Starting phenix.real_space_refine (version: dev) on Sun Dec 11 22:56:41 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sca_25031/12_2022/7sca_25031_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sca_25031/12_2022/7sca_25031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sca_25031/12_2022/7sca_25031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sca_25031/12_2022/7sca_25031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sca_25031/12_2022/7sca_25031_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sca_25031/12_2022/7sca_25031_updated.pdb" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.174 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "AA GLU 109": "OE1" <-> "OE2" Residue "AA ASP 116": "OD1" <-> "OD2" Residue "AA ASP 123": "OD1" <-> "OD2" Residue "AA GLU 131": "OE1" <-> "OE2" Residue "AB ASP 25": "OD1" <-> "OD2" Residue "AB GLU 136": "OE1" <-> "OE2" Residue "AC GLU 7": "OE1" <-> "OE2" Residue "AC ASP 108": "OD1" <-> "OD2" Residue "AC GLU 109": "OE1" <-> "OE2" Residue "AC ASP 123": "OD1" <-> "OD2" Residue "AC ASP 145": "OD1" <-> "OD2" Residue "AC GLU 149": "OE1" <-> "OE2" Residue "AC ASP 155": "OD1" <-> "OD2" Residue "AD ASP 25": "OD1" <-> "OD2" Residue "AD GLU 136": "OE1" <-> "OE2" Residue "AD ASP 140": "OD1" <-> "OD2" Residue "AD ASP 144": "OD1" <-> "OD2" Residue "AD ASP 152": "OD1" <-> "OD2" Residue "AE GLU 7": "OE1" <-> "OE2" Residue "AE ASP 77": "OD1" <-> "OD2" Residue "AE GLU 109": "OE1" <-> "OE2" Residue "AE ASP 116": "OD1" <-> "OD2" Residue "AE ASP 123": "OD1" <-> "OD2" Residue "AF GLU 17": "OE1" <-> "OE2" Residue "AF GLU 62": "OE1" <-> "OE2" Residue "AF GLU 87": "OE1" <-> "OE2" Residue "AF ASP 140": "OD1" <-> "OD2" Residue "AG TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG ASP 123": "OD1" <-> "OD2" Residue "AG ASP 155": "OD1" <-> "OD2" Residue "AH GLU 33": "OE1" <-> "OE2" Residue "AH ASP 107": "OD1" <-> "OD2" Residue "AH GLU 159": "OE1" <-> "OE2" Residue "AH ASP 165": "OD1" <-> "OD2" Residue "AI GLU 7": "OE1" <-> "OE2" Residue "AI ASP 46": "OD1" <-> "OD2" Residue "AI ASP 116": "OD1" <-> "OD2" Residue "AI GLU 117": "OE1" <-> "OE2" Residue "AI GLU 149": "OE1" <-> "OE2" Residue "AJ GLU 62": "OE1" <-> "OE2" Residue "AJ GLU 115": "OE1" <-> "OE2" Residue "AJ GLU 159": "OE1" <-> "OE2" Residue "AK GLU 131": "OE1" <-> "OE2" Residue "AK GLU 149": "OE1" <-> "OE2" Residue "AL ASP 25": "OD1" <-> "OD2" Residue "AL GLU 62": "OE1" <-> "OE2" Residue "AL ASP 101": "OD1" <-> "OD2" Residue "AL ASP 144": "OD1" <-> "OD2" Residue "AM GLU 23": "OE1" <-> "OE2" Residue "AM ASP 116": "OD1" <-> "OD2" Residue "AM GLU 117": "OE1" <-> "OE2" Residue "AM GLU 131": "OE1" <-> "OE2" Residue "AM ASP 148": "OD1" <-> "OD2" Residue "AM GLU 149": "OE1" <-> "OE2" Residue "AN ASP 25": "OD1" <-> "OD2" Residue "AN GLU 33": "OE1" <-> "OE2" Residue "AN ASP 39": "OD1" <-> "OD2" Residue "AN ASP 101": "OD1" <-> "OD2" Residue "AN GLU 106": "OE1" <-> "OE2" Residue "AN GLU 115": "OE1" <-> "OE2" Residue "AN ASP 144": "OD1" <-> "OD2" Residue "AN ASP 152": "OD1" <-> "OD2" Residue "AO GLU 23": "OE1" <-> "OE2" Residue "AO GLU 117": "OE1" <-> "OE2" Residue "AO ASP 123": "OD1" <-> "OD2" Residue "AO ASP 145": "OD1" <-> "OD2" Residue "AO ASP 148": "OD1" <-> "OD2" Residue "AO GLU 149": "OE1" <-> "OE2" Residue "AP ASP 25": "OD1" <-> "OD2" Residue "AP GLU 33": "OE1" <-> "OE2" Residue "AP ASP 39": "OD1" <-> "OD2" Residue "AP ASP 152": "OD1" <-> "OD2" Residue "AQ GLU 7": "OE1" <-> "OE2" Residue "AQ ASP 123": "OD1" <-> "OD2" Residue "AQ GLU 131": "OE1" <-> "OE2" Residue "AQ ASP 148": "OD1" <-> "OD2" Residue "AQ GLU 149": "OE1" <-> "OE2" Residue "AR GLU 17": "OE1" <-> "OE2" Residue "AR GLU 87": "OE1" <-> "OE2" Residue "AR ASP 107": "OD1" <-> "OD2" Residue "AR GLU 115": "OE1" <-> "OE2" Residue "AR ASP 140": "OD1" <-> "OD2" Residue "AR ASP 152": "OD1" <-> "OD2" Residue "AR TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AS GLU 7": "OE1" <-> "OE2" Residue "AS TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AS ASP 82": "OD1" <-> "OD2" Residue "AS ASP 116": "OD1" <-> "OD2" Residue "AS GLU 117": "OE1" <-> "OE2" Residue "AS GLU 131": "OE1" <-> "OE2" Residue "AT GLU 33": "OE1" <-> "OE2" Residue "AT GLU 115": "OE1" <-> "OE2" Residue "AT ASP 144": "OD1" <-> "OD2" Residue "AT ASP 165": "OD1" <-> "OD2" Residue "AU ASP 46": "OD1" <-> "OD2" Residue "AU GLU 131": "OE1" <-> "OE2" Residue "AV ASP 39": "OD1" <-> "OD2" Residue "AV ASP 140": "OD1" <-> "OD2" Residue "AW ASP 46": "OD1" <-> "OD2" Residue "AW GLU 109": "OE1" <-> "OE2" Residue "AW GLU 131": "OE1" <-> "OE2" Residue "AW GLU 149": "OE1" <-> "OE2" Residue "AX GLU 17": "OE1" <-> "OE2" Residue "AX GLU 106": "OE1" <-> "OE2" Residue "AX ASP 107": "OD1" <-> "OD2" Residue "AX GLU 136": "OE1" <-> "OE2" Residue "AX ASP 140": "OD1" <-> "OD2" Residue "AX ASP 165": "OD1" <-> "OD2" Residue "AY ASP 77": "OD1" <-> "OD2" Residue "AY ASP 82": "OD1" <-> "OD2" Residue "AY GLU 109": "OE1" <-> "OE2" Residue "AY ASP 116": "OD1" <-> "OD2" Residue "AY GLU 117": "OE1" <-> "OE2" Residue "AY ASP 123": "OD1" <-> "OD2" Residue "AY GLU 131": "OE1" <-> "OE2" Residue "AZ ASP 3": "OD1" <-> "OD2" Residue "AZ ASP 39": "OD1" <-> "OD2" Residue "AZ ASP 101": "OD1" <-> "OD2" Residue "AZ GLU 136": "OE1" <-> "OE2" Residue "AZ ASP 140": "OD1" <-> "OD2" Residue "AZ ASP 144": "OD1" <-> "OD2" Residue "BA ASP 46": "OD1" <-> "OD2" Residue "BA GLU 117": "OE1" <-> "OE2" Residue "BA ASP 123": "OD1" <-> "OD2" Residue "BA GLU 131": "OE1" <-> "OE2" Residue "BA ASP 145": "OD1" <-> "OD2" Residue "BA ASP 155": "OD1" <-> "OD2" Residue "BB ASP 25": "OD1" <-> "OD2" Residue "BB GLU 33": "OE1" <-> "OE2" Residue "BB ASP 39": "OD1" <-> "OD2" Residue "BB GLU 87": "OE1" <-> "OE2" Residue "BB GLU 106": "OE1" <-> "OE2" Residue "BB ASP 107": "OD1" <-> "OD2" Residue "BB ASP 144": "OD1" <-> "OD2" Residue "BC GLU 7": "OE1" <-> "OE2" Residue "BC ASP 77": "OD1" <-> "OD2" Residue "BC GLU 117": "OE1" <-> "OE2" Residue "BC ASP 123": "OD1" <-> "OD2" Residue "BC GLU 149": "OE1" <-> "OE2" Residue "BD ASP 25": "OD1" <-> "OD2" Residue "BD GLU 62": "OE1" <-> "OE2" Residue "BD GLU 115": "OE1" <-> "OE2" Residue "BD GLU 136": "OE1" <-> "OE2" Residue "BD ASP 140": "OD1" <-> "OD2" Residue "BD ASP 144": "OD1" <-> "OD2" Residue "BD ASP 152": "OD1" <-> "OD2" Residue "BE GLU 7": "OE1" <-> "OE2" Residue "BE GLU 109": "OE1" <-> "OE2" Residue "BE GLU 117": "OE1" <-> "OE2" Residue "BE GLU 131": "OE1" <-> "OE2" Residue "BE ASP 155": "OD1" <-> "OD2" Residue "BF GLU 17": "OE1" <-> "OE2" Residue "BF ASP 39": "OD1" <-> "OD2" Residue "BF GLU 87": "OE1" <-> "OE2" Residue "BF ASP 101": "OD1" <-> "OD2" Residue "BF GLU 106": "OE1" <-> "OE2" Residue "BF ASP 144": "OD1" <-> "OD2" Residue "BF ASP 152": "OD1" <-> "OD2" Residue "BG ASP 13": "OD1" <-> "OD2" Residue "BG GLU 23": "OE1" <-> "OE2" Residue "BG TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BG ASP 77": "OD1" <-> "OD2" Residue "BG GLU 109": "OE1" <-> "OE2" Residue "BG ASP 155": "OD1" <-> "OD2" Residue "BH GLU 33": "OE1" <-> "OE2" Residue "BH GLU 106": "OE1" <-> "OE2" Residue "BI TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BI GLU 109": "OE1" <-> "OE2" Residue "BI ASP 116": "OD1" <-> "OD2" Residue "BJ GLU 17": "OE1" <-> "OE2" Residue "BJ ASP 25": "OD1" <-> "OD2" Residue "BJ GLU 87": "OE1" <-> "OE2" Residue "BJ GLU 106": "OE1" <-> "OE2" Residue "BJ ASP 140": "OD1" <-> "OD2" Residue "BJ ASP 152": "OD1" <-> "OD2" Residue "BJ GLU 159": "OE1" <-> "OE2" Residue "BK TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BK ASP 145": "OD1" <-> "OD2" Residue "BK ASP 182": "OD1" <-> "OD2" Residue "BL ASP 47": "OD1" <-> "OD2" Residue "BL GLU 183": "OE1" <-> "OE2" Residue "BM TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BM ASP 145": "OD1" <-> "OD2" Residue "BM GLU 