Starting phenix.real_space_refine on Wed Jan 17 18:52:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sag_10130/01_2024/6sag_10130_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sag_10130/01_2024/6sag_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_10130/01_2024/6sag_10130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sag_10130/01_2024/6sag_10130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sag_10130/01_2024/6sag_10130_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sag_10130/01_2024/6sag_10130_updated.pdb" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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 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. 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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 21.54, per 1000 atoms: 0.40 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: 20.08 Conformation dependent library (CDL) restraints added in 6.9 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: 18.33 Creating SS restraints... Processing helix chain 'A' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE A 10 " --> pdb=" O PRO A 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL A 11 " --> pdb=" O SER A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU A 31 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY A 32 " --> pdb=" O THR A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 50 Processing helix chain 'A' and resid 74 through 86 Proline residue: A 78 - end of helix Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU A 131 " --> pdb=" O ASN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 Processing helix chain 'B' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE B 10 " --> pdb=" O PRO B 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL B 11 " --> pdb=" O SER B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 32 removed outlier: 3.621A pdb=" N LEU B 31 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY B 32 " --> pdb=" O THR B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 50 Processing helix chain 'B' and resid 74 through 86 Proline residue: B 78 - end of helix Processing helix chain 'B' and resid 92 through 96 Processing helix chain 'B' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU B 131 " --> pdb=" O ASN B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 148 Processing helix chain 'D' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE D 10 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL D 11 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU D 31 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY D 32 " --> pdb=" O THR D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 74 through 86 Proline residue: D 78 - end of helix Processing helix chain 'D' and resid 92 through 96 Processing helix chain 'D' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU D 131 " --> pdb=" O ASN D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 148 Processing helix chain 'F' and resid 7 through 13 removed outlier: 3.706A pdb=" N PHE F 10 " --> pdb=" O PRO F 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL F 11 " --> pdb=" O SER F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU F 31 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY F 32 " --> pdb=" O THR F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 50 Processing helix chain 'F' and resid 74 through 86 Proline residue: F 78 - end of helix Processing helix chain 'F' and resid 92 through 96 Processing helix chain 'F' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU F 131 " --> pdb=" O ASN F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 148 Processing helix chain 'H' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE H 10 " --> pdb=" O PRO H 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL H 11 " --> pdb=" O SER H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 32 removed outlier: 3.619A pdb=" N LEU H 31 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY H 32 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 74 through 86 Proline residue: H 78 - end of helix Processing helix chain 'H' and resid 92 through 96 Processing helix chain 'H' and resid 104 through 133 removed outlier: 3.704A pdb=" N GLU H 131 " --> pdb=" O ASN H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 148 Processing helix chain 'J' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE J 10 " --> pdb=" O PRO J 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL J 11 " --> pdb=" O SER J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU J 31 " --> pdb=" O CYS J 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY J 32 " --> pdb=" O THR J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 50 Processing helix chain 'J' and resid 74 through 86 Proline residue: J 78 - end of helix Processing helix chain 