Starting phenix.real_space_refine (version: dev) on Thu May 12 17:13:41 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sag_10130/05_2022/6sag_10130_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sag_10130/05_2022/6sag_10130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sag_10130/05_2022/6sag_10130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sag_10130/05_2022/6sag_10130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sag_10130/05_2022/6sag_10130_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sag_10130/05_2022/6sag_10130_updated.pdb" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 19": "OD1" <-> "OD2" Residue "A PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 19": "OD1" <-> "OD2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 19": "OD1" <-> "OD2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 19": "OD1" <-> "OD2" Residue "F PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 19": "OD1" <-> "OD2" Residue "H PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 19": "OD1" <-> "OD2" Residue "J PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 19": "OD1" <-> "OD2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 19": "OD1" <-> "OD2" Residue "N PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 19": "OD1" <-> "OD2" Residue "P PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 19": "OD1" <-> "OD2" Residue "S PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 19": "OD1" <-> "OD2" Residue "U PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 19": "OD1" <-> "OD2" Residue "W PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 19": "OD1" <-> "OD2" Residue "Y PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ASP 19": "OD1" <-> "OD2" Residue "0 PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 19": "OD1" <-> "OD2" Residue "2 PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 19": "OD1" <-> "OD2" Residue "4 PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 19": "OD1" <-> "OD2" Residue "6 PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 19": "OD1" <-> "OD2" Residue "8 PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 19": "OD1" <-> "OD2" Residue "a PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 19": "OD1" <-> "OD2" Residue "c PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 19": "OD1" <-> "OD2" Residue "e PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 19": "OD1" <-> "OD2" Residue "g PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 19": "OD1" <-> "OD2" Residue "i PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 19": "OD1" <-> "OD2" Residue "k PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 19": "OD1" <-> "OD2" Residue "m PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 19": "OD1" <-> "OD2" Residue "o PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 19": "OD1" <-> "OD2" Residue "q PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 19": "OD1" <-> "OD2" Residue "s PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ASP 19": "OD1" <-> "OD2" Residue "u PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 19": "OD1" <-> "OD2" Residue "w PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ASP 19": "OD1" <-> "OD2" Residue "y PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA ASP 19": "OD1" <-> "OD2" Residue "AA PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AC ASP 19": "OD1" <-> "OD2" Residue "AC PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AC PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AC TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AE ASP 19": "OD1" <-> "OD2" Residue "AE PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AE PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AE TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG ASP 19": "OD1" <-> "OD2" Residue "AG PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AI ASP 19": "OD1" <-> "OD2" Residue "AI PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AI PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AI TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AK ASP 19": "OD1" <-> "OD2" Residue "AK PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AK PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AK TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM ASP 19": "OD1" <-> "OD2" Residue "AM PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AO ASP 19": "OD1" <-> "OD2" Residue "AO PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AO PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AO TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AQ ASP 19": "OD1" <-> "OD2" Residue "AQ PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AQ PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AQ TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 54080 Number of models: 1 Model: "" Number of chains: 240 Chain: "A" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "R" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "I" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "K" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "M" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "O" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "O" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "Q" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "P" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "Q" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "T" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "S" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "V" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "U" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "V" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "X" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "W" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "X" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "Z" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "Y" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "Z" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "0" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "1" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "0" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "1" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "3" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "2" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "3" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "4" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "5" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "4" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "5" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "7" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "6" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "7" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "8" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "9" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "8" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "9" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "b" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "a" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "b" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "d" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "c" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "d" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "f" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "e" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "f" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "h" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "g" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "h" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "i" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "j" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "i" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "j" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "k" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "l" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "k" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "l" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "m" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "n" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "m" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "n" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "o" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "p" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "o" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "p" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "r" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "q" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "r" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "s" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "t" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "s" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "s" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "t" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "u" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "v" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "u" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "v" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "w" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "x" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "w" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "x" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "y" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "z" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "y" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "z" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AA" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "AB" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "AA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "AB" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AA" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "AB" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AC" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "AD" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "AC" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "AD" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AC" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "AD" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AE" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "AF" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "AE" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "AF" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AE" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "AF" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AG" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "AH" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "AG" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "AH" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AG" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "AH" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AI" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "AJ" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "AI" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "AJ" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AI" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "AJ" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AK" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "AL" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "AK" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "AL" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AK" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "AL" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AM" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "AN" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "AM" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "AN" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AM" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "AN" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AO" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "AP" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "AO" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "AP" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AO" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "AP" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AQ" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1, 'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145, 'ACE_C-N': 1} Chain: "AR" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "AQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "AR" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AQ" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "AR" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 23.77, per 1000 atoms: 0.44 Number of scatterers: 54080 At special positions: 0 Unit cell: (188.21, 188.21, 101.442, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 40 19.99 S 40 16.00 P 120 15.00 Mg 160 11.99 O 13080 8.00 N 9000 7.00 C 31640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.38 Conformation dependent library (CDL) restraints added in 5.4 seconds 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11840 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 280 helices and 40 sheets defined 58.2% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.15 Creating SS restraints... Processing helix chain 'A' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE A 10 " --> pdb=" O PRO A 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL A 11 " --> pdb=" O SER A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU A 31 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY A 32 " --> pdb=" O THR A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 50 Processing helix chain 'A' and resid 74 through 86 Proline residue: A 78 - end of helix Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU A 131 " --> pdb=" O ASN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 Processing helix chain 'B' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE B 10 " --> pdb=" O PRO B 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL B 11 " --> pdb=" O SER B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 32 removed outlier: 3.621A pdb=" N LEU B 31 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY B 32 " --> pdb=" O THR B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 50 Processing helix chain 'B' and resid 74 through 86 Proline residue: B 78 - end of helix Processing helix chain 'B' and resid 92 through 96 Processing helix chain 'B' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU B 131 " --> pdb=" O ASN B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 148 Processing helix chain 'D' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE D 10 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL D 11 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU D 31 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY D 32 " --> pdb=" O THR D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 74 through 86 Proline residue: D 78 - end of helix Processing helix chain 'D' and resid 92 through 96 Processing helix chain 'D' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU D 131 " --> pdb=" O ASN D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 148 Processing helix chain 'F' and resid 7 through 13 removed outlier: 3.706A pdb=" N PHE F 10 " --> pdb=" O PRO F 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL F 11 " --> pdb=" O SER F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU F 31 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY F 32 " --> pdb=" O THR F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 50 Processing helix chain 'F' and resid 74 through 86 Proline residue: F 78 - end of helix Processing helix chain 'F' and resid 92 through 96 Processing helix chain 'F' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU F 131 " --> pdb=" O ASN F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 148 Processing helix chain 'H' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE H 10 " --> pdb=" O PRO H 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL H 11 " --> pdb=" O SER H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 32 removed outlier: 3.619A pdb=" N LEU H 31 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY H 32 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 74 through 86 Proline residue: H 78 - end of helix Processing helix chain 'H' and resid 92 through 96 Processing helix chain 'H' and resid 104 through 133 removed outlier: 3.704A pdb=" N GLU H 131 " --> pdb=" O ASN H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 148 Processing helix chain 'J' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE J 10 " --> pdb=" O PRO J 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL J 11 " --> pdb=" O SER J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU J 31 " --> pdb=" O CYS J 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY J 32 " --> pdb=" O THR J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 50 Processing helix chain 'J' and resid 74 through 86 Proline residue: J 78 - end of helix Processing helix chain 'J' and resid 92 through 96 Processing helix chain 'J' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU J 131 " --> pdb=" O ASN J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 148 Processing helix chain 'L' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE L 10 " --> pdb=" O PRO L 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL L 11 " --> pdb=" O SER L 8 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU L 31 " --> pdb=" O CYS L 27 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY L 32 " --> pdb=" O