245": "OE1" <-> "OE2" Residue "BN GLU 23": "OE1" <-> "OE2" Residue "BN GLU 34": "OE1" <-> "OE2" Residue "BN ASP 39": "OD1" <-> "OD2" Residue "BN GLU 58": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 55437 Number of models: 1 Model: "" Number of chains: 116 Chain: "AA" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "AB" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "AC" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "AD" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "AE" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "AF" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "AG" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "AH" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "AI" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "AJ" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "AK" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "AL" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "AM" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "AN" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "AO" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "AP" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "AQ" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "AR" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "AS" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "AT" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "AU" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "AV" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "AW" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "AX" Number of atoms: 1269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1269 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "AY" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "AZ" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "BA" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "BB" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "BC" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "BD" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "BE" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "BF" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "BG" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "BH" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "BI" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "BJ" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "BK" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1617 Classifications: {'peptide': 194} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 185} Chain: "BL" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2282 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 275} Chain: "BM" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2122 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 260} Chain breaks: 2 Chain: "BN" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 590 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "AA" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AB" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AC" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AD" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AE" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AF" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AG" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AH" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AI" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AJ" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AK" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AL" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AM" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AN" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AO" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AP" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AQ" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AR" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AS" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AT" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AU" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AV" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AW" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AX" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AY" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AZ" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BA" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BB" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BC" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BD" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BE" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BF" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BG" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BH" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BI" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BJ" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AA" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "AB" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "AC" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "AD" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "AE" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "AF" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "AG" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "AH" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "AI" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "AJ" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "AK" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "AL" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "AM" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "AN" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "AO" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "AP" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "AQ" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "AR" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "AS" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "AT" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "AU" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "AV" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "AW" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "AX" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "AY" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "AZ" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "BA" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "BB" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "BC" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "BD" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "BE" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "BF" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "BG" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "BH" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "BI" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "BJ" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "BK" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "BL" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "BM" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "BN" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 22.73, per 1000 atoms: 0.41 Number of scatterers: 55437 At special positions: 0 Unit cell: (126, 127.05, 189, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 191 16.00 O 11862 8.00 N 9391 7.00 C 33993 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=54, symmetry=0 Number of additional bonds: simple=54, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.36 Conformation dependent library (CDL) restraints added in 5.8 seconds 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12588 