Starting phenix.real_space_refine (version: dev) on Sat Feb 25 15:09:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hxx_0297/02_2023/6hxx_0297_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hxx_0297/02_2023/6hxx_0297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hxx_0297/02_2023/6hxx_0297.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hxx_0297/02_2023/6hxx_0297.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hxx_0297/02_2023/6hxx_0297_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hxx_0297/02_2023/6hxx_0297_neut.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.003 sd= 0.024 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 Process input model Symmetric amino acids flipped Residue "AA ARG 46": "NH1" <-> "NH2" Residue "AA PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB ARG 46": "NH1" <-> "NH2" Residue "AB PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AC ARG 46": "NH1" <-> "NH2" Residue "AC PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AD ARG 46": "NH1" <-> "NH2" Residue "AD PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AE ARG 46": "NH1" <-> "NH2" Residue "AE PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AF ARG 46": "NH1" <-> "NH2" Residue "AF PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG ARG 46": "NH1" <-> "NH2" Residue "AG PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AH ARG 46": "NH1" <-> "NH2" Residue "AH PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AI ARG 46": "NH1" <-> "NH2" Residue "AI PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AJ ARG 46": "NH1" <-> "NH2" Residue "AJ PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AK ARG 46": "NH1" <-> "NH2" Residue "AK PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AL ARG 46": "NH1" <-> "NH2" Residue "AL PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM ARG 46": "NH1" <-> "NH2" Residue "AM PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AN ARG 46": "NH1" <-> "NH2" Residue "AN PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AO ARG 46": "NH1" <-> "NH2" Residue "AO PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AP ARG 46": "NH1" <-> "NH2" Residue "AP PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AQ ARG 46": "NH1" <-> "NH2" Residue "AQ PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AR ARG 46": "NH1" <-> "NH2" Residue "AR PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AS ARG 46": "NH1" <-> "NH2" Residue "AS PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AT ARG 46": "NH1" <-> "NH2" Residue "AT PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AU ARG 46": "NH1" <-> "NH2" Residue "AU PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AV ARG 46": "NH1" <-> "NH2" Residue "AV PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AW ARG 46": "NH1" <-> "NH2" Residue "AW PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AX ARG 46": "NH1" <-> "NH2" Residue "AX PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AY ARG 46": "NH1" <-> "NH2" Residue "AY PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AZ ARG 46": "NH1" <-> "NH2" Residue "AZ PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA ARG 46": "NH1" <-> "NH2" Residue "BA PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BB ARG 46": "NH1" <-> "NH2" Residue "BB PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC ARG 46": "NH1" <-> "NH2" Residue "BC PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BD ARG 46": "NH1" <-> "NH2" Residue "BD PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE ARG 46": "NH1" <-> "NH2" Residue "BE PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BF ARG 46": "NH1" <-> "NH2" Residue "BF PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BG ARG 46": "NH1" <-> "NH2" Residue "BG PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BH ARG 46": "NH1" <-> "NH2" Residue "BH PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BI ARG 46": "NH1" <-> "NH2" Residue "BI PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 65765 Number of models: 1 Model: "" Number of chains: 70 Chain: "AA" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Aa" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "AB" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Ab" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "AC" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Ac" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "AD" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Ad" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "AE" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Ae" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "AF" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Af" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "AG" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Ag" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "AH" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Ah" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "AI" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Ai" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "AJ" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Aj" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "AK" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Ak" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "AL" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Al" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "AM" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Am" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "AN" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "An" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "AO" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Ao" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "AP" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Ap" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "AQ" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Aq" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "AR" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Ar" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "AS" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "As" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "AT" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "At" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "AU" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Au" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "AV" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Av" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "AW" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Aw" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "AX" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Ax" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "AY" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Ay" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "AZ" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Az" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "BA" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Ba" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "BB" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Bb" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "BC" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Bc" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "BD" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Bd" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "BE" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Be" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "BF" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Bf" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "BG" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Bg" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "BH" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Bh" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "BI" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1779 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "Bi" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Time building chain proxies: 26.55, per 1000 atoms: 0.40 Number of scatterers: 65765 At special positions: 0 Unit cell: (143.235, 143.235, 253.579, 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 490 16.00 P 175 15.00 O 13265 8.00 N 11235 7.00 C 40600 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: 21.08 Conformation dependent library (CDL) restraints added in 6.7 seconds 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14840 Finding SS restraints... Secondary structure from input PDB file: 315 helices and 70 sheets defined 44.6% alpha, 5.4% beta 0 base pairs and 70 stacking pairs defined. Time for finding SS restraints: 16.34 Creating SS restraints... Processing helix chain 'AA' and resid 66 through 72 removed outlier: 3.894A pdb=" N GLUAA 72 " --> pdb=" O GLUAA 68 " (cutoff:3.500A) Processing helix chain 'AA' and resid 86 through 100 Processing helix chain 'AA' and resid 107 through 122 removed outlier: 3.719A pdb=" N VALAA 111 " --> pdb=" O GLUAA 107 " (cutoff:3.500A) Processing helix chain 'AA' and resid 145 through 152 Processing helix chain 'AA' and resid 155 through 161 removed outlier: 3.604A pdb=" N ILEAA 159 " --> pdb=" O THRAA 155 " (cutoff:3.500A) Processing helix chain 'AA' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAA 177 " --> pdb=" O METAA 173 " (cutoff:3.500A) Processing helix chain 'AA' and resid 182 through 189 Processing helix chain 'AA' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAA 197 " --> pdb=" O SERAA 194 " (cutoff:3.500A) Processing helix chain 'AA' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAA 226 " --> pdb=" O ALAAA 222 " (cutoff:3.500A) Processing helix chain 'AB' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAB 72 " --> pdb=" O GLUAB 68 " (cutoff:3.500A) Processing helix chain 'AB' and resid 86 through 100 Processing helix chain 'AB' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAB 111 " --> pdb=" O GLUAB 107 " (cutoff:3.500A) Processing helix chain 'AB' and resid 145 through 152 Processing helix chain 'AB' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAB 159 " --> pdb=" O THRAB 155 " (cutoff:3.500A) Processing helix chain 'AB' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAB 177 " --> pdb=" O METAB 173 " (cutoff:3.500A) Processing helix chain 'AB' and resid 182 through 189 Processing helix chain 'AB' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAB 197 " --> pdb=" O SERAB 194 " (cutoff:3.500A) Processing helix chain 'AB' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAB 226 " --> pdb=" O ALAAB 222 " (cutoff:3.500A) Processing helix chain 'AC' and resid 66 through 72 removed outlier: 3.894A pdb=" N GLUAC 72 " --> pdb=" O GLUAC 68 " (cutoff:3.500A) Processing helix chain 'AC' and resid 86 through 100 Processing helix chain 'AC' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAC 111 " --> pdb=" O GLUAC 107 " (cutoff:3.500A) Processing helix chain 'AC' and resid 145 through 152 Processing helix chain 'AC' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAC 159 " --> pdb=" O THRAC 155 " (cutoff:3.500A) Processing helix chain 'AC' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAC 177 " --> pdb=" O METAC 173 " (cutoff:3.500A) Processing helix chain 'AC' and resid 182 through 189 Processing helix chain 'AC' and resid 193 through 198 removed outlier: 4.041A pdb=" N ARGAC 197 " --> pdb=" O SERAC 194 " (cutoff:3.500A) Processing helix chain 'AC' and resid 210 through 226 removed outlier: 3.725A pdb=" N LYSAC 226 " --> pdb=" O ALAAC 222 " (cutoff:3.500A) Processing helix chain 'AD' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAD 72 " --> pdb=" O GLUAD 68 " (cutoff:3.500A) Processing helix chain 'AD' and resid 86 through 100 Processing helix chain 'AD' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAD 111 " --> pdb=" O GLUAD 107 " (cutoff:3.500A) Processing helix chain 'AD' and resid 145 through 152 Processing helix chain 'AD' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAD 159 " --> pdb=" O THRAD 155 " (cutoff:3.500A) Processing helix chain 'AD' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAD 177 " --> pdb=" O METAD 173 " (cutoff:3.500A) Processing helix chain 'AD' and resid 182 through 189 Processing helix chain 'AD' and resid 193 through 198 removed outlier: 4.043A pdb=" N ARGAD 197 " --> pdb=" O SERAD 194 " (cutoff:3.500A) Processing helix chain 'AD' and resid 210 through 226 removed outlier: 3.726A pdb=" N LYSAD 226 " --> pdb=" O ALAAD 222 " (cutoff:3.500A) Processing helix chain 'AE' and resid 66 through 72 removed outlier: 3.894A pdb=" N GLUAE 72 " --> pdb=" O GLUAE 68 " (cutoff:3.500A) Processing helix chain 'AE' and resid 86 through 100 Processing helix chain 'AE' and resid 107 through 122 removed outlier: 3.719A pdb=" N VALAE 111 " --> pdb=" O GLUAE 107 " (cutoff:3.500A) Processing helix chain 'AE' and resid 145 through 152 Processing helix chain 'AE' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAE 159 " --> pdb=" O THRAE 155 " (cutoff:3.500A) Processing helix chain 'AE' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAE 177 " --> pdb=" O METAE 173 " (cutoff:3.500A) Processing helix chain 'AE' and resid 182 through 189 Processing helix chain 'AE' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAE 197 " --> pdb=" O SERAE 194 " (cutoff:3.500A) Processing helix chain 'AE' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAE 226 " --> pdb=" O ALAAE 222 " (cutoff:3.500A) Processing helix chain 'AF' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAF 72 " --> pdb=" O GLUAF 68 " (cutoff:3.500A) Processing helix chain 'AF' and resid 86 through 100 Processing helix chain 'AF' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAF 111 " --> pdb=" O GLUAF 107 " (cutoff:3.500A) Processing helix chain 'AF' and resid 145 through 152 Processing helix chain 'AF' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAF 159 " --> pdb=" O THRAF 155 " (cutoff:3.500A) Processing helix chain 'AF' and resid 163 through 178 removed outlier: 3.983A pdb=" N LYSAF 177 " --> pdb=" O METAF 173 " (cutoff:3.500A) Processing helix chain 'AF' and resid 182 through 189 Processing helix chain 'AF' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAF 197 " --> pdb=" O SERAF 194 " (cutoff:3.500A) Processing helix chain 'AF' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAF 226 " --> pdb=" O ALAAF 222 " (cutoff:3.500A) Processing helix chain 'AG' and resid 66 through 72 removed outlier: 3.894A pdb=" N GLUAG 72 " --> pdb=" O GLUAG 68 " (cutoff:3.500A) Processing helix chain 'AG' and resid 86 through 100 Processing helix chain 'AG' and resid 107 through 122 removed outlier: 3.719A pdb=" N VALAG 111 " --> pdb=" O GLUAG 107 " (cutoff:3.500A) Processing helix chain 'AG' and resid 145 through 152 Processing helix chain 'AG' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAG 159 " --> pdb=" O THRAG 155 " (cutoff:3.500A) Processing helix chain 'AG' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAG 177 " --> pdb=" O METAG 173 " (cutoff:3.500A) Processing helix chain 'AG' and resid 182 through 189 Processing helix chain 'AG' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAG 197 " --> pdb=" O SERAG 194 " (cutoff:3.500A) Processing helix chain 'AG' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAG 226 " --> pdb=" O ALAAG 222 " (cutoff:3.500A) Processing helix chain 'AH' and resid 66 through 72 removed outlier: 3.894A pdb=" N GLUAH 72 " --> pdb=" O GLUAH 68 " (cutoff:3.500A) Processing helix chain 'AH' and resid 86 through 100 Processing helix chain 'AH' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAH 111 " --> pdb=" O GLUAH 107 " (cutoff:3.500A) Processing helix chain 'AH' and resid 145 through 152 Processing helix chain 'AH' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAH 159 " --> pdb=" O THRAH 155 " (cutoff:3.500A) Processing helix chain 'AH' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAH 177 " --> pdb=" O METAH 173 " (cutoff:3.500A) Processing helix chain 'AH' and resid 182 through 189 Processing helix chain 'AH' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAH 197 " --> pdb=" O SERAH 194 " (cutoff:3.500A) Processing helix chain 'AH' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAH 226 " --> pdb=" O ALAAH 222 " (cutoff:3.500A) Processing helix chain 'AI' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAI 72 " --> pdb=" O GLUAI 68 " (cutoff:3.500A) Processing helix chain 'AI' and resid 86 through 100 Processing helix chain 'AI' and resid 107 through 122 removed outlier: 3.719A pdb=" N VALAI 111 " --> pdb=" O GLUAI 107 " (cutoff:3.500A) Processing helix chain 'AI' and resid 145 through 152 Processing helix chain 'AI' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAI 159 " --> pdb=" O THRAI 155 " (cutoff:3.500A) Processing helix chain 'AI' and resid 163 through 178 removed outlier: 3.985A pdb=" N LYSAI 177 " --> pdb=" O METAI 173 " (cutoff:3.500A) Processing helix chain 'AI' and resid 182 through 189 Processing helix chain 'AI' and resid 193 through 198 removed outlier: 4.041A pdb=" N ARGAI 197 " --> pdb=" O SERAI 194 " (cutoff:3.500A) Processing helix chain 'AI' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAI 226 " --> pdb=" O ALAAI 222 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAJ 72 " --> pdb=" O GLUAJ 68 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 86 through 100 Processing helix chain 'AJ' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAJ 111 " --> pdb=" O GLUAJ 107 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 145 through 152 Processing helix chain 'AJ' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAJ 159 " --> pdb=" O THRAJ 155 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAJ 177 " --> pdb=" O METAJ 173 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 182 through 189 Processing helix chain 'AJ' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAJ 197 " --> pdb=" O SERAJ 194 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAJ 226 " --> pdb=" O ALAAJ 222 " (cutoff:3.500A) Processing helix chain 'AK' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAK 72 " --> pdb=" O GLUAK 68 " (cutoff:3.500A) Processing helix chain 'AK' and resid 86 through 100 Processing helix chain 'AK' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAK 111 " --> pdb=" O GLUAK 107 " (cutoff:3.500A) Processing helix chain 'AK' and resid 145 through 152 Processing helix chain 'AK' and resid 155 through 161 removed outlier: 3.602A pdb=" N ILEAK 159 " --> pdb=" O THRAK 155 " (cutoff:3.500A) Processing helix chain 'AK' and resid 163 through 178 removed outlier: 3.983A pdb=" N LYSAK 177 " --> pdb=" O METAK 173 " (cutoff:3.500A) Processing helix chain 'AK' and resid 182 through 189 Processing helix chain 'AK' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAK 197 " --> pdb=" O SERAK 194 " (cutoff:3.500A) Processing helix chain 'AK' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAK 226 " --> pdb=" O ALAAK 222 " (cutoff:3.500A) Processing helix chain 'AL' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAL 72 " --> pdb=" O GLUAL 68 " (cutoff:3.500A) Processing helix chain 'AL' and resid 86 through 100 Processing helix chain 'AL' and resid 107 through 122 removed outlier: 3.719A pdb=" N VALAL 111 " --> pdb=" O GLUAL 107 " (cutoff:3.500A) Processing helix chain 'AL' and resid 145 through 152 Processing helix chain 'AL' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAL 159 " --> pdb=" O THRAL 155 " (cutoff:3.500A) Processing helix chain 'AL' and resid 163 through 178 removed outlier: 3.983A pdb=" N LYSAL 177 " --> pdb=" O METAL 173 " (cutoff:3.500A) Processing helix chain 'AL' and resid 182 through 189 Processing helix chain 'AL' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAL 197 " --> pdb=" O SERAL 194 " (cutoff:3.500A) Processing helix chain 'AL' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAL 226 " --> pdb=" O ALAAL 222 " (cutoff:3.500A) Processing helix chain 'AM' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAM 72 " --> pdb=" O GLUAM 68 " (cutoff:3.500A) Processing helix chain 'AM' and resid 86 through 100 Processing helix chain 'AM' and resid 107 through 122 removed outlier: 3.719A pdb=" N VALAM 111 " --> pdb=" O GLUAM 107 " (cutoff:3.500A) Processing helix chain 'AM' and resid 145 through 152 Processing helix chain 'AM' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAM 159 " --> pdb=" O THRAM 155 " (cutoff:3.500A) Processing helix chain 'AM' and resid 163 through 178 removed outlier: 3.983A pdb=" N LYSAM 177 " --> pdb=" O METAM 173 " (cutoff:3.500A) Processing helix chain 'AM' and resid 182 through 189 Processing helix chain 'AM' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAM 197 " --> pdb=" O SERAM 194 " (cutoff:3.500A) Processing helix chain 'AM' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAM 226 " --> pdb=" O ALAAM 222 " (cutoff:3.500A) Processing helix chain 'AN' and resid 66 through 72 removed outlier: 3.894A pdb=" N GLUAN 72 " --> pdb=" O GLUAN 68 " (cutoff:3.500A) Processing helix chain 'AN' and resid 86 through 100 Processing helix chain 'AN' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAN 111 " --> pdb=" O GLUAN 107 " (cutoff:3.500A) Processing helix chain 'AN' and resid 145 through 152 Processing helix chain 'AN' and resid 155 through 161 removed outlier: 3.602A pdb=" N ILEAN 159 " --> pdb=" O THRAN 155 " (cutoff:3.500A) Processing helix chain 'AN' and resid 163 through 178 removed outlier: 3.983A pdb=" N LYSAN 177 " --> pdb=" O METAN 173 " (cutoff:3.500A) Processing helix chain 'AN' and resid 182 through 189 Processing helix chain 'AN' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAN 197 " --> pdb=" O SERAN 194 " (cutoff:3.500A) Processing helix chain 'AN' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAN 226 " --> pdb=" O ALAAN 222 " (cutoff:3.500A) Processing helix chain 'AO' and resid 66 through 72 removed outlier: 3.894A pdb=" N GLUAO 72 " --> pdb=" O GLUAO 68 " (cutoff:3.500A) Processing helix chain 'AO' and resid 86 through 100 Processing helix chain 'AO' and resid 107 through 122 removed outlier: 3.717A pdb=" N VALAO 111 " --> pdb=" O GLUAO 107 " (cutoff:3.500A) Processing helix chain 'AO' and resid 145 through 152 Processing helix chain 'AO' and resid 155 through 161 removed outlier: 3.602A pdb=" N ILEAO 159 " --> pdb=" O THRAO 155 " (cutoff:3.500A) Processing helix chain 'AO' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAO 177 " --> pdb=" O METAO 173 " (cutoff:3.500A) Processing helix chain 'AO' and resid 182 through 189 Processing helix chain 'AO' and resid 193 through 198 removed outlier: 4.043A pdb=" N ARGAO 197 " --> pdb=" O SERAO 194 " (cutoff:3.500A) Processing helix chain 'AO' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAO 226 " --> pdb=" O ALAAO 222 " (cutoff:3.500A) Processing helix chain 'AP' and resid 66 through 72 removed outlier: 3.894A pdb=" N GLUAP 72 " --> pdb=" O GLUAP 68 " (cutoff:3.500A) Processing helix chain 'AP' and resid 86 through 100 Processing helix chain 'AP' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAP 111 " --> pdb=" O GLUAP 107 " (cutoff:3.500A) Processing helix chain 'AP' and resid 145 through 152 Processing helix chain 'AP' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAP 159 " --> pdb=" O THRAP 155 " (cutoff:3.500A) Processing helix chain 'AP' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAP 177 " --> pdb=" O METAP 173 " (cutoff:3.500A) Processing helix chain 'AP' and resid 182 through 189 Processing helix chain 'AP' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAP 197 " --> pdb=" O SERAP 194 " (cutoff:3.500A) Processing helix chain 'AP' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAP 226 " --> pdb=" O ALAAP 222 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 66 through 72 removed outlier: 3.896A pdb=" N GLUAQ 72 " --> pdb=" O GLUAQ 68 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 86 through 100 Processing helix chain 'AQ' and resid 107 through 122 removed outlier: 3.719A pdb=" N VALAQ 111 " --> pdb=" O GLUAQ 107 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 145 through 152 Processing helix chain 'AQ' and resid 155 through 161 removed outlier: 3.602A pdb=" N ILEAQ 159 " --> pdb=" O THRAQ 155 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAQ 177 " --> pdb=" O METAQ 173 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 182 through 189 Processing helix chain 'AQ' and resid 193 through 198 removed outlier: 4.041A pdb=" N ARGAQ 197 " --> pdb=" O SERAQ 194 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAQ 226 " --> pdb=" O ALAAQ 222 " (cutoff:3.500A) Processing helix chain 'AR' and resid 66 through 72 removed outlier: 3.893A pdb=" N GLUAR 72 " --> pdb=" O GLUAR 68 " (cutoff:3.500A) Processing helix chain 'AR' and resid 86 through 100 Processing helix chain 'AR' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAR 111 " --> pdb=" O GLUAR 107 " (cutoff:3.500A) Processing helix chain 'AR' and resid 145 through 152 Processing helix chain 'AR' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAR 159 " --> pdb=" O THRAR 155 " (cutoff:3.500A) Processing helix chain 'AR' and resid 163 through 178 removed outlier: 3.983A pdb=" N LYSAR 177 " --> pdb=" O METAR 173 " (cutoff:3.500A) Processing helix chain 'AR' and resid 182 through 189 Processing helix chain 'AR' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAR 197 " --> pdb=" O SERAR 194 " (cutoff:3.500A) Processing helix chain 'AR' and resid 210 through 226 removed outlier: 3.726A pdb=" N LYSAR 226 " --> pdb=" O ALAAR 222 " (cutoff:3.500A) Processing helix chain 'AS' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAS 72 " --> pdb=" O GLUAS 68 " (cutoff:3.500A) Processing helix chain 'AS' and resid 86 through 100 Processing helix chain 'AS' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAS 111 " --> pdb=" O GLUAS 107 " (cutoff:3.500A) Processing helix chain 'AS' and resid 145 through 152 Processing helix chain 'AS' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAS 159 " --> pdb=" O THRAS 155 " (cutoff:3.500A) Processing helix chain 'AS' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAS 177 " --> pdb=" O METAS 173 " (cutoff:3.500A) Processing helix chain 'AS' and resid 182 through 189 Processing helix chain 'AS' and resid 193 through 198 removed outlier: 4.041A pdb=" N ARGAS 197 " --> pdb=" O SERAS 194 " (cutoff:3.500A) Processing helix chain 'AS' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAS 226 " --> pdb=" O ALAAS 222 " (cutoff:3.500A) Processing helix chain 'AT' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAT 72 " --> pdb=" O GLUAT 68 " (cutoff:3.500A) Processing helix chain 'AT' and resid 86 through 100 Processing helix chain 'AT' and resid 107 through 122 removed outlier: 3.719A pdb=" N VALAT 111 " --> pdb=" O GLUAT 107 " (cutoff:3.500A) Processing helix chain 'AT' and resid 145 through 152 Processing helix chain 'AT' and resid 155 through 161 removed outlier: 3.604A pdb=" N ILEAT 159 " --> pdb=" O THRAT 155 " (cutoff:3.500A) Processing helix chain 'AT' and resid 163 through 178 removed outlier: 3.985A pdb=" N LYSAT 177 " --> pdb=" O METAT 173 " (cutoff:3.500A) Processing helix