THR L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 50 Processing helix chain 'L' and resid 74 through 86 Proline residue: L 78 - end of helix Processing helix chain 'L' and resid 92 through 96 Processing helix chain 'L' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU L 131 " --> pdb=" O ASN L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 148 Processing helix chain 'N' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE N 10 " --> pdb=" O PRO N 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL N 11 " --> pdb=" O SER N 8 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU N 31 " --> pdb=" O CYS N 27 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY N 32 " --> pdb=" O THR N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 50 Processing helix chain 'N' and resid 74 through 86 Proline residue: N 78 - end of helix Processing helix chain 'N' and resid 92 through 96 Processing helix chain 'N' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU N 131 " --> pdb=" O ASN N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 141 through 148 Processing helix chain 'P' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE P 10 " --> pdb=" O PRO P 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL P 11 " --> pdb=" O SER P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU P 31 " --> pdb=" O CYS P 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY P 32 " --> pdb=" O THR P 28 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 50 Processing helix chain 'P' and resid 74 through 86 Proline residue: P 78 - end of helix Processing helix chain 'P' and resid 92 through 96 Processing helix chain 'P' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU P 131 " --> pdb=" O ASN P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 141 through 148 Processing helix chain 'S' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE S 10 " --> pdb=" O PRO S 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL S 11 " --> pdb=" O SER S 8 " (cutoff:3.500A) Processing helix chain 'S' and resid 20 through 32 removed outlier: 3.619A pdb=" N LEU S 31 " --> pdb=" O CYS S 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY S 32 " --> pdb=" O THR S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 50 Processing helix chain 'S' and resid 74 through 86 Proline residue: S 78 - end of helix Processing helix chain 'S' and resid 92 through 96 Processing helix chain 'S' and resid 104 through 133 removed outlier: 3.704A pdb=" N GLU S 131 " --> pdb=" O ASN S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 141 through 148 Processing helix chain 'U' and resid 7 through 13 removed outlier: 3.704A pdb=" N PHE U 10 " --> pdb=" O PRO U 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL U 11 " --> pdb=" O SER U 8 " (cutoff:3.500A) Processing helix chain 'U' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU U 31 " --> pdb=" O CYS U 27 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY U 32 " --> pdb=" O THR U 28 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 50 Processing helix chain 'U' and resid 74 through 86 Proline residue: U 78 - end of helix Processing helix chain 'U' and resid 92 through 96 Processing helix chain 'U' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU U 131 " --> pdb=" O ASN U 127 " (cutoff:3.500A) Processing helix chain 'U' and resid 141 through 148 Processing helix chain 'W' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE W 10 " --> pdb=" O PRO W 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL W 11 " --> pdb=" O SER W 8 " (cutoff:3.500A) Processing helix chain 'W' and resid 20 through 32 removed outlier: 3.619A pdb=" N LEU W 31 " --> pdb=" O CYS W 27 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY W 32 " --> pdb=" O THR W 28 " (cutoff:3.500A) Processing helix chain 'W' and resid 38 through 50 Processing helix chain 'W' and resid 74 through 86 Proline residue: W 78 - end of helix Processing helix chain 'W' and resid 92 through 96 Processing helix chain 'W' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU W 131 " --> pdb=" O ASN W 127 " (cutoff:3.500A) Processing helix chain 'W' and resid 141 through 148 Processing helix chain 'Y' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE Y 10 " --> pdb=" O PRO Y 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL Y 11 " --> pdb=" O SER Y 8 " (cutoff:3.500A) Processing helix chain 'Y' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU Y 31 " --> pdb=" O CYS Y 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY Y 32 " --> pdb=" O THR Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 38 through 50 Processing helix chain 'Y' and resid 74 through 86 Proline residue: Y 78 - end of helix Processing helix chain 'Y' and resid 92 through 96 Processing helix chain 'Y' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU Y 131 " --> pdb=" O ASN Y 127 " (cutoff:3.500A) Processing helix chain 'Y' and resid 141 through 148 Processing helix chain '0' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE 0 10 " --> pdb=" O PRO 0 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL 0 11 " --> pdb=" O SER 0 8 " (cutoff:3.500A) Processing helix chain '0' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU 0 31 " --> pdb=" O CYS 0 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY 0 32 " --> pdb=" O THR 0 28 " (cutoff:3.500A) Processing helix chain '0' and resid 38 through 50 Processing helix chain '0' and resid 74 through 86 Proline residue: 0 78 - end of helix Processing helix chain '0' and resid 92 through 96 Processing helix chain '0' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU 0 131 " --> pdb=" O ASN 0 127 " (cutoff:3.500A) Processing helix chain '0' and resid 141 through 148 Processing helix chain '2' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE 2 10 " --> pdb=" O PRO 2 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL 2 11 " --> pdb=" O SER 2 8 " (cutoff:3.500A) Processing helix chain '2' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU 2 31 " --> pdb=" O CYS 2 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY 2 32 " --> pdb=" O THR 2 28 " (cutoff:3.500A) Processing helix chain '2' and resid 38 through 50 Processing helix chain '2' and resid 74 through 86 Proline residue: 2 78 - end of helix Processing helix chain '2' and resid 92 through 96 Processing helix chain '2' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU 2 131 " --> pdb=" O ASN 2 127 " (cutoff:3.500A) Processing helix chain '2' and resid 141 through 148 Processing helix chain '4' and resid 7 through 13 removed outlier: 3.704A pdb=" N PHE 4 10 " --> pdb=" O PRO 4 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL 4 11 " --> pdb=" O SER 4 8 " (cutoff:3.500A) Processing helix chain '4' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU 4 31 " --> pdb=" O CYS 4 27 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY 4 32 " --> pdb=" O THR 4 28 " (cutoff:3.500A) Processing helix chain '4' and resid 38 through 50 Processing helix chain '4' and resid 74 through 86 Proline residue: 4 78 - end of helix Processing helix chain '4' and resid 92 through 96 Processing helix chain '4' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU 4 131 " --> pdb=" O ASN 4 127 " (cutoff:3.500A) Processing helix chain '4' and resid 141 through 148 Processing helix chain '6' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE 6 10 " --> pdb=" O PRO 6 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL 6 11 " --> pdb=" O SER 6 8 " (cutoff:3.500A) Processing helix chain '6' and resid 20 through 32 removed outlier: 3.619A pdb=" N LEU 6 31 " --> pdb=" O CYS 6 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY 6 32 " --> pdb=" O THR 6 28 " (cutoff:3.500A) Processing helix chain '6' and resid 38 through 50 Processing helix chain '6' and resid 74 through 86 Proline residue: 6 78 - end of helix Processing helix chain '6' and resid 92 through 96 Processing helix chain '6' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU 6 131 " --> pdb=" O ASN 6 127 " (cutoff:3.500A) Processing helix chain '6' and resid 141 through 148 Processing helix chain '8' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE 8 10 " --> pdb=" O PRO 8 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL 8 11 " --> pdb=" O SER 8 8 " (cutoff:3.500A) Processing helix chain '8' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU 8 31 " --> pdb=" O CYS 8 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY 8 32 " --> pdb=" O THR 8 28 " (cutoff:3.500A) Processing helix chain '8' and resid 38 through 50 Processing helix chain '8' and resid 74 through 86 Proline residue: 8 78 - end of helix Processing helix chain '8' and resid 92 through 96 Processing helix chain '8' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU 8 131 " --> pdb=" O ASN 8 127 " (cutoff:3.500A) Processing helix chain '8' and resid 141 through 148 Processing helix chain 