58 optimal weight: 0.8980 chunk 253 optimal weight: 50.0000 chunk 357 optimal weight: 0.6980 chunk 534 optimal weight: 0.6980 chunk 565 optimal weight: 0.0970 chunk 279 optimal weight: 30.0000 chunk 506 optimal weight: 0.0020 chunk 152 optimal weight: 20.0000 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN G 201 GLN I 14 ASN ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 305 GLN M 149 ASN O 201 GLN Q 304 GLN S 304 GLN ** U 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 304 GLN Y 202 GLN 0 345 ASN 2 345 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5929 moved from start: 0.6000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.061 49005 Z= 0.145 Angle : 0.507 8.678 66750 Z= 0.260 Chirality : 0.038 0.206 7725 Planarity : 0.004 0.066 8235 Dihedral : 5.365 42.934 7485 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 1.22 % 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: -0.77 (0.11), residues: 5880 helix: 0.96 (0.09), residues: 3480 sheet: -3.38 (0.19), residues: 330 loop : -2.63 (0.12), residues: 2070 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 4980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 898 time to evaluate : 5.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 31 residues processed: 932 average time/residue: 0.5667 time to fit residues: 884.9368 Evaluate side-chains 791 residues out of total 4980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 760 time to evaluate : 4.643 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.4598 time to fit residues: 33.5051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 470 optimal weight: 50.0000 chunk 320 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 421 optimal weight: 0.5980 chunk 233 optimal weight: 50.0000 chunk 482 optimal weight: 8.9990 chunk 390 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 288 optimal weight: 5.9990 chunk 507 optimal weight: 50.0000 chunk 142 optimal weight: 1.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 202 GLN I 221 ASN K 305 GLN M 149 ASN S 134 GLN U 14 ASN ** U 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 202 GLN ** Y 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 345 ASN 2 149 ASN 2 345 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6065 moved from start: 0.6585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 49005 Z= 0.311 Angle : 0.613 9.611 66750 Z= 0.312 Chirality : 0.042 0.220 7725 Planarity : 0.004 0.055 8235 Dihedral : 5.718 45.567 7485 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer Outliers : 2.07 % 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: 5880 helix: 1.01 (0.09), residues: 3390 sheet: -2.96 (0.21), residues: 330 loop : -2.57 (0.11), residues: 2160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 4980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 755 time to evaluate : 5.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 62 residues processed: 810 average time/residue: 0.5999 time to fit residues: 809.0213 Evaluate side-chains 755 residues out of total 4980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 693 time to evaluate : 5.219 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 0.4528 time to fit residues: 59.9424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 190 optimal weight: 50.0000 chunk 509 optimal weight: 50.0000 chunk 111 optimal weight: 7.9990 chunk 331 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 566 optimal weight: 10.0000 chunk 469 optimal weight: 1.9990 chunk 262 optimal weight: 50.0000 chunk 47 optimal weight: 0.0270 chunk 187 optimal weight: 0.2980 chunk 297 optimal weight: 10.0000 overall best weight: 0.8642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 106 GLN K 305 GLN M 149 ASN Q 305 GLN U 145 HIS Y 321 GLN 0 345 ASN 2 149 ASN 2 345 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5976 moved from start: 0.6684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 49005 Z= 0.144 Angle : 0.498 9.951 66750 Z= 0.255 Chirality : 0.038 0.183 7725 Planarity : 0.004 0.052 8235 Dihedral : 5.220 44.156 7485 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 0.96 % 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 (0.11), residues: 5880 helix: 1.12 (0.09), residues: 3465 sheet: -2.78 (0.22), residues: 330 loop : -2.54 (0.12), residues: 2085 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 4980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 789 time to evaluate : 5.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 24 residues processed: 819 average time/residue: 0.5637 time to fit residues: 768.4834 Evaluate side-chains 747 residues out of total 4980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 723 time to evaluate : 5.012 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.4032 time to fit residues: 25.6795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 545 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 322 optimal weight: 40.0000 chunk 413 optimal weight: 4.9990 chunk 320 optimal weight: 5.9990 chunk 476 optimal weight: 50.0000 chunk 316 optimal weight: 2.9990 chunk 563 optimal weight: 0.0470 chunk 352 optimal weight: 0.6980 chunk 343 optimal weight: 0.6980 chunk 260 optimal weight: 50.0000 overall best weight: 1.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 86 GLN A 33 HIS D 351 ASN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 305 GLN M 149 ASN U 14 ASN U 145 HIS Y 321 GLN 2 149 ASN 2 345 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5998 moved from start: 0.6877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 49005 Z= 0.166 Angle : 0.506 10.184 66750 Z= 0.258 Chirality : 0.038 0.166 7725 Planarity : 0.004 0.048 8235 Dihedral : 5.117 43.735 7485 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.37 (0.11), residues: 5880 helix: 1.29 (0.09), residues: 3390 sheet: -2.57 (0.22), residues: 330 loop : -2.45 (0.12), residues: 2160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 4980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 756 time to evaluate : 5.