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 368 helices and 3 sheets defined 72.5% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'AA' and resid 4 through 14 Processing helix chain 'AA' and resid 21 through 46 removed outlier: 4.499A pdb=" N ASNAA 35 " --> pdb=" O LEUAA 31 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ALAAA 36 " --> pdb=" O ARGAA 32 " (cutoff:3.500A) Processing helix chain 'AA' and resid 48 through 62 Processing helix chain 'AA' and resid 64 through 68 removed outlier: 3.586A pdb=" N GLNAA 68 " --> pdb=" O PROAA 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'AA' and resid 64 through 68' Processing helix chain 'AA' and resid 78 through 101 Processing helix chain 'AA' and resid 105 through 110 Processing helix chain 'AA' and resid 115 through 122 Processing helix chain 'AA' and resid 126 through 139 Processing helix chain 'AA' and resid 144 through 161 Processing helix chain 'AB' and resid 4 through 15 removed outlier: 3.928A pdb=" N VALAB 8 " --> pdb=" O VALAB 4 " (cutoff:3.500A) Processing helix chain 'AB' and resid 21 through 61 removed outlier: 4.394A pdb=" N ASNAB 35 " --> pdb=" O VALAB 31 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LYSAB 36 " --> pdb=" O ALAAB 32 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N SERAB 49 " --> pdb=" O THRAB 45 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ALAAB 50 " --> pdb=" O GLYAB 46 " (cutoff:3.500A) Processing helix chain 'AB' and resid 64 through 66 No H-bonds generated for 'chain 'AB' and resid 64 through 66' Processing helix chain 'AB' and resid 76 through 99 Processing helix chain 'AB' and resid 103 through 108 Processing helix chain 'AB' and resid 113 through 120 Processing helix chain 'AB' and resid 124 through 142 Processing helix chain 'AB' and resid 154 through 171 Processing helix chain 'AC' and resid 4 through 14 Processing helix chain 'AC' and resid 21 through 46 removed outlier: 4.236A pdb=" N ASNAC 35 " --> pdb=" O LEUAC 31 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ALAAC 36 " --> pdb=" O ARGAC 32 " (cutoff:3.500A) Processing helix chain 'AC' and resid 48 through 62 Processing helix chain 'AC' and resid 64 through 68 removed outlier: 3.589A pdb=" N GLNAC 68 " --> pdb=" O TYRAC 65 " (cutoff:3.500A) Processing helix chain 'AC' and resid 78 through 101 Processing helix chain 'AC' and resid 105 through 110 Processing helix chain 'AC' and resid 115 through 121 Processing helix chain 'AC' and resid 126 through 139 Processing helix chain 'AC' and resid 145 through 161 Processing helix chain 'AD' and resid 4 through 15 removed outlier: 3.884A pdb=" N VALAD 8 " --> pdb=" O VALAD 4 " (cutoff:3.500A) Processing helix chain 'AD' and resid 21 through 32 Processing helix chain 'AD' and resid 34 through 62 removed outlier: 5.454A pdb=" N SERAD 49 " --> pdb=" O THRAD 45 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALAAD 50 " --> pdb=" O GLYAD 46 " (cutoff:3.500A) Processing helix chain 'AD' and resid 64 through 66 No H-bonds generated for 'chain 'AD' and resid 64 through 66' Processing helix chain 'AD' and resid 76 through 99 Processing helix chain 'AD' and resid 103 through 108 Processing helix chain 'AD' and resid 113 through 120 Processing helix chain 'AD' and resid 124 through 142 Processing helix chain 'AD' and resid 154 through 171 Processing helix chain 'AE' and resid 4 through 14 Processing helix chain 'AE' and resid 21 through 46 removed outlier: 4.283A pdb=" N ASNAE 35 " --> pdb=" O LEUAE 31 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ALAAE 36 " --> pdb=" O ARGAE 32 " (cutoff:3.500A) Processing helix chain 'AE' and resid 48 through 62 Processing helix chain 'AE' and resid 64 through 67 Processing helix chain 'AE' and resid 78 through 101 Processing helix chain 'AE' and resid 105 through 110 Processing helix chain 'AE' and resid 115 through 122 Processing helix chain 'AE' and resid 126 through 139 Processing helix chain 'AE' and resid 144 through 161 Processing helix chain 'AF' and resid 4 through 15 removed outlier: 3.999A pdb=" N VALAF 8 " --> pdb=" O VALAF 4 " (cutoff:3.500A) Processing helix chain 'AF' and resid 21 through 61 removed outlier: 4.599A pdb=" N ASNAF 35 " --> pdb=" O VALAF 31 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N LYSAF 36 " --> pdb=" O ALAAF 32 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N SERAF 49 " --> pdb=" O THRAF 45 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALAAF 50 " --> pdb=" O GLYAF 46 " (cutoff:3.500A) Processing helix chain 'AF' and resid 64 through 66 No H-bonds generated for 'chain 'AF' and resid 64 through 66' Processing helix chain 'AF' and resid 76 through 99 Processing helix chain 'AF' and resid 103 through 108 Processing helix chain 'AF' and resid 113 through 120 Processing helix chain 'AF' and resid 124 through 142 Processing helix chain 'AF' and resid 154 through 171 Processing helix chain 'AG' and resid 4 through 14 Processing helix chain 'AG' and resid 21 through 46 removed outlier: 4.380A pdb=" N ASNAG 35 " --> pdb=" O LEUAG 31 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ALAAG 36 " --> pdb=" O ARGAG 32 " (cutoff:3.500A) Processing helix chain 'AG' and resid 48 through 62 Processing helix chain 'AG' and resid 64 through 67 Processing helix chain 'AG' and resid 78 through 101 Processing helix chain 'AG' and resid 105 through 110 Processing helix chain 'AG' and resid 115 through 121 Processing helix chain 'AG' and resid 126 through 139 Processing helix chain 'AG' and resid 144 through 161 Processing helix chain 'AH' and resid 4 through 15 removed outlier: 3.963A pdb=" N VALAH 8 " --> pdb=" O VALAH 4 " (cutoff:3.500A) Processing helix chain 'AH' and resid 21 through 32 Processing helix chain 'AH' and resid 34 through 62 removed outlier: 3.581A pdb=" N ASNAH 47 " --> pdb=" O ARGAH 43 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SERAH 49 " --> pdb=" O THRAH 45 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALAAH 50 " --> pdb=" O GLYAH 46 " (cutoff:3.500A) Processing helix chain 'AH' and resid 64 through 67 No H-bonds generated for 'chain 'AH' and resid 64 through 67' Processing helix chain 'AH' and resid 76 through 99 Processing helix chain 'AH' and resid 103 through 108 Processing helix chain 'AH' and resid 113 through 120 Processing helix chain 'AH' and resid 124 through 142 Processing helix chain 'AH' and resid 154 through 171 Processing helix chain 'AI' and resid 4 through 14 Processing helix chain 'AI' and resid 21 through 46 removed outlier: 4.228A pdb=" N ASNAI 35 " --> pdb=" O LEUAI 31 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ALAAI 36 " --> pdb=" O ARGAI 32 " (cutoff:3.500A) Processing helix chain 'AI' and resid 48 through 62 Processing helix chain 'AI' and resid 64 through 68 removed outlier: 3.522A pdb=" N GLNAI 68 " --> pdb=" O TYRAI 65 " (cutoff:3.500A) Processing helix chain 'AI' and resid 78 through 101 Processing helix chain 'AI' and resid 105 through 110 Processing helix chain 'AI' and resid 115 through 121 Processing helix chain 'AI' and resid 126 through 139 Processing helix chain 'AI' and resid 144 through 161 Processing helix chain 'AJ' and resid 4 through 15 removed outlier: 4.160A pdb=" N VALAJ 8 " --> pdb=" O VALAJ 4 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 21 through 32 Processing helix chain 'AJ' and resid 34 through 62 removed outlier: 5.085A pdb=" N SERAJ 49 " --> pdb=" O THRAJ 45 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALAAJ 50 " --> pdb=" O GLYAJ 46 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 64 through 66 No H-bonds generated for 'chain 'AJ' and resid 64 through 66' Processing helix chain 'AJ' and resid 76 through 99 Processing helix chain 'AJ' and resid 103 through 