'a' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE a 10 " --> pdb=" O PRO a 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL a 11 " --> pdb=" O SER a 8 " (cutoff:3.500A) Processing helix chain 'a' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU a 31 " --> pdb=" O CYS a 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY a 32 " --> pdb=" O THR a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 50 Processing helix chain 'a' and resid 74 through 86 Proline residue: a 78 - end of helix Processing helix chain 'a' and resid 92 through 96 Processing helix chain 'a' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU a 131 " --> pdb=" O ASN a 127 " (cutoff:3.500A) Processing helix chain 'a' and resid 141 through 148 Processing helix chain 'c' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE c 10 " --> pdb=" O PRO c 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL c 11 " --> pdb=" O SER c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU c 31 " --> pdb=" O CYS c 27 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY c 32 " --> pdb=" O THR c 28 " (cutoff:3.500A) Processing helix chain 'c' and resid 38 through 50 Processing helix chain 'c' and resid 74 through 86 Proline residue: c 78 - end of helix Processing helix chain 'c' and resid 92 through 96 Processing helix chain 'c' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU c 131 " --> pdb=" O ASN c 127 " (cutoff:3.500A) Processing helix chain 'c' and resid 141 through 148 Processing helix chain 'e' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE e 10 " --> pdb=" O PRO e 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL e 11 " --> pdb=" O SER e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU e 31 " --> pdb=" O CYS e 27 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY e 32 " --> pdb=" O THR e 28 " (cutoff:3.500A) Processing helix chain 'e' and resid 38 through 50 Processing helix chain 'e' and resid 74 through 86 Proline residue: e 78 - end of helix Processing helix chain 'e' and resid 92 through 96 Processing helix chain 'e' and resid 104 through 133 removed outlier: 3.704A pdb=" N GLU e 131 " --> pdb=" O ASN e 127 " (cutoff:3.500A) Processing helix chain 'e' and resid 141 through 148 Processing helix chain 'g' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE g 10 " --> pdb=" O PRO g 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL g 11 " --> pdb=" O SER g 8 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 32 removed outlier: 3.619A pdb=" N LEU g 31 " --> pdb=" O CYS g 27 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY g 32 " --> pdb=" O THR g 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 38 through 50 Processing helix chain 'g' and resid 74 through 86 Proline residue: g 78 - end of helix Processing helix chain 'g' and resid 92 through 96 Processing helix chain 'g' and resid 104 through 133 removed outlier: 3.704A pdb=" N GLU g 131 " --> pdb=" O ASN g 127 " (cutoff:3.500A) Processing helix chain 'g' and resid 141 through 148 Processing helix chain 'i' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE i 10 " --> pdb=" O PRO i 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL i 11 " --> pdb=" O SER i 8 " (cutoff:3.500A) Processing helix chain 'i' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU i 31 " --> pdb=" O CYS i 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY i 32 " --> pdb=" O THR i 28 " (cutoff:3.500A) Processing helix chain 'i' and resid 38 through 50 Processing helix chain 'i' and resid 74 through 86 Proline residue: i 78 - end of helix Processing helix chain 'i' and resid 92 through 96 Processing helix chain 'i' and resid 104 through 133 removed outlier: 3.704A pdb=" N GLU i 131 " --> pdb=" O ASN i 127 " (cutoff:3.500A) Processing helix chain 'i' and resid 141 through 148 Processing helix chain 'k' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE k 10 " --> pdb=" O PRO k 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL k 11 " --> pdb=" O SER k 8 " (cutoff:3.500A) Processing helix chain 'k' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU k 31 " --> pdb=" O CYS k 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY k 32 " --> pdb=" O THR k 28 " (cutoff:3.500A) Processing helix chain 'k' and resid 38 through 50 Processing helix chain 'k' and resid 74 through 86 Proline residue: k 78 - end of helix Processing helix chain 'k' and resid 92 through 96 Processing helix chain 'k' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU k 131 " --> pdb=" O ASN k 127 " (cutoff:3.500A) Processing helix chain 'k' and resid 141 through 148 Processing helix chain 'm' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE m 10 " --> pdb=" O PRO m 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL m 11 " --> pdb=" O SER m 8 " (cutoff:3.500A) Processing helix chain 'm' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU m 31 " --> pdb=" O CYS m 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY m 32 " --> pdb=" O THR m 28 " (cutoff:3.500A) Processing helix chain 'm' and resid 38 through 50 Processing helix chain 'm' and resid 74 through 86 Proline residue: m 78 - end of helix Processing helix chain 'm' and resid 92 through 96 Processing helix chain 'm' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU m 131 " --> pdb=" O ASN m 127 " (cutoff:3.500A) Processing helix chain 'm' and resid 141 through 148 Processing helix chain 'o' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE o 10 " --> pdb=" O PRO o 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL o 11 " --> pdb=" O SER o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU o 31 " --> pdb=" O CYS o 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY o 32 " --> pdb=" O THR o 28 " (cutoff:3.500A) Processing helix chain 'o' and resid 38 through 50 Processing helix chain 'o' and resid 74 through 86 Proline residue: o 78 - end of helix Processing helix chain 'o' and resid 92 through 96 Processing helix chain 'o' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU o 131 " --> pdb=" O ASN o 127 " (cutoff:3.500A) Processing helix chain 'o' and resid 141 through 148 Processing helix chain 'q' and resid 7 through 13 removed outlier: 3.704A pdb=" N PHE q 10 " --> pdb=" O PRO q 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL q 11 " --> pdb=" O SER q 8 " (cutoff:3.500A) Processing helix chain 'q' and resid 20 through 32 removed outlier: 3.619A pdb=" N LEU q 31 " --> pdb=" O CYS q 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY q 32 " --> pdb=" O THR q 28 " (cutoff:3.500A) Processing helix chain 'q' and resid 38 through 50 Processing helix chain 'q' and resid 74 through 86 Proline residue: q 78 - end of helix Processing helix chain 'q' and resid 92 through 96 Processing helix chain 'q' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU q 131 " --> pdb=" O ASN q 127 " (cutoff:3.500A) Processing helix chain 'q' and resid 141 through 148 Processing helix chain 's' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE s 10 " --> pdb=" O PRO s 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL s 11 " --> pdb=" O SER s 8 " (cutoff:3.500A) Processing helix chain 's' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU s 31 " --> pdb=" O CYS s 27 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY s 32 " --> pdb=" O THR s 28 " (cutoff:3.500A) Processing helix chain 's' and resid 38 through 50 Processing helix chain 's' and resid 74 through 86 Proline residue: s 78 - end of helix Processing helix chain 's' and resid 92 through 96 Processing helix chain 's' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU s 131 " --> pdb=" O ASN s 127 " (cutoff:3.500A) Processing helix chain 's' and resid 141 through 148 Processing helix chain 'u' and resid 7 through 13 removed outlier: 3.704A pdb=" N PHE u 10 " --> pdb=" O PRO u 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL u 11 " --> pdb=" O SER u 8 " (cutoff:3.500A) Processing helix chain 'u' and resid 20 through 32 removed outlier: 3.619A pdb=" N LEU u 31 " --> pdb=" O CYS u 27 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY u 32 " --> pdb=" O THR u 28 " (cutoff:3.500A) Processing helix chain 'u' and resid 38 through 50 Processing helix chain 'u' and resid 74 through 86 Proline residue: u 78 - end of helix Processing helix chain 'u' and resid 92 through 96 Processing helix chain 'u' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU u 131 " --> pdb=" O ASN u 127 " (cutoff:3.500A) Processing helix chain 'u' and resid 141 through 148 Processing helix chain 'w' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE w 10 " --> pdb=" O PRO w 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL w 11 " --> pdb=" O SER w 8 " (cutoff:3.500A) Processing helix chain 'w' and resid 20 through 32 removed outlier: 3.619A pdb=" N LEU w 31 " --> pdb=" O CYS w 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY w 32 " --> pdb=" O THR w 28 " (cutoff:3.500A) Processing helix