chain 'AT' and resid 182 through 189 Processing helix chain 'AT' and resid 193 through 198 removed outlier: 4.041A pdb=" N ARGAT 197 " --> pdb=" O SERAT 194 " (cutoff:3.500A) Processing helix chain 'AT' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAT 226 " --> pdb=" O ALAAT 222 " (cutoff:3.500A) Processing helix chain 'AU' and resid 66 through 72 removed outlier: 3.896A pdb=" N GLUAU 72 " --> pdb=" O GLUAU 68 " (cutoff:3.500A) Processing helix chain 'AU' and resid 86 through 100 Processing helix chain 'AU' and resid 107 through 122 removed outlier: 3.719A pdb=" N VALAU 111 " --> pdb=" O GLUAU 107 " (cutoff:3.500A) Processing helix chain 'AU' and resid 145 through 152 Processing helix chain 'AU' and resid 155 through 161 removed outlier: 3.602A pdb=" N ILEAU 159 " --> pdb=" O THRAU 155 " (cutoff:3.500A) Processing helix chain 'AU' and resid 163 through 178 removed outlier: 3.983A pdb=" N LYSAU 177 " --> pdb=" O METAU 173 " (cutoff:3.500A) Processing helix chain 'AU' and resid 182 through 189 Processing helix chain 'AU' and resid 193 through 198 removed outlier: 4.041A pdb=" N ARGAU 197 " --> pdb=" O SERAU 194 " (cutoff:3.500A) Processing helix chain 'AU' and resid 210 through 226 removed outlier: 3.728A pdb=" N LYSAU 226 " --> pdb=" O ALAAU 222 " (cutoff:3.500A) Processing helix chain 'AV' and resid 66 through 72 removed outlier: 3.894A pdb=" N GLUAV 72 " --> pdb=" O GLUAV 68 " (cutoff:3.500A) Processing helix chain 'AV' and resid 86 through 100 Processing helix chain 'AV' and resid 107 through 122 removed outlier: 3.717A pdb=" N VALAV 111 " --> pdb=" O GLUAV 107 " (cutoff:3.500A) Processing helix chain 'AV' and resid 145 through 152 Processing helix chain 'AV' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAV 159 " --> pdb=" O THRAV 155 " (cutoff:3.500A) Processing helix chain 'AV' and resid 163 through 178 removed outlier: 3.983A pdb=" N LYSAV 177 " --> pdb=" O METAV 173 " (cutoff:3.500A) Processing helix chain 'AV' and resid 182 through 189 Processing helix chain 'AV' and resid 193 through 198 removed outlier: 4.041A pdb=" N ARGAV 197 " --> pdb=" O SERAV 194 " (cutoff:3.500A) Processing helix chain 'AV' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAV 226 " --> pdb=" O ALAAV 222 " (cutoff:3.500A) Processing helix chain 'AW' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAW 72 " --> pdb=" O GLUAW 68 " (cutoff:3.500A) Processing helix chain 'AW' and resid 86 through 100 Processing helix chain 'AW' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAW 111 " --> pdb=" O GLUAW 107 " (cutoff:3.500A) Processing helix chain 'AW' and resid 145 through 152 Processing helix chain 'AW' and resid 155 through 161 removed outlier: 3.601A pdb=" N ILEAW 159 " --> pdb=" O THRAW 155 " (cutoff:3.500A) Processing helix chain 'AW' and resid 163 through 178 removed outlier: 3.983A pdb=" N LYSAW 177 " --> pdb=" O METAW 173 " (cutoff:3.500A) Processing helix chain 'AW' and resid 182 through 189 Processing helix chain 'AW' and resid 193 through 198 removed outlier: 4.043A pdb=" N ARGAW 197 " --> pdb=" O SERAW 194 " (cutoff:3.500A) Processing helix chain 'AW' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAW 226 " --> pdb=" O ALAAW 222 " (cutoff:3.500A) Processing helix chain 'AX' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAX 72 " --> pdb=" O GLUAX 68 " (cutoff:3.500A) Processing helix chain 'AX' and resid 86 through 100 Processing helix chain 'AX' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAX 111 " --> pdb=" O GLUAX 107 " (cutoff:3.500A) Processing helix chain 'AX' and resid 145 through 152 Processing helix chain 'AX' and resid 155 through 161 removed outlier: 3.602A pdb=" N ILEAX 159 " --> pdb=" O THRAX 155 " (cutoff:3.500A) Processing helix chain 'AX' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAX 177 " --> pdb=" O METAX 173 " (cutoff:3.500A) Processing helix chain 'AX' and resid 182 through 189 Processing helix chain 'AX' and resid 193 through 198 removed outlier: 4.041A pdb=" N ARGAX 197 " --> pdb=" O SERAX 194 " (cutoff:3.500A) Processing helix chain 'AX' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAX 226 " --> pdb=" O ALAAX 222 " (cutoff:3.500A) Processing helix chain 'AY' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAY 72 " --> pdb=" O GLUAY 68 " (cutoff:3.500A) Processing helix chain 'AY' and resid 86 through 100 Processing helix chain 'AY' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALAY 111 " --> pdb=" O GLUAY 107 " (cutoff:3.500A) Processing helix chain 'AY' and resid 145 through 152 Processing helix chain 'AY' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAY 159 " --> pdb=" O THRAY 155 " (cutoff:3.500A) Processing helix chain 'AY' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAY 177 " --> pdb=" O METAY 173 " (cutoff:3.500A) Processing helix chain 'AY' and resid 182 through 189 Processing helix chain 'AY' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGAY 197 " --> pdb=" O SERAY 194 " (cutoff:3.500A) Processing helix chain 'AY' and resid 210 through 226 removed outlier: 3.726A pdb=" N LYSAY 226 " --> pdb=" O ALAAY 222 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUAZ 72 " --> pdb=" O GLUAZ 68 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 86 through 100 Processing helix chain 'AZ' and resid 107 through 122 removed outlier: 3.717A pdb=" N VALAZ 111 " --> pdb=" O GLUAZ 107 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 145 through 152 Processing helix chain 'AZ' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEAZ 159 " --> pdb=" O THRAZ 155 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSAZ 177 " --> pdb=" O METAZ 173 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 182 through 189 Processing helix chain 'AZ' and resid 193 through 198 removed outlier: 4.043A pdb=" N ARGAZ 197 " --> pdb=" O SERAZ 194 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSAZ 226 " --> pdb=" O ALAAZ 222 " (cutoff:3.500A) Processing helix chain 'BA' and resid 66 through 72 removed outlier: 3.894A pdb=" N GLUBA 72 " --> pdb=" O GLUBA 68 " (cutoff:3.500A) Processing helix chain 'BA' and resid 86 through 100 Processing helix chain 'BA' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALBA 111 " --> pdb=" O GLUBA 107 " (cutoff:3.500A) Processing helix chain 'BA' and resid 145 through 152 Processing helix chain 'BA' and resid 155 through 161 removed outlier: 3.602A pdb=" N ILEBA 159 " --> pdb=" O THRBA 155 " (cutoff:3.500A) Processing helix chain 'BA' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSBA 177 " --> pdb=" O METBA 173 " (cutoff:3.500A) Processing helix chain 'BA' and resid 182 through 189 Processing helix chain 'BA' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGBA 197 " --> pdb=" O SERBA 194 " (cutoff:3.500A) Processing helix chain 'BA' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSBA 226 " --> pdb=" O ALABA 222 " (cutoff:3.500A) Processing helix chain 'BB' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUBB 72 " --> pdb=" O GLUBB 68 " (cutoff:3.500A) Processing helix chain 'BB' and resid 86 through 100 Processing helix chain 'BB' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALBB 111 " --> pdb=" O GLUBB 107 " (cutoff:3.500A) Processing helix chain 'BB' and resid 145 through 152 Processing helix chain 'BB' and resid 155 through 161 removed outlier: 3.602A pdb=" N ILEBB 159 " --> pdb=" O THRBB 155 " (cutoff:3.500A) Processing helix chain 'BB' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSBB 177 " --> pdb=" O METBB 173 " (cutoff:3.500A) Processing helix chain 'BB' and resid 182 through 189 Processing helix chain 'BB' and resid 193 through 198 removed outlier: 4.041A pdb=" N ARGBB 197 " --> pdb=" O SERBB 194 " (cutoff:3.500A) Processing helix chain 'BB' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSBB 226 " --> pdb=" O ALABB 222 " (cutoff:3.500A) Processing helix chain 'BC' and resid 66 through 72 removed outlier: 3.896A pdb=" N GLUBC 72 " --> pdb=" O GLUBC 68 " (cutoff:3.500A) Processing helix chain 'BC' and resid 86 through 100 Processing helix chain 'BC' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALBC 111 " --> pdb=" O GLUBC 107 " (cutoff:3.500A) Processing helix chain 'BC' and resid 145 through 152 Processing helix chain 'BC' and resid 155 through 161 removed outlier: 3.602A pdb=" N ILEBC 159 " --> pdb=" O THRBC 155 " (cutoff:3.500A) Processing helix chain 'BC' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSBC 177 " --> pdb=" O METBC 173 " (cutoff:3.500A) Processing helix chain 'BC' and resid 182 through 189 Processing helix chain 'BC' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGBC 197 " --> pdb=" O SERBC 194 " (cutoff:3.500A) Processing helix chain 'BC' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSBC 226 " --> pdb=" O ALABC 222 " (cutoff:3.500A) Processing helix chain 'BD' and resid 66 through 72 removed outlier: 3.894A pdb=" N GLUBD 72 " --> pdb=" O GLUBD 68 " (cutoff:3.500A) Processing helix chain 'BD' and resid 86 through 100 Processing helix chain 'BD' and resid 107 through 122 removed outlier: 3.719A pdb=" N VALBD 111 " --> pdb=" O GLUBD 