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 30 residues processed: 782 average time/residue: 0.5850 time to fit residues: 760.8639 Evaluate side-chains 748 residues out of total 4980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 718 time to evaluate : 5.093 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.4578 time to fit residues: 33.4887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 348 optimal weight: 1.9990 chunk 225 optimal weight: 7.9990 chunk 336 optimal weight: 7.9990 chunk 169 optimal weight: 0.5980 chunk 110 optimal weight: 0.0870 chunk 109 optimal weight: 2.9990 chunk 358 optimal weight: 0.9980 chunk 384 optimal weight: 0.7980 chunk 278 optimal weight: 6.9990 chunk 52 optimal weight: 0.2980 chunk 443 optimal weight: 7.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 33 HIS D 351 ASN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 201 GLN I 201 GLN K 305 GLN M 149 ASN 0 345 ASN 2 149 ASN 2 345 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5949 moved from start: 0.6962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.053 49005 Z= 0.135 Angle : 0.496 9.763 66750 Z= 0.251 Chirality : 0.038 0.157 7725 Planarity : 0.004 0.048 8235 Dihedral : 4.914 46.811 7485 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.22 (0.11), residues: 5880 helix: 1.35 (0.09), residues: 3375 sheet: -2.41 (0.23), residues: 330 loop : -2.26 (0.12), residues: 2175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 4980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 791 time to evaluate : 5.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 14 residues processed: 802 average time/residue: 0.6017 time to fit residues: 795.8811 Evaluate side-chains 754 residues out of total 4980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 740 time to evaluate : 5.035 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.4355 time to fit residues: 18.8013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 512 optimal weight: 9.9990 chunk 540 optimal weight: 3.9990 chunk 492 optimal weight: 8.9990 chunk 525 optimal weight: 0.6980 chunk 316 optimal weight: 0.8980 chunk 228 optimal weight: 50.0000 chunk 412 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 474 optimal weight: 30.0000 chunk 496 optimal weight: 3.9990 chunk 523 optimal weight: 20.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 86 GLN D 134 GLN D 351 ASN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 305 GLN M 149 ASN S 202 GLN W 304 GLN 2 149 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 moved from start: 0.7268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 49005 Z= 0.255 Angle : 0.575 14.325 66750 Z= 0.293 Chirality : 0.040 0.198 7725 Planarity : 0.004 0.058 8235 Dihedral : 5.355 45.469 7485 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.34 (0.11), residues: 5880 helix: 1.23 (0.09), residues: 3450 sheet: -2.12 (0.23), residues: 330 loop : -2.47 (0.12), residues: 2100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 4980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 738 time to evaluate : 5.358 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 16 residues processed: 750 average time/residue: 0.5908 time to fit residues: 735.4033 Evaluate side-chains 724 residues out of total 4980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 708 time to evaluate : 5.043 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.4202 time to fit residues: 19.9956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 345 optimal weight: 0.9990 chunk 555 optimal weight: 50.0000 chunk 339 optimal weight: 0.7980 chunk 263 optimal weight: 10.0000 chunk 386 optimal weight: 0.9980 chunk 582 optimal weight: 4.9990 chunk 536 optimal weight: 9.9990 chunk 464 optimal weight: 0.7980 chunk 48 optimal weight: 10.0000 chunk 358 optimal weight: 0.7980 chunk 284 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 33 HIS D 351 ASN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 201 GLN ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 HIS K 305 GLN M 149 ASN ** Q 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5989 moved from start: 0.7326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.057 49005 Z= 0.155 Angle : 0.527 12.534 66750 Z= 0.267 Chirality : 0.039 0.221 7725 Planarity : 0.004 0.060 8235 Dihedral : 5.012 46.138 7485 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 0.22 % 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: -0.20 (0.11), residues: 5880 helix: 1.29 (0.09), residues: 3435 sheet: -2.01 (0.24), residues: 330 loop : -2.29 (0.12), residues: 2115 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 4980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 743 time to evaluate : 5.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 747 average time/residue: 0.5776 time to fit residues: 719.6430 Evaluate side-chains 714 residues out of total 4980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 711 time to evaluate : 5.096 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4370 time to fit residues: 9.7330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 368 optimal weight: 1.9990 chunk 494 optimal weight: 0.8980 chunk 142 optimal weight: 4.9990 chunk 427 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 128 optimal weight: 20.0000 chunk 464 optimal weight: 0.8980 chunk 194 optimal weight: 50.0000 chunk 477 optimal weight: 50.0000 chunk 58 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 ASN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 201 GLN K 14 ASN K 305 GLN M 149 ASN ** Q 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 304 GLN 2 149 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.255877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.198774 restraints weight = 74352.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.174877 restraints weight = 93052.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.170197 restraints weight = 73022.334| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.7431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 49005 Z= 0.175 Angle : 0.538 17.534 66750 Z= 0.272 Chirality : 0.039 0.247 7725 Planarity : 0.004 0.058 8235 Dihedral : 5.020 45.175 7485 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 0.34 % 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: -0.15 (0.11), residues: 5880 helix: 1.33 (0.09), residues: 3420 sheet: -2.00 (0.37), residues: 150 loop : -2.26 (0.11), residues: 2310 =============================================================================== Job complete usr+sys time: 12546.78 seconds wall clock time: 224 minutes 12.86 seconds (13452.86 seconds total)