chain 'w' and resid 38 through 50 Processing helix chain 'w' and resid 74 through 86 Proline residue: w 78 - end of helix Processing helix chain 'w' and resid 92 through 96 Processing helix chain 'w' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU w 131 " --> pdb=" O ASN w 127 " (cutoff:3.500A) Processing helix chain 'w' and resid 141 through 148 Processing helix chain 'y' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE y 10 " --> pdb=" O PRO y 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL y 11 " --> pdb=" O SER y 8 " (cutoff:3.500A) Processing helix chain 'y' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU y 31 " --> pdb=" O CYS y 27 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY y 32 " --> pdb=" O THR y 28 " (cutoff:3.500A) Processing helix chain 'y' and resid 38 through 50 Processing helix chain 'y' and resid 74 through 86 Proline residue: y 78 - end of helix Processing helix chain 'y' and resid 92 through 96 Processing helix chain 'y' and resid 104 through 133 removed outlier: 3.702A pdb=" N GLU y 131 " --> pdb=" O ASN y 127 " (cutoff:3.500A) Processing helix chain 'y' and resid 141 through 148 Processing helix chain 'AA' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHEAA 10 " --> pdb=" O PROAA 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALAA 11 " --> pdb=" O SERAA 8 " (cutoff:3.500A) Processing helix chain 'AA' and resid 20 through 32 removed outlier: 3.619A pdb=" N LEUAA 31 " --> pdb=" O CYSAA 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLYAA 32 " --> pdb=" O THRAA 28 " (cutoff:3.500A) Processing helix chain 'AA' and resid 38 through 50 Processing helix chain 'AA' and resid 74 through 86 Proline residue: AA 78 - end of helix Processing helix chain 'AA' and resid 92 through 96 Processing helix chain 'AA' and resid 104 through 133 removed outlier: 3.704A pdb=" N GLUAA 131 " --> pdb=" O ASNAA 127 " (cutoff:3.500A) Processing helix chain 'AA' and resid 141 through 148 Processing helix chain 'AC' and resid 7 through 13 removed outlier: 3.704A pdb=" N PHEAC 10 " --> pdb=" O PROAC 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALAC 11 " --> pdb=" O SERAC 8 " (cutoff:3.500A) Processing helix chain 'AC' and resid 20 through 32 removed outlier: 3.619A pdb=" N LEUAC 31 " --> pdb=" O CYSAC 27 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLYAC 32 " --> pdb=" O THRAC 28 " (cutoff:3.500A) Processing helix chain 'AC' and resid 38 through 50 Processing helix chain 'AC' and resid 74 through 86 Proline residue: AC 78 - end of helix Processing helix chain 'AC' and resid 92 through 96 Processing helix chain 'AC' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLUAC 131 " --> pdb=" O ASNAC 127 " (cutoff:3.500A) Processing helix chain 'AC' and resid 141 through 148 Processing helix chain 'AE' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHEAE 10 " --> pdb=" O PROAE 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALAE 11 " --> pdb=" O SERAE 8 " (cutoff:3.500A) Processing helix chain 'AE' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEUAE 31 " --> pdb=" O CYSAE 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLYAE 32 " --> pdb=" O THRAE 28 " (cutoff:3.500A) Processing helix chain 'AE' and resid 38 through 50 Processing helix chain 'AE' and resid 74 through 86 Proline residue: AE 78 - end of helix Processing helix chain 'AE' and resid 92 through 96 Processing helix chain 'AE' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLUAE 131 " --> pdb=" O ASNAE 127 " (cutoff:3.500A) Processing helix chain 'AE' and resid 141 through 148 Processing helix chain 'AG' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHEAG 10 " --> pdb=" O PROAG 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALAG 11 " --> pdb=" O SERAG 8 " (cutoff:3.500A) Processing helix chain 'AG' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEUAG 31 " --> pdb=" O CYSAG 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLYAG 32 " --> pdb=" O THRAG 28 " (cutoff:3.500A) Processing helix chain 'AG' and resid 38 through 50 Processing helix chain 'AG' and resid 74 through 86 Proline residue: AG 78 - end of helix Processing helix chain 'AG' and resid 92 through 96 Processing helix chain 'AG' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLUAG 131 " --> pdb=" O ASNAG 127 " (cutoff:3.500A) Processing helix chain 'AG' and resid 141 through 148 Processing helix chain 'AI' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHEAI 10 " --> pdb=" O PROAI 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALAI 11 " --> pdb=" O SERAI 8 " (cutoff:3.500A) Processing helix chain 'AI' and resid 20 through 32 removed outlier: 3.619A pdb=" N LEUAI 31 " --> pdb=" O CYSAI 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLYAI 32 " --> pdb=" O THRAI 28 " (cutoff:3.500A) Processing helix chain 'AI' and resid 38 through 50 Processing helix chain 'AI' and resid 74 through 86 Proline residue: AI 78 - end of helix Processing helix chain 'AI' and resid 92 through 96 Processing helix chain 'AI' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLUAI 131 " --> pdb=" O ASNAI 127 " (cutoff:3.500A) Processing helix chain 'AI' and resid 141 through 148 Processing helix chain 'AK' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHEAK 10 " --> pdb=" O PROAK 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALAK 11 " --> pdb=" O SERAK 8 " (cutoff:3.500A) Processing helix chain 'AK' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEUAK 31 " --> pdb=" O CYSAK 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLYAK 32 " --> pdb=" O THRAK 28 " (cutoff:3.500A) Processing helix chain 'AK' and resid 38 through 50 Processing helix chain 'AK' and resid 74 through 86 Proline residue: AK 78 - end of helix Processing helix chain 'AK' and resid 92 through 96 Processing helix chain 'AK' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLUAK 131 " --> pdb=" O ASNAK 127 " (cutoff:3.500A) Processing helix chain 'AK' and resid 141 through 148 Processing helix chain 'AM' and resid 7 through 13 removed outlier: 3.706A pdb=" N PHEAM 10 " --> pdb=" O PROAM 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALAM 11 " --> pdb=" O SERAM 8 " (cutoff:3.500A) Processing helix chain 'AM' and resid 20 through 32 removed outlier: 3.619A pdb=" N LEUAM 31 " --> pdb=" O CYSAM 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLYAM 32 " --> pdb=" O THRAM 28 " (cutoff:3.500A) Processing helix chain 'AM' and resid 38 through 50 Processing helix chain 'AM' and resid 74 through 86 Proline residue: AM 78 - end of helix Processing helix chain 'AM' and resid 92 through 96 Processing helix chain 'AM' and resid 104 through 133 removed outlier: 3.704A pdb=" N GLUAM 131 " --> pdb=" O ASNAM 127 " (cutoff:3.500A) Processing helix chain 'AM' and resid 141 through 148 Processing helix chain 'AO' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHEAO 10 " --> pdb=" O PROAO 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALAO 11 " --> pdb=" O SERAO 8 " (cutoff:3.500A) Processing helix chain 'AO' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEUAO 31 " --> pdb=" O CYSAO 27 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLYAO 32 " --> pdb=" O THRAO 28 " (cutoff:3.500A) Processing helix chain 'AO' and resid 38 through 50 Processing helix chain 'AO' and resid 74 through 86 Proline residue: AO 78 - end of helix Processing helix chain 'AO' and resid 92 through 96 Processing helix chain 'AO' and resid 104 through 133 removed outlier: 3.704A pdb=" N GLUAO 131 " --> pdb=" O ASNAO 127 " (cutoff:3.500A) Processing helix chain 'AO' and resid 141 through 148 Processing helix chain 'AQ' and resid 7 through 13 removed outlier: 3.704A pdb=" N PHEAQ 10 " --> pdb=" O PROAQ 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALAQ 11 " --> pdb=" O SERAQ 8 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 20 through 32 removed outlier: 3.619A pdb=" N LEUAQ 31 " --> pdb=" O CYSAQ 27 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLYAQ 32 " --> pdb=" O THRAQ 28 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 38 through 50 Processing helix chain 'AQ' and resid 74 through 86 Proline residue: AQ 78 - end of helix Processing helix chain 'AQ' and resid 92 through 96 Processing helix chain 'AQ' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLUAQ 131 " --> pdb=" O ASNAQ 127 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 141 through 148 Processing sheet with id= A, first strand: chain 'A' and resid 17 through 19 Processing sheet with id= B, first strand: chain 'B' and resid 17 through 19 Processing sheet with id= C, first strand: chain 'D' and resid 17 through 19 Processing sheet with id= D, first strand: chain 'F' and resid 17 through 19 Processing sheet with id= E, first strand: chain 'H' and resid 17 through 19 Processing sheet with id= F, first strand: chain 'J' and resid 17 through 19 Processing sheet with id= G, first strand: chain 'L' and resid 