107 Processing helix chain 'AJ' and resid 113 through 120 Processing helix chain 'AJ' and resid 124 through 142 Processing helix chain 'AJ' and resid 154 through 171 Processing helix chain 'AK' and resid 4 through 14 Processing helix chain 'AK' and resid 21 through 46 removed outlier: 4.668A pdb=" N ASNAK 35 " --> pdb=" O LEUAK 31 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ALAAK 36 " --> pdb=" O ARGAK 32 " (cutoff:3.500A) Processing helix chain 'AK' and resid 48 through 62 Processing helix chain 'AK' and resid 64 through 67 Processing helix chain 'AK' and resid 78 through 101 Processing helix chain 'AK' and resid 105 through 110 Processing helix chain 'AK' and resid 115 through 121 Processing helix chain 'AK' and resid 126 through 139 Processing helix chain 'AK' and resid 144 through 161 Processing helix chain 'AL' and resid 4 through 15 removed outlier: 4.004A pdb=" N VALAL 8 " --> pdb=" O VALAL 4 " (cutoff:3.500A) Processing helix chain 'AL' and resid 21 through 32 Processing helix chain 'AL' and resid 34 through 46 Processing helix chain 'AL' and resid 48 through 62 Processing helix chain 'AL' and resid 64 through 67 No H-bonds generated for 'chain 'AL' and resid 64 through 67' Processing helix chain 'AL' and resid 76 through 99 Processing helix chain 'AL' and resid 103 through 108 Processing helix chain 'AL' and resid 113 through 120 Processing helix chain 'AL' and resid 124 through 142 Processing helix chain 'AL' and resid 154 through 171 Processing helix chain 'AM' and resid 4 through 14 Processing helix chain 'AM' and resid 21 through 46 removed outlier: 4.617A pdb=" N ASNAM 35 " --> pdb=" O LEUAM 31 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ALAAM 36 " --> pdb=" O ARGAM 32 " (cutoff:3.500A) Processing helix chain 'AM' and resid 48 through 62 Processing helix chain 'AM' and resid 64 through 67 Processing helix chain 'AM' and resid 78 through 101 Processing helix chain 'AM' and resid 105 through 110 Processing helix chain 'AM' and resid 115 through 121 Processing helix chain 'AM' and resid 126 through 139 Processing helix chain 'AM' and resid 144 through 161 Processing helix chain 'AN' and resid 4 through 15 removed outlier: 3.803A pdb=" N VALAN 8 " --> pdb=" O VALAN 4 " (cutoff:3.500A) Processing helix chain 'AN' and resid 21 through 62 removed outlier: 4.830A pdb=" N ASNAN 35 " --> pdb=" O VALAN 31 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LYSAN 36 " --> pdb=" O ALAAN 32 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N SERAN 49 " --> pdb=" O THRAN 45 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALAAN 50 " --> pdb=" O GLYAN 46 " (cutoff:3.500A) Processing helix chain 'AN' and resid 64 through 66 No H-bonds generated for 'chain 'AN' and resid 64 through 66' Processing helix chain 'AN' and resid 76 through 99 Processing helix chain 'AN' and resid 103 through 108 Processing helix chain 'AN' and resid 113 through 120 Processing helix chain 'AN' and resid 124 through 142 Processing helix chain 'AN' and resid 154 through 171 Processing helix chain 'AO' and resid 4 through 14 Processing helix chain 'AO' and resid 21 through 46 removed outlier: 4.308A pdb=" N ASNAO 35 " --> pdb=" O LEUAO 31 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ALAAO 36 " --> pdb=" O ARGAO 32 " (cutoff:3.500A) Processing helix chain 'AO' and resid 48 through 62 Processing helix chain 'AO' and resid 64 through 67 Processing helix chain 'AO' and resid 78 through 101 Processing helix chain 'AO' and resid 105 through 110 Processing helix chain 'AO' and resid 115 through 121 Processing helix chain 'AO' and resid 126 through 139 Processing helix chain 'AO' and resid 144 through 161 Processing helix chain 'AP' and resid 4 through 15 removed outlier: 4.112A pdb=" N VALAP 8 " --> pdb=" O VALAP 4 " (cutoff:3.500A) Processing helix chain 'AP' and resid 21 through 32 Processing helix chain 'AP' and resid 34 through 62 removed outlier: 5.126A pdb=" N SERAP 49 " --> pdb=" O THRAP 45 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALAAP 50 " --> pdb=" O GLYAP 46 " (cutoff:3.500A) Processing helix chain 'AP' and resid 64 through 66 No H-bonds generated for 'chain 'AP' and resid 64 through 66' Processing helix chain 'AP' and resid 76 through 99 Processing helix chain 'AP' and resid 103 through 108 Processing helix chain 'AP' and resid 113 through 120 Processing helix chain 'AP' and resid 124 through 142 Processing helix chain 'AP' and resid 154 through 171 Processing helix chain 'AQ' and resid 4 through 14 Processing helix chain 'AQ' and resid 21 through 46 removed outlier: 4.454A pdb=" N ASNAQ 35 " --> pdb=" O LEUAQ 31 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ALAAQ 36 " --> pdb=" O ARGAQ 32 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 48 through 62 Processing helix chain 'AQ' and resid 64 through 68 Processing helix chain 'AQ' and resid 78 through 101 Processing helix chain 'AQ' and resid 105 through 110 Processing helix chain 'AQ' and resid 115 through 121 Processing helix chain 'AQ' and resid 126 through 139 Processing helix chain 'AQ' and resid 144 through 161 Processing helix chain 'AR' and resid 4 through 15 removed outlier: 3.706A pdb=" N VALAR 8 " --> pdb=" O VALAR 4 " (cutoff:3.500A) Processing helix chain 'AR' and resid 21 through 32 Processing helix chain 'AR' and resid 34 through 62 removed outlier: 5.133A pdb=" N SERAR 49 " --> pdb=" O THRAR 45 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ALAAR 50 " --> pdb=" O GLYAR 46 " (cutoff:3.500A) Processing helix chain 'AR' and resid 64 through 66 No H-bonds generated for 'chain 'AR' and resid 64 through 66' Processing helix chain 'AR' and resid 76 through 99 Processing helix chain 'AR' and resid 103 through 108 Processing helix chain 'AR' and resid 113 through 120 Processing helix chain 'AR' and resid 124 through 142 Processing helix chain 'AR' and resid 154 through 171 Processing helix chain 'AS' and resid 4 through 14 Processing helix chain 'AS' and resid 21 through 46 removed outlier: 4.569A pdb=" N ASNAS 35 " --> pdb=" O LEUAS 31 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ALAAS 36 " --> pdb=" O ARGAS 32 " (cutoff:3.500A) Processing helix chain 'AS' and resid 48 through 62 Processing helix chain 'AS' and resid 64 through 67 Processing helix chain 'AS' and resid 78 through 101 Processing helix chain 'AS' and resid 105 through 110 Processing helix chain 'AS' and resid 115 through 121 Processing helix chain 'AS' and resid 126 through 139 Processing helix chain 'AS' and resid 144 through 161 Processing helix chain 'AT' and resid 4 through 15 removed outlier: 4.092A pdb=" N VALAT 8 " --> pdb=" O VALAT 4 " (cutoff:3.500A) Processing helix chain 'AT' and resid 21 through 32 Processing helix chain 'AT' and resid 34 through 46 Processing helix chain 'AT' and resid 48 through 62 Processing helix chain 'AT' and resid 64 through 66 No H-bonds generated for 'chain 'AT' and resid 64 through 66' Processing helix chain 'AT' and resid 76 through 99 Processing helix chain 'AT' and resid 103 through 108 Processing helix chain 'AT' and resid 113 through 120 Processing helix chain 'AT' and resid 124 through 142 Processing helix chain 'AT' and resid 154 through 171 removed outlier: 3.565A pdb=" N VALAT 171 " --> pdb=" O ALAAT 167 " (cutoff:3.500A) Processing helix chain 'AU' and resid 4 through 14 Processing helix chain 'AU' and resid 21 through 46 removed outlier: 4.376A pdb=" N ASNAU 35 " --> pdb=" O LEUAU 31 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ALAAU 36 " --> pdb=" O ARGAU 32 " (cutoff:3.500A) Processing helix chain 'AU' and resid 48 through 62 Processing helix chain 'AU' and resid 64 through 67 Processing helix chain 'AU' and resid 78 through 101 Processing helix chain 