107 " (cutoff:3.500A) Processing helix chain 'BD' and resid 145 through 152 Processing helix chain 'BD' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEBD 159 " --> pdb=" O THRBD 155 " (cutoff:3.500A) Processing helix chain 'BD' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSBD 177 " --> pdb=" O METBD 173 " (cutoff:3.500A) Processing helix chain 'BD' and resid 182 through 189 Processing helix chain 'BD' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGBD 197 " --> pdb=" O SERBD 194 " (cutoff:3.500A) Processing helix chain 'BD' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSBD 226 " --> pdb=" O ALABD 222 " (cutoff:3.500A) Processing helix chain 'BE' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUBE 72 " --> pdb=" O GLUBE 68 " (cutoff:3.500A) Processing helix chain 'BE' and resid 86 through 100 Processing helix chain 'BE' and resid 107 through 122 removed outlier: 3.719A pdb=" N VALBE 111 " --> pdb=" O GLUBE 107 " (cutoff:3.500A) Processing helix chain 'BE' and resid 145 through 152 Processing helix chain 'BE' and resid 155 through 161 removed outlier: 3.604A pdb=" N ILEBE 159 " --> pdb=" O THRBE 155 " (cutoff:3.500A) Processing helix chain 'BE' and resid 163 through 178 removed outlier: 3.982A pdb=" N LYSBE 177 " --> pdb=" O METBE 173 " (cutoff:3.500A) Processing helix chain 'BE' and resid 182 through 189 Processing helix chain 'BE' and resid 193 through 198 removed outlier: 4.041A pdb=" N ARGBE 197 " --> pdb=" O SERBE 194 " (cutoff:3.500A) Processing helix chain 'BE' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSBE 226 " --> pdb=" O ALABE 222 " (cutoff:3.500A) Processing helix chain 'BF' and resid 66 through 72 removed outlier: 3.896A pdb=" N GLUBF 72 " --> pdb=" O GLUBF 68 " (cutoff:3.500A) Processing helix chain 'BF' and resid 86 through 100 Processing helix chain 'BF' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALBF 111 " --> pdb=" O GLUBF 107 " (cutoff:3.500A) Processing helix chain 'BF' and resid 145 through 152 Processing helix chain 'BF' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEBF 159 " --> pdb=" O THRBF 155 " (cutoff:3.500A) Processing helix chain 'BF' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSBF 177 " --> pdb=" O METBF 173 " (cutoff:3.500A) Processing helix chain 'BF' and resid 182 through 189 Processing helix chain 'BF' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGBF 197 " --> pdb=" O SERBF 194 " (cutoff:3.500A) Processing helix chain 'BF' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSBF 226 " --> pdb=" O ALABF 222 " (cutoff:3.500A) Processing helix chain 'BG' and resid 66 through 72 removed outlier: 3.895A pdb=" N GLUBG 72 " --> pdb=" O GLUBG 68 " (cutoff:3.500A) Processing helix chain 'BG' and resid 86 through 100 Processing helix chain 'BG' and resid 107 through 122 removed outlier: 3.717A pdb=" N VALBG 111 " --> pdb=" O GLUBG 107 " (cutoff:3.500A) Processing helix chain 'BG' and resid 145 through 152 Processing helix chain 'BG' and resid 155 through 161 removed outlier: 3.603A pdb=" N ILEBG 159 " --> pdb=" O THRBG 155 " (cutoff:3.500A) Processing helix chain 'BG' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSBG 177 " --> pdb=" O METBG 173 " (cutoff:3.500A) Processing helix chain 'BG' and resid 182 through 189 Processing helix chain 'BG' and resid 193 through 198 removed outlier: 4.042A pdb=" N ARGBG 197 " --> pdb=" O SERBG 194 " (cutoff:3.500A) Processing helix chain 'BG' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSBG 226 " --> pdb=" O ALABG 222 " (cutoff:3.500A) Processing helix chain 'BH' and resid 66 through 72 removed outlier: 3.896A pdb=" N GLUBH 72 " --> pdb=" O GLUBH 68 " (cutoff:3.500A) Processing helix chain 'BH' and resid 86 through 100 Processing helix chain 'BH' and resid 107 through 122 removed outlier: 3.718A pdb=" N VALBH 111 " --> pdb=" O GLUBH 107 " (cutoff:3.500A) Processing helix chain 'BH' and resid 145 through 152 Processing helix chain 'BH' and resid 155 through 161 removed outlier: 3.604A pdb=" N ILEBH 159 " --> pdb=" O THRBH 155 " (cutoff:3.500A) Processing helix chain 'BH' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSBH 177 " --> pdb=" O METBH 173 " (cutoff:3.500A) Processing helix chain 'BH' and resid 182 through 189 Processing helix chain 'BH' and resid 193 through 198 removed outlier: 4.043A pdb=" N ARGBH 197 " --> pdb=" O SERBH 194 " (cutoff:3.500A) Processing helix chain 'BH' and resid 210 through 226 removed outlier: 3.726A pdb=" N LYSBH 226 " --> pdb=" O ALABH 222 " (cutoff:3.500A) Processing helix chain 'BI' and resid 66 through 72 removed outlier: 3.896A pdb=" N GLUBI 72 " --> pdb=" O GLUBI 68 " (cutoff:3.500A) Processing helix chain 'BI' and resid 86 through 100 Processing helix chain 'BI' and resid 107 through 122 removed outlier: 3.717A pdb=" N VALBI 111 " --> pdb=" O GLUBI 107 " (cutoff:3.500A) Processing helix chain 'BI' and resid 145 through 152 Processing helix chain 'BI' and resid 155 through 161 removed outlier: 3.602A pdb=" N ILEBI 159 " --> pdb=" O THRBI 155 " (cutoff:3.500A) Processing helix chain 'BI' and resid 163 through 178 removed outlier: 3.984A pdb=" N LYSBI 177 " --> pdb=" O METBI 173 " (cutoff:3.500A) Processing helix chain 'BI' and resid 182 through 189 Processing helix chain 'BI' and resid 193 through 198 removed outlier: 4.041A pdb=" N ARGBI 197 " --> pdb=" O SERBI 194 " (cutoff:3.500A) Processing helix chain 'BI' and resid 210 through 226 removed outlier: 3.727A pdb=" N LYSBI 226 " --> pdb=" O ALABI 222 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'AA' and resid 58 through 59 Processing sheet with id=AA2, first strand: chain 'AA' and resid 131 through 136 Processing sheet with id=AA3, first strand: chain 'AB' and resid 58 through 59 Processing sheet with id=AA4, first strand: chain 'AB' and resid 131 through 136 Processing sheet with id=AA5, first strand: chain 'AC' and resid 58 through 59 Processing sheet with id=AA6, first strand: chain 'AC' and resid 131 through 136 Processing sheet with id=AA7, first strand: chain 'AD' and resid 58 through 59 Processing sheet with id=AA8, first strand: chain 'AD' and resid 131 through 136 Processing sheet with id=AA9, first strand: chain 'AE' and resid 58 through 59 Processing sheet with id=AB1, first strand: chain 'AE' and resid 131 through 136 Processing sheet with id=AB2, first strand: chain 'AF' and resid 58 through 59 Processing sheet with id=AB3, first strand: chain 'AF' and resid 131 through 136 Processing sheet with id=AB4, first strand: chain 'AG' and resid 58 through 59 Processing sheet with id=AB5, first strand: chain 'AG' and resid 131 through 136 Processing sheet with id=AB6, first strand: chain 'AH' and resid 58 through 59 Processing sheet with id=AB7, first strand: chain 'AH' and resid 131 through 136 Processing sheet with id=AB8, first strand: chain 'AI' and resid 58 through 59 Processing sheet with id=AB9, first strand: chain 'AI' and resid 131 through 136 Processing sheet with id=AC1, first strand: chain 'AJ' and resid 58 through 59 Processing sheet with id=AC2, first strand: chain 'AJ' and resid 131 through 136 Processing sheet with id=AC3, first strand: chain 'AK' and resid 58 through 59 Processing sheet with id=AC4, first strand: chain 'AK' and resid 131 through 136 Processing sheet with id=AC5, first strand: chain 'AL' and resid 58 through 59 Processing sheet with id=AC6, first strand: chain 'AL' and resid 131 through 136 Processing sheet with id=AC7, first strand: chain 'AM' and resid 58 through 59 Processing sheet with id=AC8, first strand: chain 'AM' and resid 131 through 136 Processing sheet with id=AC9, first strand: chain 'AN' and resid 58 through 59 Processing sheet with id=AD1, first strand: chain 'AN' and resid 131 through 136 Processing sheet with id=AD2, first strand: chain 'AO' and resid 58 through 59 Processing sheet with id=AD3, first strand: chain 'AO' and resid 131 through 136 Processing sheet with id=AD4, first strand: chain 'AP' and resid 58 through 59 Processing sheet with id=AD5, first strand: chain 'AP' and resid 131 through 136 Processing sheet with id=AD6, first strand: chain 'AQ' and resid 58 through 59 Processing sheet with id=AD7, first strand: chain 'AQ' and resid 131 through 136 Processing sheet with id=AD8, first strand: chain 'AR' and resid 58 through 59 Processing sheet with id=AD9, first strand: chain 'AR' and resid 131 through 136 Processing sheet with id=AE1, first strand: chain 'AS' and resid 58 through 59 Processing sheet with id=AE2, first strand: chain 'AS' and resid 131 through 136 Processing sheet with id=AE3, first strand: chain 'AT' and resid 58 through 59 Processing sheet with id=AE4, first strand: chain 'AT' and resid 131 through 136 Processing sheet with id=AE5, first strand: chain 'AU' and resid 58 through 59 Processing sheet with id=AE6, first strand: chain 'AU' and resid 131 through 136 Processing sheet with id=AE7, first strand: chain 'AV' and resid 58 through 59 Processing sheet with id=AE8, first strand: chain 'AV' and resid 131 through 136 Processing sheet with id=AE9, first strand: chain 'AW' and resid 58 through 59 