'J' and resid 92 through 96 Processing helix chain 'J' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU J 131 " --> pdb=" O ASN J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 148 Processing helix chain 'L' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE L 10 " --> pdb=" O PRO L 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL L 11 " --> pdb=" O SER L 8 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU L 31 " --> pdb=" O CYS L 27 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY L 32 " --> pdb=" O THR L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 50 Processing helix chain 'L' and resid 74 through 86 Proline residue: L 78 - end of helix Processing helix chain 'L' and resid 92 through 96 Processing helix chain 'L' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU L 131 " --> pdb=" O ASN L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 148 Processing helix chain 'N' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE N 10 " --> pdb=" O PRO N 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL N 11 " --> pdb=" O SER N 8 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU N 31 " --> pdb=" O CYS N 27 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY N 32 " --> pdb=" O THR N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 50 Processing helix chain 'N' and resid 74 through 86 Proline residue: N 78 - end of helix Processing helix chain 'N' and resid 92 through 96 Processing helix chain 'N' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU N 131 " --> pdb=" O ASN N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 141 through 148 Processing helix chain 'P' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE P 10 " --> pdb=" O PRO P 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL P 11 " --> pdb=" O SER P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU P 31 " --> pdb=" O CYS P 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY P 32 " --> pdb=" O THR P 28 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 50 Processing helix chain 'P' and resid 74 through 86 Proline residue: P 78 - end of helix Processing helix chain 'P' and resid 92 through 96 Processing helix chain 'P' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU P 131 " --> pdb=" O ASN P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 141 through 148 Processing helix chain 'S' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE S 10 " --> pdb=" O PRO S 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL S 11 " --> pdb=" O SER S 8 " (cutoff:3.500A) Processing helix chain 'S' and resid 20 through 32 removed outlier: 3.619A pdb=" N LEU S 31 " --> pdb=" O CYS S 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY S 32 " --> pdb=" O THR S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 50 Processing helix chain 'S' and resid 74 through 86 Proline residue: S 78 - end of helix Processing helix chain 'S' and resid 92 through 96 Processing helix chain 'S' and resid 104 through 133 removed outlier: 3.704A pdb=" N GLU S 131 " --> pdb=" O ASN S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 141 through 148 Processing helix chain 'U' and resid 7 through 13 removed outlier: 3.704A pdb=" N PHE U 10 " --> pdb=" O PRO U 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL U 11 " --> pdb=" O SER U 8 " (cutoff:3.500A) Processing helix chain 'U' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU U 31 " --> pdb=" O CYS U 27 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY U 32 " --> pdb=" O THR U 28 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 50 Processing helix chain 'U' and resid 74 through 86 Proline residue: U 78 - end of helix Processing helix chain 'U' and resid 92 through 96 Processing helix chain 'U' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU U 131 " --> pdb=" O ASN U 127 " (cutoff:3.500A) Processing helix chain 'U' and resid 141 through 148 Processing helix chain 'W' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE W 10 " --> pdb=" O PRO W 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL W 11 " --> pdb=" O SER W 8 " (cutoff:3.500A) Processing helix chain 'W' and resid 20 through 32 removed outlier: 3.619A pdb=" N LEU W 31 " --> pdb=" O CYS W 27 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY W 32 " --> pdb=" O THR W 28 " (cutoff:3.500A) Processing helix chain 'W' and resid 38 through 50 Processing helix chain 'W' and resid 74 through 86 Proline residue: W 78 - end of helix Processing helix chain 'W' and resid 92 through 96 Processing helix chain 'W' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU W 131 " --> pdb=" O ASN W 127 " (cutoff:3.500A) Processing helix chain 'W' and resid 141 through 148 Processing helix chain 'Y' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE Y 10 " --> pdb=" O PRO Y 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL Y 11 " --> pdb=" O SER Y 8 " (cutoff:3.500A) Processing helix chain 'Y' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU Y 31 " --> pdb=" O CYS Y 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY Y 32 " --> pdb=" O THR Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 38 through 50 Processing helix chain 'Y' and resid 74 through 86 Proline residue: Y 78 - end of helix Processing helix chain 'Y' and resid 92 through 96 Processing helix chain 'Y' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU Y 131 " --> pdb=" O ASN Y 127 " (cutoff:3.500A) Processing helix chain 'Y' and resid 141 through 148 Processing helix chain '0' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE 0 10 " --> pdb=" O PRO 0 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL 0 11 " --> pdb=" O SER 0 8 " (cutoff:3.500A) Processing helix chain '0' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU 0 31 " --> pdb=" O CYS 0 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY 0 32 " --> pdb=" O THR 0 28 " (cutoff:3.500A) Processing helix chain '0' and resid 38 through 50 Processing helix chain '0' and resid 74 through 86 Proline residue: 0 78 - end of helix Processing helix chain '0' and resid 92 through 96 Processing helix chain '0' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU 0 131 " --> pdb=" O ASN 0 127 " (cutoff:3.500A) Processing helix chain '0' and resid 141 through 148 Processing helix chain '2' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE 2 10 " --> pdb=" O PRO 2 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL 2 11 " --> pdb=" O SER 2 8 " (cutoff:3.500A) Processing helix chain '2' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU 2 31 " --> pdb=" O CYS 2 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY 2 32 " --> pdb=" O THR 2 28 " (cutoff:3.500A) Processing helix chain '2' and resid 38 through 50 Processing helix chain '2' and resid 74 through 86 Proline residue: 2 78 - end of helix Processing helix chain '2' and resid 92 through 96 Processing helix chain '2' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU 2 131 " --> pdb=" O ASN 2 127 " (cutoff:3.500A) Processing helix chain '2' and resid 141 through 148 Processing helix chain '4' and resid 7 through 13 removed outlier: 3.704A pdb=" N PHE 4 10 " --> pdb=" O PRO 4 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL 4 11 " --> pdb=" O SER 4 8 " (cutoff:3.500A) Processing helix chain '4' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU 4 31 " --> pdb=" O CYS 4 27 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY 4 32 " --> pdb=" O THR 4 28 " (cutoff:3.500A) Processing helix chain '4' and resid 38 through 50 Processing helix chain '4' and resid 74 through 86 Proline residue: 4 78 - end of helix Processing helix chain '4' and resid 92 through 96 Processing helix chain '4' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU 4 131 " --> pdb=" O ASN 4 127 " (cutoff:3.500A) Processing helix chain '4' and resid 141 through 148 Processing helix chain '6' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE 6 10 " --> pdb=" O PRO 6 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL 6 11 " --> pdb=" O SER 6 8 " (cutoff:3.500A) Processing helix chain '6' and resid 20 through 32 removed outlier: 3.619A pdb=" N LEU 6 31 " --> pdb=" O CYS 6 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY 6 32 " --> pdb=" O THR 6 28 " (cutoff:3.500A) Processing helix chain '6' and resid 38 through 50 Processing helix chain '6' and resid 74 through 86 Proline residue: 6 78 - end of helix Processing helix chain '6' and resid 92 through 96 Processing helix chain '6' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU 6 131 " --> pdb=" O ASN 6 127 " (cutoff:3.500A) Processing helix chain '6' and resid 141 through 148 Processing helix chain '8' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE 8 10 " --> pdb=" O PRO 8 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL 8 11 " --> pdb=" O SER 8 8 " (cutoff:3.500A) Processing helix chain '8' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU 8 31 " --> pdb=" O CYS 8 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY 8 32 " --> pdb=" O THR 8 28 " (cutoff:3.500A) Processing helix chain '8' and resid 38 through 50 Processing helix chain '8' and resid 74 through 86 Proline residue: 8 78 - end of helix Processing helix chain '8' and resid 92 through 96 Processing helix chain '8' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU 8 131 " --> pdb=" O ASN 8 127 " (cutoff:3.500A) Processing helix chain '8' and resid 141 through 148 Processing helix chain 'a' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE a 10 " --> pdb=" O PRO a 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL a 11 " --> pdb=" O SER a 8 " (cutoff:3.500A) Processing helix chain 'a' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU a 