17 through 19 Processing sheet with id= H, first strand: chain 'N' and resid 17 through 19 Processing sheet with id= I, first strand: chain 'P' and resid 17 through 19 Processing sheet with id= J, first strand: chain 'S' and resid 17 through 19 Processing sheet with id= K, first strand: chain 'U' and resid 17 through 19 Processing sheet with id= L, first strand: chain 'W' and resid 17 through 19 Processing sheet with id= M, first strand: chain 'Y' and resid 17 through 19 Processing sheet with id= N, first strand: chain '0' and resid 17 through 19 Processing sheet with id= O, first strand: chain '2' and resid 17 through 19 Processing sheet with id= P, first strand: chain '4' and resid 17 through 19 Processing sheet with id= Q, first strand: chain '6' and resid 17 through 19 Processing sheet with id= R, first strand: chain '8' and resid 17 through 19 Processing sheet with id= S, first strand: chain 'a' and resid 17 through 19 Processing sheet with id= T, first strand: chain 'c' and resid 17 through 19 Processing sheet with id= U, first strand: chain 'e' and resid 17 through 19 Processing sheet with id= V, first strand: chain 'g' and resid 17 through 19 Processing sheet with id= W, first strand: chain 'i' and resid 17 through 19 Processing sheet with id= X, first strand: chain 'k' and resid 17 through 19 Processing sheet with id= Y, first strand: chain 'm' and resid 17 through 19 Processing sheet with id= Z, first strand: chain 'o' and resid 17 through 19 Processing sheet with id= AA, first strand: chain 'q' and resid 17 through 19 Processing sheet with id= AB, first strand: chain 's' and resid 17 through 19 Processing sheet with id= AC, first strand: chain 'u' and resid 17 through 19 Processing sheet with id= AD, first strand: chain 'w' and resid 17 through 19 Processing sheet with id= AE, first strand: chain 'y' and resid 17 through 19 Processing sheet with id= AF, first strand: chain 'AA' and resid 17 through 19 Processing sheet with id= AG, first strand: chain 'AC' and resid 17 through 19 Processing sheet with id= AH, first strand: chain 'AE' and resid 17 through 19 Processing sheet with id= AI, first strand: chain 'AG' and resid 17 through 19 Processing sheet with id= AJ, first strand: chain 'AI' and resid 17 through 19 Processing sheet with id= AK, first strand: chain 'AK' and resid 17 through 19 Processing sheet with id= AL, first strand: chain 'AM' and resid 17 through 19 Processing sheet with id= AM, first strand: chain 'AO' and resid 17 through 19 Processing sheet with id= AN, first strand: chain 'AQ' and resid 17 through 19 2240 hydrogen bonds defined for protein. 6480 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 16.64 Time building geometry restraints manager: 19.91 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: 16683 1.34 - 1.45: 7642 1.45 - 1.57: 27755 1.57 - 1.68: 200 1.68 - 1.80: 40 Bond restraints: 52320 Sorted by residual: bond pdb=" C ALA a 100 " pdb=" N ASN a 101 " ideal model delta sigma weight residual 1.332 1.322 0.009 8.60e-03 1.35e+04 1.17e+00 bond pdb=" C ALAAA 100 " pdb=" N ASNAA 101 " ideal model delta sigma weight residual 1.332 1.323 0.009 8.60e-03 1.35e+04 1.16e+00 bond pdb=" C ALA 4 100 " pdb=" N ASN 4 101 " ideal model delta sigma weight residual 1.332 1.323 0.009 8.60e-03 1.35e+04 1.15e+00 bond pdb=" C ALA J 100 " pdb=" N ASN J 101 " ideal model delta sigma weight residual 1.332 1.323 0.009 8.60e-03 1.35e+04 1.14e+00 bond pdb=" C ALA U 100 " pdb=" N ASN U 101 " ideal model delta sigma weight residual 1.332 1.323 0.009 8.60e-03 1.35e+04 1.12e+00 ... (remaining 52315 not shown) Histogram of bond angle deviations from ideal: 100.88 - 107.50: 2363 107.50 - 114.13: 30299 114.13 - 120.75: 22528 120.75 - 127.38: 15901 127.38 - 134.00: 909 Bond angle restraints: 72000 Sorted by residual: angle pdb=" C PRO 6 54 " pdb=" N SER 6 55 " pdb=" CA SER 6 55 " ideal model delta sigma weight residual 121.80 116.10 5.70 2.44e+00 1.68e-01 5.47e+00 angle pdb=" C PROAE 54 " pdb=" N SERAE 55 " pdb=" CA SERAE 55 " ideal model delta sigma weight residual 121.80 116.10 5.70 2.44e+00 1.68e-01 5.45e+00 angle pdb=" C PRO 4 54 " pdb=" N SER 4 55 " pdb=" CA SER 4 55 " ideal model delta sigma weight residual 121.80 116.11 5.69 2.44e+00 1.68e-01 5.44e+00 angle pdb=" C PRO B 54 " pdb=" N SER B 55 " pdb=" CA SER B 55 " ideal model delta sigma weight residual 121.80 116.11 5.69 2.44e+00 1.68e-01 5.44e+00 angle pdb=" C PRO k 54 " pdb=" N SER k 55 " pdb=" CA SER k 55 " ideal model delta sigma weight residual 121.80 116.12 5.68 2.44e+00 1.68e-01 5.43e+00 ... (remaining 71995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.45: 27600 14.45 - 28.89: 2499 28.89 - 43.34: 404 43.34 - 57.78: 257 57.78 - 72.23: 120 Dihedral angle restraints: 30880 sinusoidal: 12800 harmonic: 18080 Sorted by residual: dihedral pdb=" CA ASP 0 66 " pdb=" C ASP 0 66 " pdb=" N PHE 0 67 " pdb=" CA PHE 0 67 " ideal model delta harmonic sigma weight residual 180.00 160.70 19.30 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ASP W 66 " pdb=" C ASP W 66 " pdb=" N PHE W 67 " pdb=" CA PHE W 67 " ideal model delta harmonic sigma weight residual 180.00 160.70 19.30 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ASP H 66 " pdb=" C ASP H 66 " pdb=" N PHE H 67 " pdb=" CA PHE H 67 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 30877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 5768 0.039 - 0.079: 2270 0.079 - 0.118: 436 0.118 - 0.157: 6 0.157 - 0.196: 40 Chirality restraints: 8520 Sorted by residual: chirality pdb=" CA SER 0 55 " pdb=" N SER 0 55 " pdb=" C SER 0 55 " pdb=" CB SER 0 55 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.63e-01 chirality pdb=" CA SERAI 55 " pdb=" N SERAI 55 " pdb=" C SERAI 55 " pdb=" CB SERAI 55 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.60e-01 chirality pdb=" CA SER u 55 " pdb=" N SER u 55 " pdb=" C SER u 55 " pdb=" CB SER u 55 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.60e-01 ... (remaining 8517 not shown) Planarity restraints: 8920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASNAC 101 " -0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PROAC 102 " 0.066 5.00e-02 4.00e+02 pdb=" CA PROAC 102 " -0.020 5.00e-02 4.00e+02 pdb=" CD PROAC 102 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN J 101 " -0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO J 102 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO J 102 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 102 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN i 101 " -0.025 5.00e-02 4.00e+02 3.84e-02 2.35e+00 pdb=" N PRO i 102 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO i 102 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO i 102 " -0.021 5.00e-02 4.00e+02 ... (remaining 8917 not shown) Histogram of nonbonded interaction distances: 0.35 - 1.26: 109 1.26 - 2.17: 187 2.17 - 3.08: 41968 3.08 - 3.99: 175718 3.99 - 4.90: 304751 Warning: very small nonbonded interaction distances. Nonbonded interactions: 522733 Sorted by model distance: nonbonded pdb=" O3' A C 6 " pdb=" OP1 G E 4 " model vdw 0.351 3.040 nonbonded pdb=" O3' A v 6 " pdb=" OP1 G x 4 " model vdw 0.351 3.040 nonbonded pdb=" O3' AAJ 6 " pdb=" OP1 GAL 4 " model vdw 0.352 3.040 nonbonded pdb=" O3' A h 6 " pdb=" OP1 G j 4 " model vdw 0.352 3.040 nonbonded pdb=" O3' A Q 6 " pdb=" OP1 G T 4 " model vdw 0.352 3.040 ... (remaining 522728 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '2' selection = chain '4' selection = chain '6' selection = chain '8' selection = chain 'A' selection = chain 'AA' selection = chain 'AC' selection = chain 'AE' selection = chain 'AG' selection = chain 'AI' selection = chain 'AK' selection = chain 'AM' selection = chain 'AO' selection = chain 'AQ' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'k' selection = chain 'm' selection = chain 'o' selection = chain 'q' selection = chain 's' selection = chain 'u' selection = chain 'w' selection = chain 'y' } ncs_group { reference = chain '1' selection = chain '3' selection = chain '5' selection = chain '7' selection = chain '9' selection = chain 'AB' selection = chain 'AD' selection = chain 'AF' selection = chain 'AH' selection = chain 'AJ' selection = chain 'AL' selection = chain 'AN' selection = chain 'AP' selection = chain 'AR' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'j' selection = chain 'l' selection = chain 'n' selection = chain 'p' selection = chain 'r' selection = chain 't' selection = chain 'v' selection = chain 'x' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 40 9.91 5 P 120 5.49 5 Mg 160 5.21 5 S 40 5.16 5 C 31640 2.51 5 N 9000 2.21 5 O 13080 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: 4.