'AU' and resid 105 through 110 Processing helix chain 'AU' and resid 115 through 121 Processing helix chain 'AU' and resid 126 through 139 Processing helix chain 'AU' and resid 144 through 161 Processing helix chain 'AV' and resid 4 through 15 removed outlier: 3.815A pdb=" N VALAV 8 " --> pdb=" O VALAV 4 " (cutoff:3.500A) Processing helix chain 'AV' and resid 21 through 32 Processing helix chain 'AV' and resid 34 through 46 Processing helix chain 'AV' and resid 48 through 62 Processing helix chain 'AV' and resid 64 through 66 No H-bonds generated for 'chain 'AV' and resid 64 through 66' Processing helix chain 'AV' and resid 76 through 99 Processing helix chain 'AV' and resid 102 through 108 removed outlier: 3.507A pdb=" N GLUAV 106 " --> pdb=" O SERAV 103 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASPAV 107 " --> pdb=" O VALAV 104 " (cutoff:3.500A) Processing helix chain 'AV' and resid 113 through 120 Processing helix chain 'AV' and resid 124 through 142 Processing helix chain 'AV' and resid 154 through 171 removed outlier: 3.529A pdb=" N VALAV 171 " --> pdb=" O ALAAV 167 " (cutoff:3.500A) Processing helix chain 'AW' and resid 4 through 15 Processing helix chain 'AW' and resid 21 through 46 removed outlier: 4.525A pdb=" N ASNAW 35 " --> pdb=" O LEUAW 31 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ALAAW 36 " --> pdb=" O ARGAW 32 " (cutoff:3.500A) Processing helix chain 'AW' and resid 48 through 62 Processing helix chain 'AW' and resid 64 through 68 Processing helix chain 'AW' and resid 78 through 101 Processing helix chain 'AW' and resid 105 through 110 Processing helix chain 'AW' and resid 115 through 122 Processing helix chain 'AW' and resid 126 through 139 Processing helix chain 'AW' and resid 144 through 161 Processing helix chain 'AX' and resid 4 through 13 removed outlier: 3.831A pdb=" N VALAX 8 " --> pdb=" O VALAX 4 " (cutoff:3.500A) Processing helix chain 'AX' and resid 21 through 32 Processing helix chain 'AX' and resid 34 through 62 removed outlier: 3.519A pdb=" N ASNAX 47 " --> pdb=" O ARGAX 43 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N SERAX 49 " --> pdb=" O THRAX 45 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALAAX 50 " --> pdb=" O GLYAX 46 " (cutoff:3.500A) Processing helix chain 'AX' and resid 64 through 66 No H-bonds generated for 'chain 'AX' and resid 64 through 66' Processing helix chain 'AX' and resid 76 through 99 Processing helix chain 'AX' and resid 103 through 108 Processing helix chain 'AX' and resid 113 through 120 Processing helix chain 'AX' and resid 124 through 142 removed outlier: 3.818A pdb=" N ASPAX 140 " --> pdb=" O GLUAX 136 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILEAX 141 " --> pdb=" O ALAAX 137 " (cutoff:3.500A) Processing helix chain 'AX' and resid 154 through 171 Processing helix chain 'AY' and resid 4 through 14 Processing helix chain 'AY' and resid 21 through 46 removed outlier: 4.453A pdb=" N ASNAY 35 " --> pdb=" O LEUAY 31 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ALAAY 36 " --> pdb=" O ARGAY 32 " (cutoff:3.500A) Processing helix chain 'AY' and resid 48 through 62 Processing helix chain 'AY' and resid 64 through 67 Processing helix chain 'AY' and resid 78 through 101 Processing helix chain 'AY' and resid 105 through 110 Processing helix chain 'AY' and resid 115 through 121 Processing helix chain 'AY' and resid 126 through 139 Processing helix chain 'AY' and resid 144 through 161 Processing helix chain 'AZ' and resid 4 through 15 removed outlier: 3.726A pdb=" N VALAZ 8 " --> pdb=" O VALAZ 4 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 21 through 32 Processing helix chain 'AZ' and resid 34 through 46 Processing helix chain 'AZ' and resid 48 through 62 Processing helix chain 'AZ' and resid 76 through 99 Processing helix chain 'AZ' and resid 103 through 108 Processing helix chain 'AZ' and resid 113 through 120 Processing helix chain 'AZ' and resid 124 through 142 Processing helix chain 'AZ' and resid 154 through 171 Processing helix chain 'BA' and resid 4 through 15 Processing helix chain 'BA' and resid 21 through 46 removed outlier: 4.353A pdb=" N ASNBA 35 " --> pdb=" O LEUBA 31 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ALABA 36 " --> pdb=" O ARGBA 32 " (cutoff:3.500A) Processing helix chain 'BA' and resid 48 through 62 Processing helix chain 'BA' and resid 64 through 67 Processing helix chain 'BA' and resid 78 through 101 Processing helix chain 'BA' and resid 105 through 110 Processing helix chain 'BA' and resid 115 through 121 Processing helix chain 'BA' and resid 126 through 139 Processing helix chain 'BA' and resid 144 through 161 Processing helix chain 'BB' and resid 4 through 15 removed outlier: 3.598A pdb=" N VALBB 8 " --> pdb=" O VALBB 4 " (cutoff:3.500A) Processing helix chain 'BB' and resid 21 through 32 Processing helix chain 'BB' and resid 34 through 46 Processing helix chain 'BB' and resid 48 through 62 Processing helix chain 'BB' and resid 64 through 66 No H-bonds generated for 'chain 'BB' and resid 64 through 66' Processing helix chain 'BB' and resid 76 through 99 Processing helix chain 'BB' and resid 103 through 108 Processing helix chain 'BB' and resid 113 through 120 Processing helix chain 'BB' and resid 124 through 142 Processing helix chain 'BB' and resid 154 through 171 Processing helix chain 'BC' and resid 4 through 15 Processing helix chain 'BC' and resid 21 through 46 removed outlier: 4.263A pdb=" N ASNBC 35 " --> pdb=" O LEUBC 31 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ALABC 36 " --> pdb=" O ARGBC 32 " (cutoff:3.500A) Processing helix chain 'BC' and resid 48 through 62 Processing helix chain 'BC' and resid 64 through 68 Processing helix chain 'BC' and resid 78 through 101 Processing helix chain 'BC' and resid 105 through 110 Processing helix chain 'BC' and resid 115 through 121 Processing helix chain 'BC' and resid 126 through 139 Processing helix chain 'BC' and resid 144 through 161 Processing helix chain 'BD' and resid 4 through 15 removed outlier: 3.741A pdb=" N VALBD 8 " --> pdb=" O VALBD 4 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARGBD 15 " --> pdb=" O GLNBD 11 " (cutoff:3.500A) Processing helix chain 'BD' and resid 21 through 32 Processing helix chain 'BD' and resid 34 through 46 Processing helix chain 'BD' and resid 48 through 62 Processing helix chain 'BD' and resid 64 through 67 No H-bonds generated for 'chain 'BD' and resid 64 through 67' Processing helix chain 'BD' and resid 76 through 99 Processing helix chain 'BD' and resid 103 through 108 Processing helix chain 'BD' and resid 113 through 120 Processing helix chain 'BD' and resid 124 through 142 Processing helix chain 'BD' and resid 154 through 171 Processing helix chain 'BE' and resid 4 through 14 Processing helix chain 'BE' and resid 21 through 46 removed outlier: 4.271A pdb=" N ASNBE 35 " --> pdb=" O LEUBE 31 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ALABE 36 " --> pdb=" O ARGBE 32 " (cutoff:3.500A) Processing helix chain 'BE' and resid 48 through 62 Processing helix chain 'BE' and resid 64 through 67 Processing helix chain 'BE' and resid 78 through 101 Processing helix chain 'BE' and resid 105 through 110 Processing helix chain 'BE' and resid 115 through 121 Processing helix chain 'BE' and resid 126 through 139 Processing helix chain 'BE' and resid 144 through 161 Processing helix chain 'BF' and resid 4 through 15 removed outlier: 3.922A pdb=" N VALBF 8 " --> pdb=" O VALBF 4 " (cutoff:3.500A) Processing helix chain 'BF' and resid 21 through 32 Processing helix chain 'BF' and resid 34 through 62 removed outlier: 3.530A pdb=" N ASNBF 47 " --> pdb=" O ARGBF 43 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N SERBF 49 " --> pdb=" O