Starting phenix.real_space_refine (version: dev) on Wed Feb 22 03:35:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sag_10130/02_2023/6sag_10130_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sag_10130/02_2023/6sag_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_10130/02_2023/6sag_10130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sag_10130/02_2023/6sag_10130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sag_10130/02_2023/6sag_10130_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sag_10130/02_2023/6sag_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 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} 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: 23.43, per 1000 atoms: 0.43 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: 20.69 Conformation dependent library (CDL) restraints added in 5.7 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: 13.59 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: 15.88 Time building geometry restraints manager: 22.05 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: 4.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 27.220 Check model and map are aligned: 0.630 Process input model: 120.460 Find NCS groups from input model: 3.080 Set up NCS constraints: 0.900 Set refine NCS operators: 0.000 Set scattering table: 0.380 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:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 169.460 ------------------------------------------------------------------------------- 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 : 5.132 Fit side-chains outliers start: 0 outliers final: 2 residues processed: 894 average time/residue: 1.2884 time to fit residues: 1478.1052 Evaluate side-chains 733 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 731 time to evaluate : 4.884 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.4119 time to fit residues: 7.6864 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.7182 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 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 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: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.197 52320 Z= 0.451 Angle : 1.328 42.195 72000 Z= 0.701 Chirality : 0.071 1.390 8520 Planarity : 0.016 0.429 8920 Dihedral : 9.351 77.108 8080 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.55 % Favored : 95.13 % Rotamer Outliers : 2.78 % Cbeta Deviations : 0.15 % 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: -2.03 (0.10), residues: 6040 helix: -1.08 (0.08), residues: 3400 sheet: None (None), residues: 0 loop : -1.59 (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 970 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 820 time to evaluate : 4.805 Fit side-chains outliers start: 150 outliers final: 44 residues processed: 881 average time/residue: 1.2710 time to fit residues: 1445.0316 Evaluate side-chains 770 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 726 time to evaluate : 4.784 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 25 residues processed: 23 average time/residue: 0.6329 time to fit residues: 28.9771 ------------------------------------------------------------------------------- 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: 6.9990 chunk 169 optimal weight: 30.0000 chunk 453 optimal weight: 5.9990 chunk 371 optimal weight: 6.9990 chunk 150 optimal weight: 30.0000 chunk 545 optimal weight: 0.6980 chunk 589 optimal weight: 10.0000 chunk 486 optimal weight: 6.9990 chunk 541 optimal weight: 0.8980 chunk 186 optimal weight: 10.0000 chunk 437 optimal weight: 6.9990 overall best weight: 4.3186 ------------------------------------------------------------------------------- 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 0 29 ASN 6 29 ASN 8 29 ASN a 29 ASN c 29 ASN e 29 ASN g 29 ASN i 29 ASN m 29 ASN o 29 ASN u 57 GLN w 29 ASN y 29 ASN AC 29 ASN AO 29 ASN AQ 29 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 52320 Z= 0.199 Angle : 0.572 7.464 72000 Z= 0.301 Chirality : 0.040 0.215 8520 Planarity : 0.006 0.052 8920 Dihedral : 8.390 58.638 8080 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.10), residues: 6040 helix: 1.05 (0.09), residues: 3360 sheet: None (None), residues: 0 loop : -0.63 (0.12), residues: 2680 *********************** 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 902 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 804 time to evaluate : 4.879 Fit side-chains outliers start: 98 outliers final: 49 residues processed: 842 