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 24.640 Check model and map are aligned: 0.580 Convert atoms to be neutral: 0.370 Process input model: 120.030 Find NCS groups from input model: 2.950 Set up NCS constraints: 1.030 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 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 : 0.004 0.025 52320 Z= 0.245 Angle : 0.645 6.439 72000 Z= 0.363 Chirality : 0.041 0.196 8520 Planarity : 0.005 0.038 8920 Dihedral : 12.989 72.230 19040 Min Nonbonded Distance : 0.351 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 0.00 % 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: -0.33 (0.10), residues: 6040 helix: 0.38 (0.08), residues: 3440 sheet: None (None), residues: 0 loop : -0.96 (0.10), residues: 2600 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 894 time to evaluate : 4.517 Fit side-chains outliers start: 0 outliers final: 2 residues processed: 894 average time/residue: 1.1778 time to fit residues: 1364.6088 Evaluate side-chains 733 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 731 time to evaluate : 4.530 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.4120 time to fit residues: 7.4235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 506 optimal weight: 8.9990 chunk 454 optimal weight: 4.9990 chunk 252 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 306 optimal weight: 50.0000 chunk 242 optimal weight: 0.0980 chunk 470 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 285 optimal weight: 9.9990 chunk 350 optimal weight: 0.5980 chunk 544 optimal weight: 0.0980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN B 73 ASN D 73 ASN F 39 GLN F 73 ASN H 73 ASN ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 73 ASN L 73 ASN N 29 ASN N 73 ASN P 29 ASN P 73 ASN S 73 ASN U 39 GLN U 73 ASN W 73 ASN Y 29 ASN Y 39 GLN Y 73 ASN 0 73 ASN 2 73 ASN 4 29 ASN 4 39 GLN 4 73 ASN ** 6 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 39 GLN 6 73 ASN ** 8 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 73 ASN a 29 ASN a 33 ASN a 73 ASN c 29 ASN c 73 ASN e 29 ASN e 39 GLN e 73 ASN g 29 ASN g 33 ASN g 39 GLN g 73 ASN g 101 ASN i 29 ASN i 73 ASN k 29 ASN k 57 GLN k 73 ASN m 29 ASN m 73 ASN o 29 ASN o 73 ASN q 33 ASN q 73 ASN s 73 ASN u 33 ASN u 73 ASN w 29 ASN w 73 ASN y 29 ASN y 73 ASN AA 73 ASN AC 29 ASN AC 73 ASN AC 126 ASN AE 73 ASN AG 73 ASN AI 29 ASN AI 73 ASN AK 33 ASN AK 73 ASN AM 29 ASN AM 73 ASN AO 29 ASN AO 73 ASN AQ 29 ASN AQ 73 ASN AQ 127 ASN Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.235 52320 Z= 0.428 Angle : 1.291 34.368 72000 Z= 0.686 Chirality : 0.069 0.766 8520 Planarity : 0.016 0.439 8920 Dihedral : 9.445 80.097 8080 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.93 % Favored : 94.70 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.10), residues: 6040 helix: -1.19 (0.08), residues: 3400 sheet: None (None), residues: 0 loop : -1.63 (0.11), residues: 2640 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1004 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 839 time to evaluate : 4.542 Fit side-chains outliers start: 165 outliers final: 47 residues processed: 912 average time/residue: 1.1491 time to fit residues: 1365.1374 Evaluate side-chains 774 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 727 time to evaluate : 4.495 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 29 residues processed: 21 average time/residue: 0.6892 time to fit residues: 27.4707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 302 optimal weight: 8.9990 chunk 169 optimal weight: 30.0000 chunk 453 optimal weight: 10.0000 chunk 371 optimal weight: 9.9990 chunk 150 optimal weight: 30.0000 chunk 545 optimal weight: 6.9990 chunk 589 optimal weight: 9.9990 chunk 486 optimal weight: 10.0000 chunk 541 optimal weight: 6.9990 chunk 186 optimal weight: 20.0000 chunk 437 optimal weight: 5.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN F 29 ASN L 29 ASN N 29 ASN S 29 ASN U 29 ASN W 29 ASN Y 33 ASN 0 29 ASN 4 29 ASN 8 29 ASN a 29 ASN c 29 ASN g 29 ASN i 29 ASN k 29 ASN m 29 ASN m 33 ASN s 29 ASN u 29 ASN u 57 GLN u 127 ASN w 29 ASN y 29 ASN AC 29 ASN AC 126 ASN AK 34 GLN AO 29 ASN AQ 29 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 52320 Z= 0.292 Angle : 0.663 7.793 72000 Z= 0.353 Chirality : 0.044 0.217 8520 Planarity : 0.007 0.068 8920 Dihedral : 8.539 58.433 8080 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 2.09 % 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: 0.28 (0.10), residues: 6040 helix: 0.75 (0.08), residues: 3440 sheet: None (None), residues: 0 loop : -0.48 (0.12), residues: 2600 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 804 time to evaluate : 4.683 Fit side-chains outliers start: 113 outliers final: 52 residues processed: 849 average time/residue: 1.2266 time to fit residues: 1338.6707 Evaluate side-chains 792 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 740 time to evaluate : 4.537 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 33 residues processed: 24 average time/residue: 0.5516 time to fit residues: 27.4241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 539 optimal weight: 0.9990 chunk 410 optimal weight: 0.7980 chunk 283 optimal weight: 8.9990 chunk 60 optimal weight: 30.0000 chunk 260 optimal weight: 10.0000 chunk 366 optimal weight: 8.9990 chunk 547 optimal weight: 9.9990 chunk 579 optimal weight: 5.9990 chunk 286 optimal weight: 20.0000 chunk 519 optimal weight: 0.9980 chunk 156 optimal weight: 10.0000 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN N 29 ASN P 29 ASN S 29 ASN Y 29 ASN 0 29 ASN 4 29 ASN 6 29 ASN 8 29 ASN a 29 ASN e 29 ASN g 29 ASN i 29 ASN k 29 ASN m 29 ASN o 29 ASN o 57 GLN q 29 ASN u 29 ASN u 57 GLN w 29 ASN y 29 ASN AI 29 ASN AO 29 ASN AQ 29 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 52320 Z= 0.172 Angle : 0.537 6.180 72000 Z= 0.281 Chirality : 0.038 0.151 8520 Planarity : 0.006 0.062 8920 Dihedral : 8.278 58.635 8080 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 1.93 % 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: 1.19 (0.11), residues: 6040 helix: 1.63 (0.09), residues: 3360 sheet: None (None), residues: 0 loop : -0.23 (0.12), residues: 2680 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 795 time to evaluate : 4.613 Fit side-chains outliers start: 104 outliers final: 63 residues processed: 834 average time/residue: 1.2430 time to fit residues: 1330.2234 Evaluate side-chains 808 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 745 time to evaluate : 4.582 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 34 residues processed: 33 average time/residue: 0.4711 time to fit residues: 32.7302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 483 optimal weight: 10.0000 chunk 329 optimal weight: 30.0000 chunk 8 optimal weight: 20.0000 chunk 431 optimal weight: 20.0000 chunk 239 optimal weight: 10.0000 chunk 494 optimal weight: 30.0000 chunk 400 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 296 optimal weight: 40.0000 chunk 520 optimal weight: 1.9990 chunk 146 optimal weight: 30.0000 overall best weight: 8.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN J 29 ASN N 29 ASN P 29 ASN S 29 ASN Y 29 ASN 0 29 ASN 4 29 ASN 6 29 ASN 8 29 ASN a 29 ASN e 29 ASN g 29 ASN g 33 ASN i 29 ASN k 29 ASN m 29 ASN o 29 ASN q 29 ASN u 29 ASN u 57 GLN w 29 ASN y 29 ASN AI 29 ASN AO 29 ASN AQ 29 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.082 52320 Z= 0.310 Angle : 0.661 6.335 72000 Z= 0.352 Chirality : 0.044 0.209 8520 Planarity : 0.007 0.066 8920 Dihedral : 8.516 58.440 8080 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 2.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.06 (0.10), residues: 6040 helix: 1.29 (0.09), residues: 3440 sheet: None (None), residues: 0 loop : 0.01 (0.12), residues: 2600 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 783 time to evaluate : 4.636 Fit side-chains outliers start: 146 outliers final: 78 residues processed: 846 average time/residue: 1.2319 time to fit residues: 1340.9731 Evaluate side-chains 839 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 761 time to evaluate : 4.522 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 36 residues processed: 46 average time/residue: 0.4157 time to fit residues: 40.6937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 195 optimal weight: 20.0000 chunk 522 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 340 optimal weight: 1.9990 chunk 143 optimal weight: 20.0000 chunk 580 optimal weight: 6.9990 chunk 481 optimal weight: 9.9990 chunk 268 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 chunk 192 optimal weight: 10.0000 chunk 304 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN J 29 ASN N 29 ASN S 29 ASN Y 29 ASN 0 29 ASN 4 29 ASN 6 29 ASN 8 29 ASN a 29 ASN c 29 ASN e 29 ASN g 29 ASN i 29 ASN k 29 ASN m 29 ASN o 29 ASN q 29 ASN u 29 ASN w 29 ASN y 29 ASN AI 29 ASN AO 29 ASN AQ 29 ASN AQ 57 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 52320 Z= 0.253 Angle : 0.613 6.273 72000 Z= 0.325 Chirality : 0.041 0.197 8520 Planarity : 0.007 0.066 8920 Dihedral : 8.434 58.526 8080 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 2.48 % 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: 1.23 (0.10), residues: 6040 helix: 1.48 (0.09), residues: 3400 sheet: None (None), residues: 0 loop : 0.03 (0.12), residues: 2640 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 766 time to evaluate : 4.580 Fit side-chains outliers start: 134 outliers final: 72 residues processed: 825 average time/residue: 1.2579 time to fit residues: 1328.3490 Evaluate side-chains 826 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 754 time to evaluate : 4.778 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 39 residues processed: 36 average time/residue: 0.4245 time to fit residues: 33.7329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 559 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 chunk 330 optimal weight: 20.0000 chunk 423 optimal weight: 10.0000 chunk 328 optimal weight: 6.9990 chunk 488 optimal weight: 20.0000 chunk 324 optimal weight: 5.9990 chunk 578 optimal weight: 30.0000 chunk 361 optimal weight: 20.0000 chunk 352 optimal weight: 1.9990 chunk 266 optimal weight: 40.