Processing sheet with id=AF1, first strand: chain 'AW' and resid 131 through 136 Processing sheet with id=AF2, first strand: chain 'AX' and resid 58 through 59 Processing sheet with id=AF3, first strand: chain 'AX' and resid 131 through 136 Processing sheet with id=AF4, first strand: chain 'AY' and resid 58 through 59 Processing sheet with id=AF5, first strand: chain 'AY' and resid 131 through 136 Processing sheet with id=AF6, first strand: chain 'AZ' and resid 58 through 59 Processing sheet with id=AF7, first strand: chain 'AZ' and resid 131 through 136 Processing sheet with id=AF8, first strand: chain 'BA' and resid 58 through 59 Processing sheet with id=AF9, first strand: chain 'BA' and resid 131 through 136 Processing sheet with id=AG1, first strand: chain 'BB' and resid 58 through 59 Processing sheet with id=AG2, first strand: chain 'BB' and resid 131 through 136 Processing sheet with id=AG3, first strand: chain 'BC' and resid 58 through 59 Processing sheet with id=AG4, first strand: chain 'BC' and resid 131 through 136 Processing sheet with id=AG5, first strand: chain 'BD' and resid 58 through 59 Processing sheet with id=AG6, first strand: chain 'BD' and resid 131 through 136 Processing sheet with id=AG7, first strand: chain 'BE' and resid 58 through 59 Processing sheet with id=AG8, first strand: chain 'BE' and resid 131 through 136 Processing sheet with id=AG9, first strand: chain 'BF' and resid 58 through 59 Processing sheet with id=AH1, first strand: chain 'BF' and resid 131 through 136 Processing sheet with id=AH2, first strand: chain 'BG' and resid 58 through 59 Processing sheet with id=AH3, first strand: chain 'BG' and resid 131 through 136 Processing sheet with id=AH4, first strand: chain 'BH' and resid 58 through 59 Processing sheet with id=AH5, first strand: chain 'BH' and resid 131 through 136 Processing sheet with id=AH6, first strand: chain 'BI' and resid 58 through 59 Processing sheet with id=AH7, first strand: chain 'BI' and resid 131 through 136 2345 hydrogen bonds defined for protein. 6615 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 70 stacking parallelities Total time for adding SS restraints: 20.55 Time building geometry restraints manager: 23.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 20036 1.34 - 1.45: 10672 1.45 - 1.57: 35372 1.57 - 1.69: 315 1.69 - 1.81: 945 Bond restraints: 67340 Sorted by residual: bond pdb=" N PROAS 57 " pdb=" CD PROAS 57 " ideal model delta sigma weight residual 1.473 1.520 -0.047 1.40e-02 5.10e+03 1.12e+01 bond pdb=" N PROAO 57 " pdb=" CD PROAO 57 " ideal model delta sigma weight residual 1.473 1.520 -0.047 1.40e-02 5.10e+03 1.12e+01 bond pdb=" N PROBB 57 " pdb=" CD PROBB 57 " ideal model delta sigma weight residual 1.473 1.520 -0.047 1.40e-02 5.10e+03 1.11e+01 bond pdb=" N PROAH 57 " pdb=" CD PROAH 57 " ideal model delta sigma weight residual 1.473 1.520 -0.047 1.40e-02 5.10e+03 1.10e+01 bond pdb=" N PROAG 57 " pdb=" CD PROAG 57 " ideal model delta sigma weight residual 1.473 1.519 -0.046 1.40e-02 5.10e+03 1.10e+01 ... (remaining 67335 not shown) Histogram of bond angle deviations from ideal: 98.08 - 105.28: 2450 105.28 - 112.48: 33104 112.48 - 119.67: 24554 119.67 - 126.87: 30538 126.87 - 134.07: 1159 Bond angle restraints: 91805 Sorted by residual: angle pdb=" N LEUAK 261 " pdb=" CA LEUAK 261 " pdb=" C LEUAK 261 " ideal model delta sigma weight residual 110.42 102.89 7.53 1.46e+00 4.69e-01 2.66e+01 angle pdb=" N LEUAJ 261 " pdb=" CA LEUAJ 261 " pdb=" C LEUAJ 261 " ideal model delta sigma weight residual 110.42 102.90 7.52 1.46e+00 4.69e-01 2.66e+01 angle pdb=" N LEUAF 261 " pdb=" CA LEUAF 261 " pdb=" C LEUAF 261 " ideal model delta sigma weight residual 110.42 102.90 7.52 1.46e+00 4.69e-01 2.65e+01 angle pdb=" N LEUBE 261 " pdb=" CA LEUBE 261 " pdb=" C LEUBE 261 " ideal model delta sigma weight residual 110.42 102.91 7.51 1.46e+00 4.69e-01 2.65e+01 angle pdb=" N LEUAM 261 " pdb=" CA LEUAM 261 " pdb=" C LEUAM 261 " ideal model delta sigma weight residual 110.42 102.91 7.51 1.46e+00 4.69e-01 2.65e+01 ... (remaining 91800 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.55: 37049 13.55 - 27.09: 2571 27.09 - 40.64: 1015 40.64 - 54.18: 280 54.18 - 67.73: 140 Dihedral angle restraints: 41055 sinusoidal: 18095 harmonic: 22960 Sorted by residual: dihedral pdb=" CA GLNAF 76 " pdb=" C GLNAF 76 " pdb=" N GLNAF 77 " pdb=" CA GLNAF 77 " ideal model delta harmonic sigma weight residual 180.00 159.41 20.59 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA GLNAH 76 " pdb=" C GLNAH 76 " pdb=" N GLNAH 77 " pdb=" CA GLNAH 77 " ideal model delta harmonic sigma weight residual 180.00 159.41 20.59 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA GLNAQ 76 " pdb=" C GLNAQ 76 " pdb=" N GLNAQ 77 " pdb=" CA GLNAQ 77 " ideal model delta harmonic sigma weight residual 180.00 159.42 20.58 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 41052 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 8008 0.070 - 0.141: 1721 0.141 - 0.211: 526 0.211 - 0.282: 35 0.282 - 0.352: 70 Chirality restraints: 10360 Sorted by residual: chirality pdb=" CB ILEAI 50 " pdb=" CA ILEAI 50 " pdb=" CG1 ILEAI 50 " pdb=" CG2 ILEAI 50 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CB ILEBF 50 " pdb=" CA ILEBF 50 " pdb=" CG1 ILEBF 50 " pdb=" CG2 ILEBF 50 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CB ILEAJ 50 " pdb=" CA ILEAJ 50 " pdb=" CG1 ILEAJ 50 " pdb=" CG2 ILEAJ 50 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 10357 not shown) Planarity restraints: 11375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLYAU 263 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.94e+00 pdb=" C GLYAU 263 " 0.055 2.00e-02 2.50e+03 pdb=" O GLYAU 263 " -0.021 2.00e-02 2.50e+03 pdb=" N VALAU 264 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLYAW 263 " -0.016 2.00e-02 2.50e+03 3.12e-02 9.75e+00 pdb=" C GLYAW 263 " 0.054 2.00e-02 2.50e+03 pdb=" O GLYAW 263 " -0.020 2.00e-02 2.50e+03 pdb=" N VALAW 264 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLYBD 263 " -0.016 2.00e-02 2.50e+03 3.12e-02 9.74e+00 pdb=" C GLYBD 263 " 0.054 2.00e-02 2.50e+03 pdb=" O GLYBD 263 " -0.020 2.00e-02 2.50e+03 pdb=" N VALBD 264 " -0.018 2.00e-02 2.50e+03 ... (remaining 11372 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 34 2.25 - 2.91: 25891 2.91 - 3.57: 93809 3.57 - 4.24: 156400 4.24 - 4.90: 263166 Nonbonded interactions: 539300 Sorted by model distance: nonbonded pdb=" O3' UAp 11 " pdb=" P UAq 7 " model vdw 1.586 3.400 nonbonded pdb=" O3' UAg 11 " pdb=" P UAh 7 " model vdw 1.587 3.400 nonbonded pdb=" O3' UAi 11 " pdb=" P UAj 7 " model vdw 1.589 3.400 nonbonded pdb=" O3' UAl 11 " pdb=" P UAm 7 " model vdw 1.590 3.400 nonbonded pdb=" O3' UAt 11 " pdb=" P UAu 7 " model vdw 1.592 3.400 ... (remaining 539295 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 'AA' selection = chain 'AB' selection = chain 'AC' selection = chain 'AD' selection = chain 'AE' selection = chain 'AF' selection = chain 'AG' selection = chain 'AH' selection = chain 'AI' selection = chain 'AJ' selection = chain 'AK' selection = chain 'AL' selection = chain 'AM' selection = chain 'AN' selection = chain 'AO' selection = chain 'AP' selection = chain 'AQ' selection = chain 'AR' selection = chain 'AS' selection = chain 'AT' selection = chain 'AU' selection = chain 'AV' selection = chain 'AW' selection = chain 'AX' selection = chain 'AY' selection = chain 'AZ' selection = chain 'BA' selection = chain 'BB' selection = chain 'BC' selection = chain 'BD' selection = chain 'BE' selection = chain 'BF' selection = chain 'BG' selection = chain 'BH' selection = chain 'BI' } ncs_group { reference = chain 'Aa' selection = chain 'Ab' selection = chain 'Ac' selection = chain 'Ad' selection = chain 'Ae' selection = chain 'Af' selection = chain 'Ag' selection = chain 'Ah' selection = chain 'Ai' selection = chain 'Aj' selection = chain 'Ak' selection = chain 'Al' selection = chain 'Am' selection = chain 'An' selection = chain 'Ao' selection = chain 'Ap' selection = chain 'Aq' selection = chain 'Ar' selection = chain 'As' selection = chain 'At' selection = chain 'Au' selection = chain 'Av' selection = chain 'Aw' selection = chain 'Ax' selection = chain 'Ay' selection = chain 'Az' selection = chain 'Ba' selection = chain 'Bb' selection = chain 'Bc' selection = chain 'Bd' selection = chain 'Be' selection = chain 'Bf' selection = chain 'Bg' selection = chain 'Bh' selection = chain 'Bi' } 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 175 5.49 5 S 490 5.16 5 C 40600 2.51 5 N 11235 2.21 5 O 13265 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 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: 0.060 Extract box with map and model: 13.350 Check model and map are aligned: 0.730 Process input model: 139.420 Find NCS groups from input model: 3.690 Set up NCS constraints: 0.950 Set refine NCS operators: 0.000 Set scattering table: 0.440 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 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 : 0.008 0.064 67340 Z= 0.511 Angle : 1.137 8.353 91805 Z= 0.679 Chirality : 0.071 0.352 10360 Planarity : 0.008 0.070 11375 Dihedral : 12.315 67.726 26215 Min Nonbonded Distance : 1.586 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.79 (0.08), residues: 7770 helix: -2.50 (0.07), residues: 2870 sheet: -1.45 (0.22), residues: 350 loop : -2.72 (0.08), residues: 4550 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2371 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 2352 time to evaluate : 5.