31 " --> pdb=" O CYS a 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY a 32 " --> pdb=" O THR a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 50 Processing helix chain 'a' and resid 74 through 86 Proline residue: a 78 - end of helix Processing helix chain 'a' and resid 92 through 96 Processing helix chain 'a' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU a 131 " --> pdb=" O ASN a 127 " (cutoff:3.500A) Processing helix chain 'a' and resid 141 through 148 Processing helix chain 'c' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE c 10 " --> pdb=" O PRO c 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL c 11 " --> pdb=" O SER c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU c 31 " --> pdb=" O CYS c 27 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY c 32 " --> pdb=" O THR c 28 " (cutoff:3.500A) Processing helix chain 'c' and resid 38 through 50 Processing helix chain 'c' and resid 74 through 86 Proline residue: c 78 - end of helix Processing helix chain 'c' and resid 92 through 96 Processing helix chain 'c' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU c 131 " --> pdb=" O ASN c 127 " (cutoff:3.500A) Processing helix chain 'c' and resid 141 through 148 Processing helix chain 'e' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE e 10 " --> pdb=" O PRO e 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL e 11 " --> pdb=" O SER e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU e 31 " --> pdb=" O CYS e 27 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY e 32 " --> pdb=" O THR e 28 " (cutoff:3.500A) Processing helix chain 'e' and resid 38 through 50 Processing helix chain 'e' and resid 74 through 86 Proline residue: e 78 - end of helix Processing helix chain 'e' and resid 92 through 96 Processing helix chain 'e' and resid 104 through 133 removed outlier: 3.704A pdb=" N GLU e 131 " --> pdb=" O ASN e 127 " (cutoff:3.500A) Processing helix chain 'e' and resid 141 through 148 Processing helix chain 'g' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE g 10 " --> pdb=" O PRO g 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL g 11 " --> pdb=" O SER g 8 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 32 removed outlier: 3.619A pdb=" N LEU g 31 " --> pdb=" O CYS g 27 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY g 32 " --> pdb=" O THR g 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 38 through 50 Processing helix chain 'g' and resid 74 through 86 Proline residue: g 78 - end of helix Processing helix chain 'g' and resid 92 through 96 Processing helix chain 'g' and resid 104 through 133 removed outlier: 3.704A pdb=" N GLU g 131 " --> pdb=" O ASN g 127 " (cutoff:3.500A) Processing helix chain 'g' and resid 141 through 148 Processing helix chain 'i' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE i 10 " --> pdb=" O PRO i 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL i 11 " --> pdb=" O SER i 8 " (cutoff:3.500A) Processing helix chain 'i' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU i 31 " --> pdb=" O CYS i 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY i 32 " --> pdb=" O THR i 28 " (cutoff:3.500A) Processing helix chain 'i' and resid 38 through 50 Processing helix chain 'i' and resid 74 through 86 Proline residue: i 78 - end of helix Processing helix chain 'i' and resid 92 through 96 Processing helix chain 'i' and resid 104 through 133 removed outlier: 3.704A pdb=" N GLU i 131 " --> pdb=" O ASN i 127 " (cutoff:3.500A) Processing helix chain 'i' and resid 141 through 148 Processing helix chain 'k' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE k 10 " --> pdb=" O PRO k 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL k 11 " --> pdb=" O SER k 8 " (cutoff:3.500A) Processing helix chain 'k' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU k 31 " --> pdb=" O CYS k 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY k 32 " --> pdb=" O THR k 28 " (cutoff:3.500A) Processing helix chain 'k' and resid 38 through 50 Processing helix chain 'k' and resid 74 through 86 Proline residue: k 78 - end of helix Processing helix chain 'k' and resid 92 through 96 Processing helix chain 'k' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU k 131 " --> pdb=" O ASN k 127 " (cutoff:3.500A) Processing helix chain 'k' and resid 141 through 148 Processing helix chain 'm' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE m 10 " --> pdb=" O PRO m 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL m 11 " --> pdb=" O SER m 8 " (cutoff:3.500A) Processing helix chain 'm' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU m 31 " --> pdb=" O CYS m 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY m 32 " --> pdb=" O THR m 28 " (cutoff:3.500A) Processing helix chain 'm' and resid 38 through 50 Processing helix chain 'm' and resid 74 through 86 