average time/residue: 1.3573 time to fit residues: 1452.1273 Evaluate side-chains 791 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 742 time to evaluate : 4.784 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 36 residues processed: 18 average time/residue: 0.4771 time to fit residues: 21.2102 ------------------------------------------------------------------------------- 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: 9.9990 chunk 410 optimal weight: 8.9990 chunk 283 optimal weight: 8.9990 chunk 60 optimal weight: 30.0000 chunk 260 optimal weight: 9.9990 chunk 366 optimal weight: 10.0000 chunk 547 optimal weight: 9.9990 chunk 579 optimal weight: 6.9990 chunk 286 optimal weight: 0.8980 chunk 519 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 39 GLN 0 29 ASN 4 29 ASN 6 29 ASN 8 29 ASN a 29 ASN e 29 ASN g 29 ASN g 101 ASN i 29 ASN k 29 ASN k 57 GLN m 29 ASN o 29 ASN o 57 GLN q 29 ASN u 29 ASN u 57 GLN w 29 ASN y 29 ASN AE 29 ASN AI 29 ASN AO 29 ASN AQ 29 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 52320 Z= 0.207 Angle : 0.569 6.490 72000 Z= 0.300 Chirality : 0.040 0.231 8520 Planarity : 0.006 0.055 8920 Dihedral : 8.357 58.567 8080 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 2.00 % 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: 1.11 (0.11), residues: 6040 helix: 1.47 (0.09), residues: 3400 sheet: None (None), residues: 0 loop : -0.16 (0.12), residues: 2640 *********************** 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 892 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 784 time to evaluate : 4.848 Fit side-chains outliers start: 108 outliers final: 63 residues processed: 825 average time/residue: 1.3610 time to fit residues: 1428.4059 Evaluate side-chains 816 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 753 time to evaluate : 4.780 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 35 residues processed: 31 average time/residue: 0.5163 time to fit residues: 33.9339 ------------------------------------------------------------------------------- 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: 9.9990 chunk 329 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 431 optimal weight: 5.9990 chunk 239 optimal weight: 8.9990 chunk 494 optimal weight: 30.0000 chunk 400 optimal weight: 0.5980 chunk 0 optimal weight: 30.0000 chunk 296 optimal weight: 20.0000 chunk 520 optimal weight: 0.9980 chunk 146 optimal weight: 20.0000 overall best weight: 5.3186 ------------------------------------------------------------------------------- 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 k 57 GLN m 29 ASN o 29 ASN q 29 ASN u 29 ASN u 57 GLN u 127 ASN w 29 ASN y 29 ASN AE 29 ASN AI 29 ASN AO 29 ASN AQ 29 ASN AQ 57 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 52320 Z= 0.215 Angle : 0.573 6.825 72000 Z= 0.303 Chirality : 0.040 0.241 8520 Planarity : 0.006 0.055 8920 Dihedral : 8.368 58.553 8080 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 2.44 % 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: 1.31 (0.11), residues: 6040 helix: 1.65 (0.09), residues: 3360 sheet: None (None), residues: 0 loop : -0.08 (0.12), residues: 2680 *********************** 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 903 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 771 time to evaluate : 4.851 Fit side-chains outliers start: 132 outliers final: 75 residues processed: 824 average time/residue: 1.3823 time to fit residues: 1445.4925 Evaluate side-chains 827 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 752 time to evaluate : 4.825 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 39 residues processed: 40 average time/residue: 0.4470 time to fit residues: 38.5426 ------------------------------------------------------------------------------- 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: 30.0000 chunk 522 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 340 optimal weight: 0.4980 chunk 143 optimal weight: 20.0000 chunk 580 optimal weight: 8.9990 chunk 481 optimal weight: 20.0000 chunk 268 optimal weight: 2.9990 chunk 48 optimal weight: 20.0000 chunk 192 optimal weight: 30.0000 chunk 304 optimal weight: 20.0000 overall best weight: 6.4990 ------------------------------------------------------------------------------- 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 k 57 GLN m 29 ASN o 29 ASN q 29 ASN u 29 ASN u 57 GLN w 29 ASN y 29 ASN AA 29 ASN AE 29 ASN AI 29 ASN AO 29 ASN AQ 29 ASN AQ 57 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 52320 Z= 0.248 Angle : 0.606 