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN J 29 ASN N 29 ASN S 29 ASN Y 29 ASN 0 29 ASN 4 29 ASN 6 29 ASN 8 29 ASN a 29 ASN c 29 ASN e 29 ASN g 29 ASN i 29 ASN k 29 ASN m 29 ASN o 29 ASN q 29 ASN u 29 ASN w 29 ASN y 29 ASN AA 29 ASN AI 29 ASN AO 29 ASN AQ 29 ASN AQ 57 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 52320 Z= 0.254 Angle : 0.618 6.674 72000 Z= 0.328 Chirality : 0.042 0.254 8520 Planarity : 0.006 0.062 8920 Dihedral : 8.460 58.498 8080 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 2.24 % 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: 1.28 (0.10), residues: 6040 helix: 1.50 (0.09), residues: 3400 sheet: None (None), residues: 0 loop : 0.09 (0.12), residues: 2640 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 769 time to evaluate : 4.637 Fit side-chains outliers start: 121 outliers final: 75 residues processed: 819 average time/residue: 1.2685 time to fit residues: 1330.2367 Evaluate side-chains 826 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 751 time to evaluate : 4.547 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 42 residues processed: 36 average time/residue: 0.4284 time to fit residues: 33.9232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 357 optimal weight: 10.0000 chunk 230 optimal weight: 9.9990 chunk 345 optimal weight: 8.9990 chunk 174 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 chunk 367 optimal weight: 20.0000 chunk 393 optimal weight: 9.9990 chunk 285 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 454 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN J 29 ASN N 29 ASN S 29 ASN Y 29 ASN 0 29 ASN 4 29 ASN 6 29 ASN 8 29 ASN a 29 ASN c 29 ASN e 29 ASN g 29 ASN i 29 ASN k 29 ASN m 29 ASN o 29 ASN q 29 ASN u 29 ASN w 29 ASN y 29 ASN AA 29 ASN AI 29 ASN AM 29 ASN AO 29 ASN AQ 29 ASN AQ 57 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 52320 Z= 0.270 Angle : 0.636 9.664 72000 Z= 0.337 Chirality : 0.042 0.251 8520 Planarity : 0.007 0.063 8920 Dihedral : 8.470 58.468 8080 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 1.83 % 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: 1.26 (0.10), residues: 6040 helix: 1.48 (0.09), residues: 3400 sheet: None (None), residues: 0 loop : 0.10 (0.12), residues: 2640 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 760 time to evaluate : 4.650 Fit side-chains outliers start: 99 outliers final: 66 residues processed: 811 average time/residue: 1.3028 time to fit residues: 1349.1915 Evaluate side-chains 819 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 753 time to evaluate : 4.625 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 42 residues processed: 27 average time/residue: 0.3979 time to fit residues: 26.1630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 526 optimal weight: 20.0000 chunk 554 optimal weight: 0.5980 chunk 505 optimal weight: 0.7980 chunk 538 optimal weight: 4.9990 chunk 553 optimal weight: 4.9990 chunk 324 optimal weight: 4.9990 chunk 234 optimal weight: 4.9990 chunk 423 optimal weight: 9.9990 chunk 165 optimal weight: 30.0000 chunk 486 optimal weight: 9.9990 chunk 509 optimal weight: 7.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN F 39 GLN J 29 ASN N 29 ASN S 29 ASN Y 29 ASN 0 29 ASN 4 29 ASN 6 29 ASN 8 29 ASN a 29 ASN c 29 ASN e 29 ASN g 29 ASN i 29 ASN k 29 ASN m 29 ASN o 29 ASN q 29 ASN u 29 ASN w 29 ASN y 29 ASN AA 29 ASN AM 29 ASN AO 29 ASN AQ 29 ASN AQ 57 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 52320 Z= 0.164 Angle : 0.531 7.375 72000 Z= 0.277 Chirality : 0.038 0.208 8520 Planarity : 0.005 0.066 8920 Dihedral : 8.244 58.599 8080 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 1.44 % 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: 1.70 (0.11), residues: 6040 helix: 1.94 (0.09), residues: 3360 sheet: None (None), residues: 0 loop : 0.16 (0.12), residues: 2680 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 768 time to evaluate : 4.792 Fit side-chains outliers start: 78 outliers final: 60 residues processed: 817 average time/residue: 1.2675 time to fit residues: 1324.3778 Evaluate side-chains 809 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 749 time to evaluate : 4.547 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 42 residues processed: 20 average time/residue: 0.3902 time to fit residues: 20.6709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 537 optimal weight: 10.0000 chunk 353 optimal weight: 9.9990 chunk 569 optimal weight: 2.9990 chunk 347 optimal weight: 8.9990 chunk 270 optimal weight: 10.0000 chunk 396 optimal weight: 10.0000 chunk 597 optimal weight: 4.9990 chunk 550 optimal weight: 5.9990 chunk 475 optimal weight: 0.5980 chunk 49 optimal weight: 30.0000 chunk 367 optimal weight: 0.9980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN J 29 ASN N 29 ASN S 29 ASN W 29 ASN Y 29 ASN 0 29 ASN 4 29 ASN 6 29 ASN 8 29 ASN a 29 ASN c 29 ASN e 29 ASN g 29 ASN i 29 ASN k 29 ASN m 29 ASN o 29 ASN q 29 ASN u 29 ASN w 29 ASN y 29 ASN AA 29 ASN AI 29 ASN AM 29 ASN AO 29 ASN AQ 29 ASN AQ 57 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 52320 Z= 0.160 Angle : 0.528 7.768 72000 Z= 0.275 Chirality : 0.038 0.224 8520 Planarity : 0.005 0.066 8920 Dihedral : 8.214 58.737 8080 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 1.09 % 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: 1.83 (0.11), residues: 6040 helix: 2.03 (0.09), residues: 3360 sheet: None (None), residues: 0 loop : 0.23 (0.12), residues: 2680 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 758 time to evaluate : 5.243 Fit side-chains outliers start: 59 outliers final: 45 residues processed: 799 average time/residue: 1.3295 time to fit residues: 1364.7909 Evaluate side-chains 794 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 749 time to evaluate : 4.639 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 40 residues processed: 8 average time/residue: 0.4249 time to fit residues: 12.4590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 291 optimal weight: 10.0000 chunk 378 optimal weight: 20.0000 chunk 507 optimal weight: 10.0000 chunk 145 optimal weight: 0.2980 chunk 438 optimal weight: 9.9990 chunk 70 optimal weight: 30.0000 chunk 132 optimal weight: 2.9990 chunk 476 optimal weight: 30.0000 chunk 199 optimal weight: 20.0000 chunk 489 optimal weight: 4.9990 chunk 60 optimal weight: 30.0000 overall best weight: 5.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN J 29 ASN N 29 ASN S 29 ASN W 29 ASN Y 29 ASN 0 29 ASN 4 29 ASN 6 29 ASN 8 29 ASN a 29 ASN c 29 ASN e 29 ASN g 29 ASN i 29 ASN k 29 ASN m 29 ASN o 29 ASN q 29 ASN u 29 ASN w 29 ASN y 29 ASN AA 29 ASN AM 29 ASN AO 29 ASN AQ 29 ASN AQ 57 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.144039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.118358 restraints weight = 40026.335| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 0.76 r_work: 0.3239 rms_B_bonded: 0.84 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 1.02 restraints_weight: 0.2500 r_work: 0.3169 rms_B_bonded: 1.42 restraints_weight: 0.1250 r_work: 0.3104 rms_B_bonded: 2.19 restraints_weight: 0.0625 r_work: 0.3000 rms_B_bonded: 3.81 restraints_weight: 0.0312 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 52320 Z= 0.227 Angle : 0.597 8.124 72000 Z= 0.314 Chirality : 0.041 0.269 8520 Planarity : 0.006 0.065 8920 Dihedral : 8.385 58.574 8080 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 1.17 % 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: 1.56 (0.11), residues: 6040 helix: 1.70 (0.09), residues: 3400 sheet: None (None), residues: 0 loop : 0.26 (0.12), residues: 2640 =============================================================================== Job complete usr+sys time: 17329.47 seconds wall clock time: 301 minutes 47.69 seconds (18107.69 seconds total)