Proline residue: m 78 - end of helix Processing helix chain 'm' and resid 92 through 96 Processing helix chain 'm' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU m 131 " --> pdb=" O ASN m 127 " (cutoff:3.500A) Processing helix chain 'm' and resid 141 through 148 Processing helix chain 'o' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE o 10 " --> pdb=" O PRO o 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL o 11 " --> pdb=" O SER o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU o 31 " --> pdb=" O CYS o 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY o 32 " --> pdb=" O THR o 28 " (cutoff:3.500A) Processing helix chain 'o' and resid 38 through 50 Processing helix chain 'o' and resid 74 through 86 Proline residue: o 78 - end of helix Processing helix chain 'o' and resid 92 through 96 Processing helix chain 'o' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU o 131 " --> pdb=" O ASN o 127 " (cutoff:3.500A) Processing helix chain 'o' and resid 141 through 148 Processing helix chain 'q' and resid 7 through 13 removed outlier: 3.704A pdb=" N PHE q 10 " --> pdb=" O PRO q 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL q 11 " --> pdb=" O SER q 8 " (cutoff:3.500A) Processing helix chain 'q' and resid 20 through 32 removed outlier: 3.619A pdb=" N LEU q 31 " --> pdb=" O CYS q 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY q 32 " --> pdb=" O THR q 28 " (cutoff:3.500A) Processing helix chain 'q' and resid 38 through 50 Processing helix chain 'q' and resid 74 through 86 Proline residue: q 78 - end of helix Processing helix chain 'q' and resid 92 through 96 Processing helix chain 'q' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU q 131 " --> pdb=" O ASN q 127 " (cutoff:3.500A) Processing helix chain 'q' and resid 141 through 148 Processing helix chain 's' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE s 10 " --> pdb=" O PRO s 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL s 11 " --> pdb=" O SER s 8 " (cutoff:3.500A) Processing helix chain 's' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU s 31 " --> pdb=" O CYS s 27 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY s 32 " --> pdb=" O THR s 28 " (cutoff:3.500A) Processing helix chain 's' and resid 38 through 50 Processing helix chain 's' and resid 74 through 86 Proline residue: s 78 - end of helix Processing helix chain 's' and resid 92 through 96 Processing helix chain 's' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU s 131 " --> pdb=" O ASN s 127 " (cutoff:3.500A) Processing helix chain 's' and resid 141 through 148 Processing helix chain 'u' and resid 7 through 13 removed outlier: 3.704A pdb=" N PHE u 10 " --> pdb=" O PRO u 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL u 11 " --> pdb=" O SER u 8 " (cutoff:3.500A) Processing helix chain 'u' and resid 20 through 32 removed outlier: 3.619A pdb=" N LEU u 31 " --> pdb=" O CYS u 27 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY u 32 " --> pdb=" O THR u 28 " (cutoff:3.500A) Processing helix chain 'u' and resid 38 through 50 Processing helix chain 'u' and resid 74 through 86 Proline residue: u 78 - end of helix Processing helix chain 'u' and resid 92 through 96 Processing helix chain 'u' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU u 131 " --> pdb=" O ASN u 127 " (cutoff:3.500A) Processing helix chain 'u' and resid 141 through 148 Processing helix chain 'w' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE w 10 " --> pdb=" O PRO w 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL w 11 " --> pdb=" O SER w 8 " (cutoff:3.500A) Processing helix chain 'w' and resid 20 through 32 removed outlier: 3.619A pdb=" N LEU w 31 " --> pdb=" O CYS w 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY w 32 " --> pdb=" O THR w 28 " (cutoff:3.500A) Processing helix chain 'w' and resid 38 through 50 Processing helix chain 'w' and resid 74 through 86 Proline residue: w 78 - end of helix Processing helix chain 'w' and resid 92 through 96 Processing helix chain 'w' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLU w 131 " --> pdb=" O ASN w 127 " (cutoff:3.500A) Processing helix chain 'w' and resid 141 through 148 Processing helix chain 'y' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHE y 10 " --> pdb=" O PRO y 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL y 11 " --> pdb=" O SER y 8 " (cutoff:3.500A) Processing helix chain 'y' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEU y 31 " --> pdb=" O CYS y 27 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY y 32 " --> pdb=" O THR y 28 " (cutoff:3.500A) Processing helix chain 'y' and resid 38 through 50 Processing helix chain 'y' and resid 74 through 86 Proline residue: y 78 - end of helix Processing helix chain 'y' and resid 92 through 96 Processing helix chain 'y' and resid 104 through 133 removed