6.460 72000 Z= 0.321 Chirality : 0.041 0.214 8520 Planarity : 0.006 0.061 8920 Dihedral : 8.428 58.506 8080 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 2.50 % 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: 1.29 (0.10), residues: 6040 helix: 1.52 (0.09), residues: 3400 sheet: None (None), residues: 0 loop : 0.06 (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 903 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 768 time to evaluate : 4.983 Fit side-chains outliers start: 135 outliers final: 73 residues processed: 829 average time/residue: 1.3805 time to fit residues: 1453.6798 Evaluate side-chains 826 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 753 time to evaluate : 4.816 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 38 residues processed: 39 average time/residue: 0.4471 time to fit residues: 37.7658 ------------------------------------------------------------------------------- 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: 6.9990 chunk 330 optimal weight: 20.0000 chunk 423 optimal weight: 10.0000 chunk 328 optimal weight: 9.9990 chunk 488 optimal weight: 20.0000 chunk 324 optimal weight: 6.9990 chunk 578 optimal weight: 30.0000 chunk 361 optimal weight: 20.0000 chunk 352 optimal weight: 4.9990 chunk 266 optimal weight: 20.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- 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 k 57 GLN m 29 ASN o 29 ASN q 29 ASN u 29 ASN u 57 GLN w 29 ASN y 29 ASN AA 29 ASN AE 29 ASN AI 29 ASN AM 29 ASN AO 29 ASN AQ 29 ASN AQ 57 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 52320 Z= 0.286 Angle : 0.641 6.751 72000 Z= 0.342 Chirality : 0.043 0.209 8520 Planarity : 0.007 0.065 8920 Dihedral : 8.484 58.432 8080 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % 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: 1.23 (0.10), residues: 6040 helix: 1.46 (0.09), residues: 3400 sheet: None (None), residues: 0 loop : 0.07 (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 889 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 768 time to evaluate : 4.806 Fit side-chains outliers start: 121 outliers final: 81 residues processed: 821 average time/residue: 1.3797 time to fit residues: 1439.5164 Evaluate side-chains 836 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 755 time to evaluate : 4.821 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 41 residues processed: 43 average time/residue: 0.4417 time to fit residues: 40.9869 ------------------------------------------------------------------------------- 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: 30.0000 chunk 230 optimal weight: 6.9990 chunk 345 optimal weight: 10.0000 chunk 174 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 chunk 367 optimal weight: 20.0000 chunk 393 optimal weight: 10.0000 chunk 285 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 454 optimal weight: 20.0000 overall best weight: 8.1994 ------------------------------------------------------------------------------- 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 k 57 GLN m 29 ASN o 29 ASN q 29 ASN u 29 ASN u 33 ASN w 29 ASN y 29 ASN AA 29 ASN AE 29 ASN AI 29 ASN AM 29 ASN AO 29 ASN AQ 29 ASN AQ 57 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 52320 Z= 0.296 Angle : 0.650 9.719 72000 Z= 0.346 Chirality : 0.044 0.202 8520 Planarity : 0.007 0.064 8920 Dihedral : 8.494 58.384 8080 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 1.91 % 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: 1.22 (0.10), residues: 6040 helix: 1.44 (0.09), residues: 3400 sheet: None (None), residues: 0 loop : 0.08 (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 871 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 768 time to evaluate : 4.882 Fit side-chains outliers start: 103 outliers final: 66 residues processed: 817 average time/residue: 1.4031 time to fit residues: 1454.9165 Evaluate side-chains 819 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 753 time to evaluate : 4.946 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 45 residues processed: 24 average time/residue: 0.5521 time to fit residues: 28.5699 ------------------------------------------------------------------------------- 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: 7.9990 chunk 505 optimal weight: 9.9990 chunk 538 optimal weight: 10.0000 chunk 553 optimal weight: 9.9990 chunk 324 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 chunk 423 optimal weight: 10.0000 chunk 165 optimal weight: 20.0000 chunk 486 optimal weight: 20.0000 chunk 