THRBF 45 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALABF 50 " --> pdb=" O GLYBF 46 " (cutoff:3.500A) Processing helix chain 'BF' and resid 64 through 66 No H-bonds generated for 'chain 'BF' and resid 64 through 66' Processing helix chain 'BF' and resid 76 through 99 Processing helix chain 'BF' and resid 103 through 108 Processing helix chain 'BF' and resid 113 through 120 Processing helix chain 'BF' and resid 124 through 143 Processing helix chain 'BF' and resid 154 through 171 Processing helix chain 'BG' and resid 4 through 14 Processing helix chain 'BG' and resid 21 through 46 removed outlier: 4.363A pdb=" N ASNBG 35 " --> pdb=" O LEUBG 31 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ALABG 36 " --> pdb=" O ARGBG 32 " (cutoff:3.500A) Processing helix chain 'BG' and resid 48 through 62 Processing helix chain 'BG' and resid 64 through 67 Processing helix chain 'BG' and resid 78 through 101 Processing helix chain 'BG' and resid 105 through 110 Processing helix chain 'BG' and resid 116 through 121 Processing helix chain 'BG' and resid 126 through 139 Processing helix chain 'BG' and resid 144 through 161 Processing helix chain 'BH' and resid 4 through 15 removed outlier: 3.948A pdb=" N VALBH 8 " --> pdb=" O VALBH 4 " (cutoff:3.500A) Processing helix chain 'BH' and resid 21 through 32 Processing helix chain 'BH' and resid 34 through 62 removed outlier: 5.252A pdb=" N SERBH 49 " --> pdb=" O THRBH 45 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALABH 50 " --> pdb=" O GLYBH 46 " (cutoff:3.500A) Processing helix chain 'BH' and resid 64 through 66 No H-bonds generated for 'chain 'BH' and resid 64 through 66' Processing helix chain 'BH' and resid 76 through 99 Processing helix chain 'BH' and resid 103 through 108 Processing helix chain 'BH' and resid 113 through 120 Processing helix chain 'BH' and resid 124 through 142 Processing helix chain 'BH' and resid 154 through 171 removed outlier: 3.668A pdb=" N VALBH 171 " --> pdb=" O ALABH 167 " (cutoff:3.500A) Processing helix chain 'BI' and resid 4 through 14 Processing helix chain 'BI' and resid 21 through 46 removed outlier: 4.387A pdb=" N ASNBI 35 " --> pdb=" O LEUBI 31 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ALABI 36 " --> pdb=" O ARGBI 32 " (cutoff:3.500A) Processing helix chain 'BI' and resid 48 through 62 Processing helix chain 'BI' and resid 64 through 68 Processing helix chain 'BI' and resid 78 through 101 Processing helix chain 'BI' and resid 105 through 110 Processing helix chain 'BI' and resid 115 through 121 Processing helix chain 'BI' and resid 126 through 139 Processing helix chain 'BI' and resid 144 through 161 Processing helix chain 'BJ' and resid 4 through 15 removed outlier: 3.542A pdb=" N VALBJ 8 " --> pdb=" O VALBJ 4 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 21 through 32 Processing helix chain 'BJ' and resid 34 through 46 Processing helix chain 'BJ' and resid 48 through 62 Processing helix chain 'BJ' and resid 64 through 66 No H-bonds generated for 'chain 'BJ' and resid 64 through 66' Processing helix chain 'BJ' and resid 76 through 99 Processing helix chain 'BJ' and resid 103 through 108 Processing helix chain 'BJ' and resid 113 through 120 Processing helix chain 'BJ' and resid 124 through 142 Processing helix chain 'BJ' and resid 154 through 171 removed outlier: 3.541A pdb=" N VALBJ 171 " --> pdb=" O ALABJ 167 " (cutoff:3.500A) Processing helix chain 'BK' and resid 39 through 54 Processing helix chain 'BK' and resid 64 through 72 Processing helix chain 'BK' and resid 77 through 85 Processing helix chain 'BK' and resid 88 through 93 Processing helix chain 'BK' and resid 101 through 104 No H-bonds generated for 'chain 'BK' and resid 101 through 104' Processing helix chain 'BK' and resid 108 through 111 No H-bonds generated for 'chain 'BK' and resid 108 through 111' Processing helix chain 'BK' and resid 119 through 132 removed outlier: 4.016A pdb=" N ILEBK 127 " --> pdb=" O ILEBK 123 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VALBK 128 " --> pdb=" O ALABK 124 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VALBK 129 " --> pdb=" O TRPBK 125 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALABK 130 " --> pdb=" O SERBK 126 " (cutoff:3.500A) Processing helix chain 'BK' and resid 134 through 142 Processing helix chain 'BK' and resid 145 through 150 Processing helix chain 'BK' and resid 174 through 177 No H-bonds generated for 'chain 'BK' and resid 174 through 177' Processing helix chain 'BK' and resid 183 through 189 Processing helix chain 'BL' and resid 13 through 16 No H-bonds generated for 'chain 'BL' and resid 13 through 16' Processing helix chain 'BL' and resid 29 through 43 Processing helix chain 'BL' and resid 51 through 53 No H-bonds generated for 'chain 'BL' and resid 51 through 53' Processing helix chain 'BL' and resid 56 through 64 Processing helix chain 'BL' and resid 69 through 78 Processing helix chain 'BL' and resid 80 through 86 Processing helix chain 'BL' and resid 92 through 103 Processing helix chain 'BL' and resid 111 through 124 Processing helix chain 'BL' and resid 126 through 134 Processing helix chain 'BL' and resid 137 through 142 Processing helix chain 'BL' and resid 161 through 170 removed outlier: 4.124A pdb=" N PHEBL 168 " --> pdb=" O PHEBL 164 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARGBL 169 " --> pdb=" O THRBL 165 " (cutoff:3.500A) Processing helix chain 'BL' and resid 190 through 195 Processing helix chain 'BL' and resid 230 through 232 No H-bonds generated for 'chain 'BL' and resid 230 through 232' Processing helix chain 'BL' and resid 265 through 277 removed outlier: 4.985A pdb=" N ASNBL 269 " --> pdb=" O GLUBL 266 " (cutoff:3.500A) Processing helix chain 'BM' and resid 4 through 10 removed outlier: 4.091A pdb=" N ARGBM 9 " --> pdb=" O VALBM 5 " (cutoff:3.500A) Processing helix chain 'BM' and resid 13 through 16 No H-bonds generated for 'chain 'BM' and resid 13 through 16' Processing helix chain 'BM' and resid 29 through 43 Processing helix chain 'BM' and resid 51 through 53 No H-bonds generated for 'chain 'BM' and resid 51 through 53' Processing helix chain 'BM' and resid 56 through 63 Processing helix chain 'BM' and resid 69 through 78 Processing helix chain 'BM' and resid 80 through 86 Processing helix chain 'BM' and resid 92 through 103 Processing helix chain 'BM' and resid 111 through 115 Processing helix chain 'BM' and resid 119 through 134 removed outlier: 8.129A pdb=" N TYRBM 126 " --> pdb=" O HISBM 122 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N GLUBM 127 " --> pdb=" O GLNBM 123 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALABM 128 " --> pdb=" O GLYBM 124 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N TYRBM 133 " --> pdb=" O GLUBM 129 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILEBM 134 " --> pdb=" O ILEBM 130 " (cutoff:3.500A) Processing helix chain 'BM' and resid 137 through 142 Processing helix chain 'BM' and resid 162 through 171 removed outlier: 3.792A pdb=" N SERBM 166 " --> pdb=" O THRBM 162 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHEBM 169 " --> pdb=" O PHEBM 165 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLNBM 170 " --> pdb=" O SERBM 166 " (cutoff:3.500A) Processing helix chain 'BM' and resid 191 through 195 Processing helix chain 'BM' and resid 250 through 262 removed outlier: 5.075A pdb=" N SERBM 254 " --> pdb=" O ASPBM 251 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALABM 255 " --> pdb=" O ASNBM 252 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARGBM 262 " --> pdb=" O GLNBM 259 " (cutoff:3.500A) Processing helix chain 'BN' and resid 31 through 33 No H-bonds generated for 'chain 'BN' and resid 31 through 33' Processing