outlier: 3.702A pdb=" N GLU y 131 " --> pdb=" O ASN y 127 " (cutoff:3.500A) Processing helix chain 'y' and resid 141 through 148 Processing helix chain 'AA' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHEAA 10 " --> pdb=" O PROAA 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALAA 11 " --> pdb=" O SERAA 8 " (cutoff:3.500A) Processing helix chain 'AA' and resid 20 through 32 removed outlier: 3.619A pdb=" N LEUAA 31 " --> pdb=" O CYSAA 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLYAA 32 " --> pdb=" O THRAA 28 " (cutoff:3.500A) Processing helix chain 'AA' and resid 38 through 50 Processing helix chain 'AA' and resid 74 through 86 Proline residue: AA 78 - end of helix Processing helix chain 'AA' and resid 92 through 96 Processing helix chain 'AA' and resid 104 through 133 removed outlier: 3.704A pdb=" N GLUAA 131 " --> pdb=" O ASNAA 127 " (cutoff:3.500A) Processing helix chain 'AA' and resid 141 through 148 Processing helix chain 'AC' and resid 7 through 13 removed outlier: 3.704A pdb=" N PHEAC 10 " --> pdb=" O PROAC 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALAC 11 " --> pdb=" O SERAC 8 " (cutoff:3.500A) Processing helix chain 'AC' and resid 20 through 32 removed outlier: 3.619A pdb=" N LEUAC 31 " --> pdb=" O CYSAC 27 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLYAC 32 " --> pdb=" O THRAC 28 " (cutoff:3.500A) Processing helix chain 'AC' and resid 38 through 50 Processing helix chain 'AC' and resid 74 through 86 Proline residue: AC 78 - end of helix Processing helix chain 'AC' and resid 92 through 96 Processing helix chain 'AC' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLUAC 131 " --> pdb=" O ASNAC 127 " (cutoff:3.500A) Processing helix chain 'AC' and resid 141 through 148 Processing helix chain 'AE' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHEAE 10 " --> pdb=" O PROAE 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALAE 11 " --> pdb=" O SERAE 8 " (cutoff:3.500A) Processing helix chain 'AE' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEUAE 31 " --> pdb=" O CYSAE 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLYAE 32 " --> pdb=" O THRAE 28 " (cutoff:3.500A) Processing helix chain 'AE' and resid 38 through 50 Processing helix chain 'AE' and resid 74 through 86 Proline residue: AE 78 - end of helix Processing helix chain 'AE' and resid 92 through 96 Processing helix chain 'AE' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLUAE 131 " --> pdb=" O ASNAE 127 " (cutoff:3.500A) Processing helix chain 'AE' and resid 141 through 148 Processing helix chain 'AG' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHEAG 10 " --> pdb=" O PROAG 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALAG 11 " --> pdb=" O SERAG 8 " (cutoff:3.500A) Processing helix chain 'AG' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEUAG 31 " --> pdb=" O CYSAG 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLYAG 32 " --> pdb=" O THRAG 28 " (cutoff:3.500A) Processing helix chain 'AG' and resid 38 through 50 Processing helix chain 'AG' and resid 74 through 86 Proline residue: AG 78 - end of helix Processing helix chain 'AG' and resid 92 through 96 Processing helix chain 'AG' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLUAG 131 " --> pdb=" O ASNAG 127 " (cutoff:3.500A) Processing helix chain 'AG' and resid 141 through 148 Processing helix chain 'AI' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHEAI 10 " --> pdb=" O PROAI 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALAI 11 " --> pdb=" O SERAI 8 " (cutoff:3.500A) Processing helix chain 'AI' and resid 20 through 32 removed outlier: 3.619A pdb=" N LEUAI 31 " --> pdb=" O CYSAI 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLYAI 32 " --> pdb=" O THRAI 28 " (cutoff:3.500A) Processing helix chain 'AI' and resid 38 through 50 Processing helix chain 'AI' and resid 74 through 86 Proline residue: AI 78 - end of helix Processing helix chain 'AI' and resid 92 through 96 Processing helix chain 'AI' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLUAI 131 " --> pdb=" O ASNAI 127 " (cutoff:3.500A) Processing helix chain 'AI' and resid 141 through 148 Processing helix chain 'AK' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHEAK 10 " --> pdb=" O PROAK 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALAK 11 " --> pdb=" O SERAK 8 " (cutoff:3.500A) Processing helix chain 'AK' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEUAK 31 " --> pdb=" O CYSAK 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLYAK 32 " --> pdb=" O THRAK 28 " (cutoff:3.500A) Processing helix chain 'AK' and resid 38 through 50 Processing helix chain 'AK' and resid 74 through 86 Proline residue: AK 78 - end of helix Processing helix chain 'AK' and resid 92 through 96 Processing helix chain 'AK' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLUAK 131 " --> pdb=" O ASNAK 127 " (cutoff:3.500A) Processing helix chain 'AK' and resid 141 through 148 Processing helix chain 'AM' and resid 7 through 13 removed outlier: 3.706A pdb=" N PHEAM 10 " --> pdb=" O PROAM 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALAM 11 " --> pdb=" O SERAM 8 " (cutoff:3.500A) Processing helix chain 'AM' and resid 20 through 32 removed outlier: 3.619A pdb=" N LEUAM 31 " --> pdb=" O CYSAM 27 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLYAM 32 " --> pdb=" O THRAM 28 " (cutoff:3.500A) Processing helix chain 'AM' and resid 38 through 50 Processing helix chain 'AM' and resid 74 through 86 Proline residue: AM 78 - end of helix Processing helix chain 'AM' and resid 92 through 96 Processing helix chain 'AM' and resid 104 through 133 removed outlier: 3.704A pdb=" N GLUAM 131 " --> pdb=" O ASNAM 127 " (cutoff:3.500A) Processing helix chain 'AM' and resid 141 through 148 Processing helix chain 'AO' and resid 7 through 13 removed outlier: 3.705A pdb=" N PHEAO 10 " --> pdb=" O PROAO 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALAO 11 " --> pdb=" O SERAO 8 " (cutoff:3.500A) Processing helix chain 'AO' and resid 20 through 32 removed outlier: 3.620A pdb=" N LEUAO 31 " --> pdb=" O CYSAO 27 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLYAO 32 " --> pdb=" O THRAO 28 " (cutoff:3.500A) Processing helix chain 'AO' and resid 38 through 50 Processing helix chain 'AO' and resid 74 through 86 Proline residue: AO 78 - end of helix Processing helix chain 'AO' and resid 92 through 96 Processing helix chain 'AO' and resid 104 through 133 removed outlier: 3.704A pdb=" N GLUAO 131 " --> pdb=" O ASNAO 127 " (cutoff:3.500A) Processing helix chain 'AO' and resid 141 through 148 Processing helix chain 'AQ' and resid 7 through 13 removed outlier: 3.704A pdb=" N PHEAQ 10 " --> pdb=" O PROAQ 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALAQ 11 " --> pdb=" O SERAQ 8 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 20 through 32 removed outlier: 3.619A pdb=" N LEUAQ 31 " --> pdb=" O CYSAQ 27 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLYAQ 32 " --> pdb=" O THRAQ 28 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 38 through 50 Processing helix chain 'AQ' and resid 74 through 86 Proline residue: AQ 78 - end of helix Processing helix chain 'AQ' and resid 92 through 96 Processing helix chain 'AQ' and resid 104 through 133 removed outlier: 3.703A pdb=" N GLUAQ 131 " --> pdb=" O ASNAQ 127 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 141 through 148 Processing sheet with id= A, first strand: chain 'A' and resid 17 through 19 Processing sheet with id= B, first strand: chain 'B' and resid 17 through 19 Processing sheet with id= C, first strand: chain 'D' and resid 17 through 19 Processing sheet with id= D, first strand: chain 'F' and resid 17 through 19 Processing sheet with id= E, first strand: chain 'H' and resid 17 through 19 Processing sheet with id= F, first strand: chain 'J' and resid 17 through 19 Processing sheet with id= G, first strand: chain 'L' and resid 17 through 19 Processing sheet with id= H, first strand: chain 'N' and resid 17 through 19 Processing sheet with id= I, first strand: chain 'P' and resid 17 through 19 Processing sheet with id= J, first strand: chain 'S' and resid 17 through 19 Processing sheet with id= K, first strand: chain 'U' and resid 17 through 19 Processing sheet with id= L, first strand: chain 'W' and resid 17 through 19 Processing sheet with id= M, first strand: chain 'Y' and resid 17 through 19 Processing sheet with id= N, first strand: chain '0' and resid 17 through 19 Processing sheet with id= O, first strand: chain '2' and resid 17 through 19 Processing sheet with id= P, first strand: chain '4' and resid 17 through 19 Processing sheet with id= Q, first strand: chain '6' and resid 17 through 19 Processing sheet with id= R, first strand: chain '8' and resid 17 through 19 Processing sheet with id= S, first strand: chain 'a' and resid 17 through 19 Processing sheet with id= T, first strand: chain 'c' and resid 17 through 19 Processing sheet with id= U, first strand: chain 'e' and resid 17 through 19 Processing sheet with id= V, first strand: chain 'g' and resid 17 through 19 Processing sheet with id= W, first strand: chain 'i' and resid 17 through 19 Processing sheet with id= X, first strand: chain 'k' and resid 17 through 19 Processing sheet with id= Y, first strand: chain 'm' and resid 17 through 19 Processing sheet with id= Z, first strand: chain 'o' and resid 17 through 19 Processing sheet with id= AA, first strand: chain 'q' and resid 17 through 19 Processing sheet with id= AB, first strand: chain 's' and resid 17 through 19 Processing sheet with id= AC, first strand: chain 'u' and resid 17 through 19 Processing sheet with id= AD, first strand: chain 'w' and resid 17 through 