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 1 residues processed: 2352 average time/residue: 0.6613 time to fit residues: 2621.2217 Evaluate side-chains 1386 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1385 time to evaluate : 5.641 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.9714 time to fit residues: 9.1199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 650 optimal weight: 0.9980 chunk 583 optimal weight: 5.9990 chunk 323 optimal weight: 0.7980 chunk 199 optimal weight: 6.9990 chunk 393 optimal weight: 1.9990 chunk 311 optimal weight: 3.9990 chunk 603 optimal weight: 0.9990 chunk 233 optimal weight: 3.9990 chunk 366 optimal weight: 6.9990 chunk 449 optimal weight: 6.9990 chunk 699 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 140 GLN AB 151 ASN AE 69 HIS AJ 127 ASN AL 69 HIS AL 140 GLN AM 151 ASN AR 69 HIS AT 151 ASN AU 69 HIS AU 127 ASN AU 151 ASN AX 151 ASN BA 151 ASN BC 158 GLN BE 151 ASN BF 69 HIS BF 127 ASN BF 151 ASN BI 69 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 67340 Z= 0.187 Angle : 0.638 10.669 91805 Z= 0.326 Chirality : 0.041 0.157 10360 Planarity : 0.004 0.037 11375 Dihedral : 7.106 47.260 10605 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer Outliers : 2.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.92 (0.09), residues: 7770 helix: -0.27 (0.09), residues: 3150 sheet: -1.21 (0.20), residues: 350 loop : -2.14 (0.09), residues: 4270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1786 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1617 time to evaluate : 6.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 169 outliers final: 63 residues processed: 1710 average time/residue: 0.7124 time to fit residues: 2040.7106 Evaluate side-chains 1392 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1329 time to evaluate : 5.650 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.5002 time to fit residues: 67.9696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 388 optimal weight: 9.9990 chunk 217 optimal weight: 1.9990 chunk 581 optimal weight: 6.9990 chunk 476 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 chunk 700 optimal weight: 9.9990 chunk 756 optimal weight: 8.9990 chunk 623 optimal weight: 7.9990 chunk 694 optimal weight: 7.9990 chunk 238 optimal weight: 10.0000 chunk 561 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 151 ASN AB 158 GLN ** AC 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 140 GLN ** AF 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 127 ASN AJ 158 GLN ** AK 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 158 GLN ** AL 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 140 GLN AM 98 GLN ** AM 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 249 HIS ** AN 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AN 158 GLN ** AO 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 158 GLN ** AP 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 140 GLN ** AQ 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 151 ASN ** AU 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 127 ASN AU 158 GLN AV 87 GLN ** AV 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 140 GLN ** AX 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 158 GLN ** AZ 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AZ 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 140 GLN BI 140 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.073 67340 Z= 0.581 Angle : 0.775 11.393 91805 Z= 0.399 Chirality : 0.049 0.221 10360 Planarity : 0.005 0.058 11375 Dihedral : 7.395 46.924 10605 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer Outliers : 4.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.28 (0.10), residues: 7770 helix: 0.20 (0.10), residues: 3115 sheet: -0.08 (0.25), residues: 350 loop : -1.77 (0.10), residues: 4305 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1606 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 1323 time to evaluate : 5.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 283 outliers final: 157 residues processed: 1535 average time/residue: 0.6481 time to fit residues: 1680.9106 Evaluate side-chains 1417 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1260 time to evaluate : 5.654 Switching outliers to nearest non-outliers outliers start: 157 outliers final: 0 residues processed: 157 average time/residue: 0.4779 time to fit residues: 151.6879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 692 optimal weight: 0.8980 chunk 526 optimal weight: 0.9980 chunk 363 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 334 optimal weight: 0.4980 chunk 470 optimal weight: 0.9980 chunk 703 optimal weight: 6.9990 chunk 744 optimal weight: 3.9990 chunk 367 optimal weight: 0.0770 chunk 666 optimal weight: 0.9990 chunk 200 optimal weight: 5.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 229 GLN ** AM 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 151 ASN AZ 77 GLN AZ 158 GLN ** BA 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 87 GLN BE 98 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 67340 Z= 0.169 Angle : 0.604 11.313 91805 Z= 0.304 Chirality : 0.040 0.163 10360 Planarity : 0.004 0.037 11375 Dihedral : 6.822 39.677 10605 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer Outliers : 0.85 % 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: -0.75 (0.10), residues: 7770 helix: 0.68 (0.10), residues: 3150 sheet: 0.03 (0.26), residues: 350 loop : -1.51 (0.10), residues: 4270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1449 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 1391 time to evaluate : 5.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 20 residues processed: 1421 average time/residue: 0.6649 time to fit residues: 1581.8222 Evaluate side-chains 1286 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1266 time to evaluate : 5.625 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.5096 time to fit residues: 26.6949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 619 optimal weight: 4.9990 chunk 422 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 554 optimal weight: 9.9990 chunk 307 optimal weight: 0.0040 chunk 635 optimal weight: 6.9990 chunk 514 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 380 optimal weight: 10.0000 chunk 668 optimal weight: 8.9990 chunk 187 optimal weight: 9.9990 overall best weight: 5.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 140 GLN ** AE 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 229 GLN ** AG 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AH 229 GLN ** AI 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 229 GLN ** AN 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 151 ASN ** AU 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 158 GLN ** BF 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.043 67340 Z= 0.443 Angle : 0.705 11.681 91805 Z= 0.355 Chirality : 0.045 0.189 10360 Planarity : 0.004 0.053 11375 Dihedral : 7.032 46.798 10605 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer Outliers : 1.68 % 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: -0.75 (0.10), residues: 7770 helix: 0.60 (0.10), residues: 3185 sheet: 0.50 (0.29), residues: 350 loop : -1.49 (0.10), residues: 4235 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1414 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1300 time to evaluate : 5.708 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 outliers start: 114 outliers final: 68 residues processed: 1377 average time/residue: 0.6761 time to fit residues: 1568.5630 Evaluate side-chains 1297 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1229 time to evaluate : 5.731 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 0 residues processed: 68 average time/residue: 0.5068 time to fit residues: 72.6885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 250 optimal weight: 3.9990 chunk 670 optimal weight: 0.3980 chunk 147 optimal weight: 0.9980 chunk 436 optimal weight: 10.0000 chunk 183 optimal weight: 0.9990 chunk 745 optimal weight: 6.9990 chunk 618 optimal weight: 3.9990 chunk 344 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 246 optimal weight: 0.9990 chunk 391 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AH 229 GLN ** AN 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 151 ASN AV 98 GLN BB 151 ASN BF 229 GLN BG 151 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 67340 Z= 0.171 Angle : 0.605 11.089 91805 Z= 0.301 Chirality : 0.040 0.168 10360 Planarity : 0.004 0.037 11375 Dihedral : 6.706 42.175 10605 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer Outliers : 0.81 % 