509 optimal weight: 0.0970 overall best weight: 5.4186 ------------------------------------------------------------------------------- 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 k 57 GLN m 29 ASN o 29 ASN q 29 ASN u 29 ASN w 29 ASN y 29 ASN AA 29 ASN AE 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: 0.8754 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 52320 Z= 0.218 Angle : 0.581 6.648 72000 Z= 0.308 Chirality : 0.040 0.258 8520 Planarity : 0.006 0.056 8920 Dihedral : 8.385 58.544 8080 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.10), residues: 6040 helix: 1.64 (0.09), residues: 3400 sheet: None (None), residues: 0 loop : 0.18 (0.12), residues: 2640 *********************** 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 856 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 758 time to evaluate : 4.969 Fit side-chains outliers start: 98 outliers final: 70 residues processed: 810 average time/residue: 1.3927 time to fit residues: 1432.7346 Evaluate side-chains 820 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 750 time to evaluate : 4.829 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 44 residues processed: 29 average time/residue: 0.4265 time to fit residues: 29.2641 ------------------------------------------------------------------------------- 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: 5.9990 chunk 353 optimal weight: 10.0000 chunk 569 optimal weight: 5.9990 chunk 347 optimal weight: 6.9990 chunk 270 optimal weight: 7.9990 chunk 396 optimal weight: 9.9990 chunk 597 optimal weight: 10.0000 chunk 550 optimal weight: 0.7980 chunk 475 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 chunk 367 optimal weight: 2.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- 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 k 57 GLN m 29 ASN o 29 ASN q 29 ASN u 29 ASN w 29 ASN y 29 ASN AA 29 ASN AE 29 ASN AI 29 ASN AM 29 ASN AO 29 ASN AQ 29 ASN AQ 57 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 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 0.046 52320 Z= 0.196 Angle : 0.562 9.772 72000 Z= 0.296 Chirality : 0.040 0.313 8520 Planarity : 0.006 0.051 8920 Dihedral : 8.340 58.584 8080 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 1.15 % 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: 1.58 (0.11), residues: 6040 helix: 1.82 (0.09), residues: 3360 sheet: None (None), residues: 0 loop : 0.14 (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 813 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 751 time to evaluate : 4.964 Fit side-chains outliers start: 62 outliers final: 52 residues processed: 794 average time/residue: 1.4435 time to fit residues: 1459.0520 Evaluate side-chains 795 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 743 time to evaluate : 4.854 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 46 residues processed: 10 average time/residue: 0.4363 time to fit residues: 14.3792 ------------------------------------------------------------------------------- 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: 9.9990 chunk 378 optimal weight: 10.0000 chunk 507 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 438 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 476 optimal weight: 20.0000 chunk 199 optimal weight: 20.0000 chunk 489 optimal weight: 4.9990 chunk 60 optimal weight: 30.0000 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 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 k 57 GLN m 29 ASN o 29 ASN q 29 ASN u 29 ASN w 29 ASN y 29 ASN AA 29 ASN AE 29 ASN AM 29 ASN AO 29 ASN AQ 29 ASN AQ 57 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.143298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.118255 restraints weight = 39967.389| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 0.70 r_work: 0.3164 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work: 0.2887 rms_B_bonded: 4.94 restraints_weight: 0.1250 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 52320 Z= 0.268 Angle : 0.630 9.982 72000 Z= 0.335 Chirality : 0.043 0.357 8520 Planarity : 0.006 0.063 8920 Dihedral : 8.459 58.485 8080 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 1.37 % 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: 1.37 (0.10), residues: 6040 helix: 1.54 (0.09), residues: 3400 sheet: None (None), residues: 0 loop : 0.18 (0.12), residues: 2640 =============================================================================== Job complete usr+sys time: 20806.37 seconds wall clock time: 360 minutes 58.89 seconds (21658.89 seconds total)