19 Processing sheet with id= AE, first strand: chain 'y' and resid 17 through 19 Processing sheet with id= AF, first strand: chain 'AA' and resid 17 through 19 Processing sheet with id= AG, first strand: chain 'AC' and resid 17 through 19 Processing sheet with id= AH, first strand: chain 'AE' and resid 17 through 19 Processing sheet with id= AI, first strand: chain 'AG' and resid 17 through 19 Processing sheet with id= AJ, first strand: chain 'AI' and resid 17 through 19 Processing sheet with id= AK, first strand: chain 'AK' and resid 17 through 19 Processing sheet with id= AL, first strand: chain 'AM' and resid 17 through 19 Processing sheet with id= AM, first strand: chain 'AO' and resid 17 through 19 Processing sheet with id= AN, first strand: chain 'AQ' and resid 17 through 19 2240 hydrogen bonds defined for protein. 6480 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 16.62 Time building geometry restraints manager: 21.43 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: 27680 14.45 - 28.89: 2499 28.89 - 43.34: 404 43.34 - 57.78: 337 57.78 - 72.23: 200 Dihedral angle restraints: 31120 sinusoidal: 13040 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 31117 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 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: 3.930 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: 0.040 Extract box with map and model: 23.330 Check model and map are aligned: 0.590 Set scattering table: 0.380 Process input model: 125.770 Find NCS groups from input model: 3.120 Set up NCS constraints: 0.990 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 169.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 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 : 13.898 72.230 19280 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 % Allowed : 2.96 % Favored : 97.04 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP a 17 PHE 0.010 0.002 PHE B 35 TYR 0.013 0.002 TYRAI 72 ARG 0.004 0.001 ARGAO 122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 894 time to evaluate : 4.597 Fit side-chains REVERT: F 72 TYR cc_start: 0.8443 (m-80) cc_final: 0.8110 (m-80) REVERT: 2 79 LEU cc_start: 0.8596 (mt) cc_final: 0.8332 (mt) REVERT: 4 145 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8185 (mt-10) REVERT: 8 128 LEU cc_start: 0.8229 (tp) cc_final: 0.7914 (mt) REVERT: i 128 LEU cc_start: 0.8258 (tp) cc_final: 0.7832 (mp) REVERT: q 84 LEU cc_start: 0.8805 (mt) cc_final: 0.8590 (mt) outliers start: 0 outliers final: 2 residues processed: 894 average time/residue: 1.2676 time to fit residues: 1455.3872 Evaluate side-chains 734 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 732 time to evaluate : 4.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 133 ILE Chi-restraints excluded: chain AG residue 133 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.262 > 50: distance: 51 - 52: 3.122 distance: 51 - 54: 3.258 distance: 52 - 53: 3.652 distance: 54 - 55: 3.091 distance: 58 - 59: 5.932 distance: 58 - 64: 5.299 distance: 59 - 60: 7.413 distance: 59 - 62: 4.474 distance: 60 - 61: 6.746 distance: 60 - 65: 18.748 distance: 61 - 90: 11.003 distance: 62 - 63: 9.645 distance: 63 - 64: 6.666 distance: 65 - 66: 9.040 distance: 66 - 67: 5.344 distance: 66 - 69: 4.576 distance: 67 - 68: 7.270 distance: 68 - 98: 18.886 distance: 69 - 70: 8.650 distance: 69 - 71: 6.474 distance: 70 - 72: 12.986 distance: 73 - 74: 4.407 distance: 74 - 77: 14.021 distance: 75 - 76: 5.722 distance: 75 - 82: 8.685 distance: 76 - 106: 23.954 distance: 77 - 78: 14.850 distance: 78 - 79: 29.068 distance: 79 - 80: 26.143 distance: 79 - 81: 18.434 distance: 82 - 83: 10.780 distance: 83 - 84: 18.868 distance: 83 - 86: 23.138 distance: 84 - 85: 13.872 distance: 84 - 90: 19.832 distance: 85 - 114: 21.817 distance: 86 - 87: 62.262 distance: 87 - 88: 4.573 distance: 87 - 89: 44.649 distance: 90 - 91: 11.597 distance: 91 - 92: 10.998 distance: 91 - 94: 4.820 distance: 93 - 120: 29.140 distance: 94 - 95: 6.147 distance: 94 - 96: 5.760 distance: 95 - 97: 3.761 distance: 98 - 99: 8.428 distance: 99 - 100: 38.949 distance: 99 - 102: 18.606 distance: 100 - 101: 41.612 distance: 100 - 106: 46.766 distance: 101 - 127: 24.718 distance: 102 - 103: 17.475 distance: 103 - 104: 9.540 distance: 103 - 105: 11.622 distance: 106 - 107: 9.309 distance: 107 - 108: 20.696 distance: 107 - 110: 14.715 distance: 108 - 109: 19.012 distance: 108 - 114: 33.590 distance: 109 - 135: 33.450 distance: 110 - 111: 21.727 distance: 111 - 112: 10.612 distance: 111 - 113: 31.870 distance: 114 - 115: 16.340 distance: 115 - 118: 22.977 distance: 116 - 117: 12.473 distance: 118 - 119: 31.040 distance: 120 - 121: 15.597 distance: 121 - 122: 13.197 distance: 121 - 124: 13.718 distance: 122 - 123: 42.351 distance: 122 - 127: 17.693 distance: 124 - 125: 7.632 distance: 124 - 126: 9.275