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: -0.45 (0.10), residues: 7770 helix: 0.83 (0.10), residues: 3185 sheet: 0.34 (0.28), residues: 350 loop : -1.28 (0.10), residues: 4235 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1402 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1347 time to evaluate : 5.640 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 outliers start: 55 outliers final: 20 residues processed: 1375 average time/residue: 0.6836 time to fit residues: 1571.3973 Evaluate side-chains 1243 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1223 time to evaluate : 5.648 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.5310 time to fit residues: 27.2759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 718 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 424 optimal weight: 8.9990 chunk 544 optimal weight: 0.1980 chunk 421 optimal weight: 8.9990 chunk 627 optimal weight: 0.5980 chunk 416 optimal weight: 9.9990 chunk 742 optimal weight: 0.9990 chunk 464 optimal weight: 10.0000 chunk 452 optimal weight: 6.9990 chunk 342 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 229 GLN ** AB 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 140 GLN ** AE 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 229 GLN AH 229 GLN AL 140 GLN AN 87 GLN ** AN 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 140 GLN ** AP 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 158 GLN AR 229 GLN AS 140 GLN AT 151 ASN ** AU 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 151 ASN BC 229 GLN BD 151 ASN BE 98 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 67340 Z= 0.254 Angle : 0.633 11.847 91805 Z= 0.316 Chirality : 0.042 0.175 10360 Planarity : 0.004 0.037 11375 Dihedral : 6.730 44.968 10605 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.10), residues: 7770 helix: 0.86 (0.10), residues: 3185 sheet: 0.42 (0.29), residues: 350 loop : -1.26 (0.10), residues: 4235 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1334 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 1262 time to evaluate : 5.696 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 outliers start: 72 outliers final: 32 residues processed: 1301 average time/residue: 0.6816 time to fit residues: 1480.8741 Evaluate side-chains 1247 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1215 time to evaluate : 5.660 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.5223 time to fit residues: 38.7218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 459 optimal weight: 5.9990 chunk 296 optimal weight: 0.9990 chunk 443 optimal weight: 1.9990 chunk 223 optimal weight: 0.5980 chunk 145 optimal weight: 0.0020 chunk 143 optimal weight: 5.9990 chunk 471 optimal weight: 1.9990 chunk 505 optimal weight: 0.9990 chunk 366 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 583 optimal weight: 2.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 229 GLN ** AE 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AH 229 GLN AL 140 GLN ** AS 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 76 GLN BH 151 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 67340 Z= 0.162 Angle : 0.606 11.600 91805 Z= 0.300 Chirality : 0.040 0.183 10360 Planarity : 0.004 0.045 11375 Dihedral : 6.607 45.042 10605 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer Outliers : 0.87 % 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: -0.31 (0.10), residues: 7770 helix: 0.92 (0.09), residues: 3185 sheet: 0.35 (0.28), residues: 350 loop : -1.17 (0.10), residues: 4235 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1399 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 1340 time to evaluate : 5.714 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 outliers start: 59 outliers final: 14 residues processed: 1373 average time/residue: 0.6955 time to fit residues: 1594.7433 Evaluate side-chains 1253 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1239 time to evaluate : 5.696 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.5293 time to fit residues: 21.7339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 675 optimal weight: 1.9990 chunk 711 optimal weight: 0.8980 chunk 648 optimal weight: 1.9990 chunk 691 optimal weight: 9.9990 chunk 710 optimal weight: 2.9990 chunk 416 optimal weight: 9.9990 chunk 301 optimal weight: 5.9990 chunk 543 optimal weight: 0.8980 chunk 212 optimal weight: 8.9990 chunk 624 optimal weight: 4.9990 chunk 654 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 229 GLN ** AB 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 98 GLN ** AL 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 151 ASN ** AN 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 140 GLN ** BA 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 229 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 67340 Z= 0.199 Angle : 0.626 12.833 91805 Z= 0.310 Chirality : 0.041 0.214 10360 Planarity : 0.004 0.053 11375 Dihedral : 6.590 45.576 10605 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer Outliers : 0.44 % 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: -0.30 (0.10), residues: 7770 helix: 0.92 (0.09), residues: 3185 sheet: 0.47 (0.28), residues: 350 loop : -1.17 (0.10), residues: 4235 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1305 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1275 time to evaluate : 5.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 12 residues processed: 1286 average time/residue: 0.6917 time to fit residues: 1485.6068 Evaluate side-chains 1242 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1230 time to evaluate : 5.644 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.5567 time to fit residues: 19.9182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 689 optimal weight: 3.9990 chunk 454 optimal weight: 2.9990 chunk 731 optimal weight: 9.9990 chunk 446 optimal weight: 0.7980 chunk 346 optimal weight: 0.6980 chunk 508 optimal weight: 0.9990 chunk 767 optimal weight: 0.9980 chunk 706 optimal weight: 20.0000 chunk 610 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 471 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 229 GLN ** AB 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 229 GLN ** AF 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 98 GLN ** AP 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 98 GLN ** AS 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 76 GLN BD 76 GLN BI 151 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 67340 Z= 0.188 Angle : 0.628 12.713 91805 Z= 0.312 Chirality : 0.040 0.201 10360 Planarity : 0.004 0.051 11375 Dihedral : 6.590 46.532 10605 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer Outliers : 0.24 % 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: -0.32 (0.10), residues: 7770 helix: 0.88 (0.09), residues: 3185 sheet: 0.50 (0.28), residues: 350 loop : -1.16 (0.11), residues: 4235 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15540 Ramachandran restraints generated. 7770 Oldfield, 0 Emsley, 7770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1298 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1282 time to evaluate : 5.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 1287 average time/residue: 0.7312 time to fit residues: 1549.9951 Evaluate side-chains 1256 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1247 time to evaluate : 5.709 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.6101 time to fit residues: 17.5159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 374 optimal weight: 0.9980 chunk 485 optimal weight: 5.9990 chunk 650 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 563 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 chunk 611 optimal weight: 4.9990 chunk 256 optimal weight: 8.9990 chunk 628 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 229 GLN ** AB 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 229 GLN ** AG 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AL 151 ASN ** AN 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 140 GLN ** AP 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 98 GLN AS 229 GLN AT 140 GLN ** BA 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 98 GLN BE 229 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.119380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.099311 restraints weight = 111906.838| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.48 r_work: 0.3249 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 67340 Z= 0.212 Angle : 0.639 12.835 91805 Z= 0.318 Chirality : 0.041 0.197 10360 Planarity : 0.004 0.048 11375 Dihedral : 6.601 45.984 10605 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer Outliers : 0.25 % 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: -0.24 (0.10), residues: 7770 helix: 1.06 (0.10), residues: 3080 sheet: 0.57 (0.28), residues: 350 loop : -1.16 (0.10), residues: 4340 =============================================================================== Job complete usr+sys time: 21962.85 seconds wall clock time: 381 minutes 54.85 seconds (22914.85 seconds total)