helix chain 'BN' and resid 52 through 64 removed outlier: 4.941A pdb=" N ASNBN 56 " --> pdb=" O ALABN 53 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLUBN 58 " --> pdb=" O METBN 55 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N METBN 59 " --> pdb=" O ASNBN 56 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'BL' and resid 259 through 264 removed outlier: 3.541A pdb=" N SERBL 284 " --> pdb=" O GLUBL 242 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N THRBL 244 " --> pdb=" O VALBL 282 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VALBL 282 " --> pdb=" O THRBL 244 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'BM' and resid 243 through 249 removed outlier: 6.242A pdb=" N ILEBM 228 " --> pdb=" O VALBM 267 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N VALBM 267 " --> pdb=" O ILEBM 228 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'BN' and resid 46 through 51 removed outlier: 3.743A pdb=" N ASNBN 71 " --> pdb=" O GLUBN 23 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N SERBN 25 " --> pdb=" O ILEBN 69 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ILEBN 69 " --> pdb=" O SERBN 25 " (cutoff:3.500A) 3434 hydrogen bonds defined for protein. 10158 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: 16.94 Time building geometry restraints manager: 22.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 9472 1.31 - 1.44: 14772 1.44 - 1.57: 30485 1.57 - 1.69: 10 1.69 - 1.82: 291 Bond restraints: 55030 Sorted by residual: bond pdb=" CG1 ILEAW 118 " pdb=" CD1 ILEAW 118 " ideal model delta sigma weight residual 1.513 1.345 0.168 3.90e-02 6.57e+02 1.85e+01 bond pdb=" CB GLNAU 15 " pdb=" CG GLNAU 15 " ideal model delta sigma weight residual 1.520 1.398 0.122 3.00e-02 1.11e+03 1.64e+01 bond pdb=" CB METAD 134 " pdb=" CG METAD 134 " ideal model delta sigma weight residual 1.520 1.403 0.117 3.00e-02 1.11e+03 1.52e+01 bond pdb=" SD METAD 134 " pdb=" CE METAD 134 " ideal model delta sigma weight residual 1.791 1.695 0.096 2.50e-02 1.60e+03 1.46e+01 bond pdb=" CG1 ILEBE 118 " pdb=" CD1 ILEBE 118 " ideal model delta sigma weight residual 1.513 1.377 0.136 3.90e-02 6.57e+02 1.21e+01 ... (remaining 55025 not shown) Histogram of bond angle deviations from ideal: 92.38 - 102.49: 135 102.49 - 112.59: 27213 112.59 - 122.70: 42589 122.70 - 132.81: 4811 132.81 - 142.92: 106 Bond angle restraints: 74854 Sorted by residual: angle pdb=" CD ARGBI 120 " pdb=" NE ARGBI 120 " pdb=" CZ ARGBI 120 " ideal model delta sigma weight residual 124.40 109.36 15.04 1.40e+00 5.10e-01 1.15e+02 angle pdb=" C ARGBD 114 " pdb=" CA ARGBD 114 " pdb=" CB ARGBD 114 " ideal model delta sigma weight residual 110.88 98.27 12.61 1.57e+00 4.06e-01 6.45e+01 angle pdb=" CG LYSBC 134 " pdb=" CD LYSBC 134 " pdb=" CE LYSBC 134 " ideal model delta sigma weight residual 111.30 96.67 14.63 2.30e+00 1.89e-01 4.05e+01 angle pdb=" CA GLNBM 259 " pdb=" CB GLNBM 259 " pdb=" CG GLNBM 259 " ideal model delta sigma weight residual 114.10 126.80 -12.70 2.00e+00 2.50e-01 4.04e+01 angle pdb=" N GLNAU 15 " pdb=" CA GLNAU 15 " pdb=" CB GLNAU 15 " ideal model delta sigma weight residual 110.44 100.98 9.46 1.53e+00 4.27e-01 3.82e+01 ... (remaining 74849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.56: 29448 18.56 - 37.12: 2176 37.12 - 55.68: 423 55.68 - 74.25: 243 74.25 - 92.81: 66 Dihedral angle restraints: 32356 sinusoidal: 12640 harmonic: 19716 Sorted by residual: dihedral pdb=" C ARGBD 114 " pdb=" N ARGBD 114 " pdb=" CA ARGBD 114 " pdb=" CB ARGBD 114 " ideal model delta harmonic sigma weight residual -122.60 -106.42 -16.18 0 2.50e+00 1.60e-01 4.19e+01 dihedral pdb=" C GLNAQ 68 " pdb=" N GLNAQ 68 " pdb=" CA GLNAQ 68 " pdb=" CB GLNAQ 68 " ideal model delta harmonic sigma weight residual -122.60 -136.03 13.43 0 2.50e+00 1.60e-01 2.88e+01 dihedral pdb=" N GLNAQ 68 " pdb=" C GLNAQ 68 " pdb=" CA GLNAQ 68 " pdb=" CB GLNAQ 68 " ideal model delta harmonic sigma weight residual 122.80 134.99 -12.19 0 2.50e+00 1.60e-01 2.38e+01 ... (remaining 32353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 7347 0.107 - 0.215: 780 0.215 - 0.322: 41 0.322 - 0.430: 10 0.430 - 0.537: 3 Chirality restraints: 8181 Sorted by residual: chirality pdb=" CA GLNAQ 68 " pdb=" N GLNAQ 68 " pdb=" C GLNAQ 68 " pdb=" CB GLNAQ 68 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.21e+00 chirality pdb=" CB ILEAM 118 " pdb=" CA ILEAM 118 " pdb=" CG1 ILEAM 118 " pdb=" CG2 ILEAM 118 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" CB VALBK 17 " pdb=" CA VALBK 17 " pdb=" CG1 VALBK 17 " pdb=" CG2 VALBK 17 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.31e+00 ... (remaining 8178 not shown) Planarity restraints: 9805 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB CYCBF 201 " 0.081 2.00e-02 2.50e+03 2.64e-01 1.56e+03 pdb=" OB CYCBF 201 " 0.143 2.00e-02 2.50e+03 pdb=" C1B CYCBF 201 " -0.071 2.00e-02 2.50e+03 pdb=" C2B CYCBF 201 " 0.134 2.00e-02 2.50e+03 pdb=" C3B CYCBF 201 " 0.106 2.00e-02 2.50e+03 pdb=" C4B CYCBF 201 " 0.123 2.00e-02 2.50e+03 pdb=" CAB CYCBF 201 " -0.522 2.00e-02 2.50e+03 pdb=" CHB CYCBF 201 " -0.369 2.00e-02 2.50e+03 pdb=" CMB CYCBF 201 " 0.375 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CYCAX 201 " -0.100 2.00e-02 2.50e+03 1.92e-01 8.28e+02 pdb=" OB CYCAX 201 " 0.205 2.00e-02 2.50e+03 pdb=" C1B CYCAX 201 " -0.046 2.00e-02 2.50e+03 pdb=" C2B CYCAX 201 " 0.121 2.00e-02 2.50e+03 pdb=" C3B CYCAX 201 " 0.145 2.00e-02 2.50e+03 pdb=" C4B CYCAX 201 " 0.025 2.00e-02 2.50e+03 pdb=" CAB CYCAX 201 " -0.397 2.00e-02 2.50e+03 pdb=" CHB CYCAX 201 " -0.179 2.00e-02 2.50e+03 pdb=" CMB CYCAX 201 " 0.226 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CYCAE 201 " 0.090 2.00e-02 2.50e+03 1.45e-01 4.72e+02 pdb=" OB CYCAE 201 " 0.037 2.00e-02 2.50e+03 pdb=" C1B CYCAE 201 " -0.057 2.00e-02 2.50e+03 pdb=" C2B CYCAE 201 " 0.058 2.00e-02 2.50e+03 pdb=" C3B CYCAE 201 " 0.087 2.00e-02 2.50e+03 pdb=" C4B CYCAE 201 " 0.079 2.00e-02 2.50e+03 pdb=" CAB CYCAE 201 " -0.277 2.00e-02 2.50e+03 pdb=" CHB CYCAE 201 " -0.210 2.00e-02 2.50e+03 pdb=" CMB CYCAE 201 " 0.194 2.00e-02 2.50e+03 ... (remaining 9802 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 1387 2.63 - 3.19: 52898 3.19 - 3.76: 107666 3.76 - 4.33: 143241 4.33 - 4.90: 223501 Nonbonded interactions: 528693 Sorted by model distance: nonbonded pdb=" NH1 ARGBD 114 " pdb=" O ALABD 172 " model vdw 2.057 2.520 nonbonded pdb=" O1D CYCBD 201 " pdb=" O HOHBD 301 " model vdw 2.165 2.440 nonbonded pdb=" O SERBL 177 " pdb=" OG SERBL 177 " model vdw 2.174 2.440 nonbonded pdb=" OG SERAN 76 " pdb=" O ALAAO 113 " model vdw 2.185 2.440 nonbonded pdb=" OD1 ASNBA 47 " pdb=" OG SERBA 50 " model vdw 2.189 2.440 ... (remaining 528688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'AA' selection = chain 'AC' selection = chain 'AE' selection = chain 'AG' selection = chain 'AI' selection = chain 'AK' selection = chain 'AM' selection = chain 'AO' selection = chain 'AQ' selection = chain 'AS' selection = chain 'AU' selection = chain 'AW' selection = chain 'AY' selection = chain 'BA' selection = chain 'BC' selection = chain 'BE' selection = chain 'BG' selection = chain 'BI' } ncs_group { reference = (chain 'AB' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'AD' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'AF' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'AH' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'AJ' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'AL' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'AN' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'AP' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'AR' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'AT' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'AV' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = chain 'AX' selection = (chain 'AZ' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'BB' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'BD' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'BF' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'BH' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'BJ' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 191 5.16 5 C 33993 2.51 5 N 9391 2.21 5 O 11862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 12.940 Check model and map are aligned: 0.610 Convert atoms to be neutral: 0.360 Process input model: 115.410 Find NCS groups from input model: 3.400 Set up NCS constraints: 0.720 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 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 : 0.011 0.168 55030 Z= 0.712 Angle : 1.136 16.822 74854 Z= 0.594 Chirality : 0.068 0.537 8181 Planarity : 0.012 0.264 9805 Dihedral : 15.334 92.808 19768 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.01 % Allowed : 0.99 % Favored : 98.99 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.10), residues: 6752 helix: 1.93 (0.07), residues: 5195 sheet: 1.04 (0.53), residues: 55 loop : -0.20 (0.16), residues: 1502 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 996 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 955 time to evaluate : 4.902 Fit side-chains TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. outliers start: 41 outliers final: 8 residues processed: 968 average time/residue: 1.6042 time to fit residues: 1897.1188 Evaluate side-chains 866 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 858 time to evaluate : 4.667 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 2 residues processed: 6 average time/residue: 1.2857 time to fit residues: 15.8288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 569 optimal weight: 0.9980 chunk 510 optimal weight: 0.9990 chunk 283 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 344 optimal weight: 1.9990 chunk 272 optimal weight: 0.9990 chunk 528 optimal weight: 0.9980 chunk 204 optimal weight: 0.7980 chunk 321 optimal weight: 0.9990 chunk 393 optimal weight: 0.9980 chunk 612 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AC 15 GLN AC 35 ASN AC 78 GLN AE 39 GLN AE 68 GLN AF 68 GLN ** AF 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 111 ASN AG 53 ASN AI 49 GLN AJ 68 GLN AL 35 ASN AL 68 GLN AM 68 GLN AN 111 ASN AO 78 GLN AQ 15 GLN AQ 39 GLN AR 68 GLN AR 111 ASN AS 15 GLN AS 68 GLN AT 132 GLN ** AU 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 39 GLN ** AW 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 68 GLN AW 78 GLN AW 139 ASN ** AX 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AX 146 ASN AY 39 GLN AY 47 ASN AY 53 ASN AY 78 GLN AZ 132 GLN BA 49 GLN BA 61 ASN BA 78 GLN BB 65 GLN BC 49 GLN BC 57 GLN BC 78 GLN ** BD 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 39 GLN BF 68 GLN BF 132 GLN BG 49 GLN BG 53 ASN ** BI 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 53 ASN BJ 11 GLN BL 89 ASN ** BM 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 12 ASN BN 14 GLN BN 71 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 55030 Z= 0.161 Angle : 0.574 9.882 74854 Z= 0.280 Chirality : 0.036 0.159 8181 Planarity : 0.004 0.050 9805 Dihedral : 10.471 85.304 8377 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.10), residues: 6752 helix: 2.22 (0.07), residues: 5193 sheet: 1.03 (0.56), residues: 55 loop : -0.18 (0.16), residues: 1504 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 998 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 953 time to evaluate : 4.727 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. outliers start: 45 outliers final: 17 residues processed: 964 average time/residue: 1.6165 time to fit residues: 1904.5799 Evaluate side-chains 910 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 893 time to evaluate : 4.655 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 8 residues processed: 9 average time/residue: 0.9325 time to fit residues: 17.5805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 340 optimal weight: 8.9990 chunk 189 optimal weight: 3.9990 chunk 509 optimal weight: 8.9990 chunk 416 optimal weight: 7.9990 chunk 168 optimal weight: 1.9990 chunk 613 optimal weight: 4.9990 chunk 662 optimal weight: 5.9990 chunk 546 optimal weight: 6.9990 chunk 608 optimal weight: 3.9990 chunk 209 optimal weight: 0.8980 chunk 491 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AC 15 GLN AC 35 ASN AC 78 GLN AE 39 GLN AE 68 GLN AE 78 GLN ** AF 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 111 ASN AG 53 ASN AL 35 ASN AL 47 ASN ** AM 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 68 GLN AN 111 ASN ** AO 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 78 GLN AQ 15 GLN AQ 39 GLN AR 68 GLN AR 111 ASN AS 68 GLN ** AU 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 47 ASN AU 78 GLN ** AW 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 78 GLN AW 139 ASN ** AX 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AX 68 GLN AX 146 ASN AY 39 GLN AY 47 ASN AY 53 ASN AY 78 GLN AZ 132 GLN ** BA 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 61 ASN BA 78 GLN BB 68 GLN BC 49 GLN BC 78 GLN ** BD 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 68 GLN BF 132 GLN BG 49 GLN BG 53 ASN BI 47 ASN BI 53 ASN BJ 11 GLN BK 188 GLN BL 89 ASN BN 14 GLN ** BN 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 55030 Z= 0.321 Angle : 0.675 10.075 74854 Z= 0.335 Chirality : 0.042 0.225 8181 Planarity : 0.005 0.059 9805 Dihedral : 10.553 88.652 8377 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.10), residues: 6752 helix: 2.04 (0.07), residues: 5202 sheet: 0.89 (0.54), residues: 46 loop : -0.10 (0.16), residues: 1504 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 912 time to evaluate : 4.731 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. outliers start: 80 outliers final: 37 residues processed: 942 average time/residue: 1.6302 time to fit residues: 1875.7973 Evaluate side-chains 917 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 880 time to evaluate : 4.662 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 19 residues processed: 18 average time/residue: 0.9478 time to fit residues: 29.4632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 605 optimal weight: 8.9990 chunk 461 optimal weight: 0.7980 chunk 318 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 292 optimal weight: 3.9990 chunk 411 optimal weight: 6.9990 chunk 615 optimal weight: 2.9990 chunk 651 optimal weight: 0.0970 chunk 321 optimal weight: 1.9990 chunk 583 optimal weight: 9.9990 chunk 175 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AC 15 GLN AC 39 GLN AC 78 GLN AE 39 GLN AE 78 GLN AF 72 ASN AF 111 ASN AG 53 ASN ** AH 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 47 ASN ** AK 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 70 GLN AL 35 ASN AL 47 ASN ** AM 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 68 GLN AN 111 ASN AO 47 ASN ** AO 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 78 GLN AQ 15 GLN AQ 39 GLN AR 68 GLN AR 111 ASN AS 68 GLN ** AU 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 47 ASN ** AW 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 78 GLN AW 139 ASN ** AX 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AX 146 ASN AY 39 GLN AY 47 ASN AY 53 ASN AY 78 GLN AZ 132 GLN BA 49 GLN BA 61 ASN BC 49 GLN BC 78 GLN BD 65 GLN ** BD 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 39 GLN BF 132 GLN BG 49 GLN BG 53 ASN BI 53 ASN BJ 11 GLN BL 89 ASN BM 259 GLN ** BN 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 55030 Z= 0.168 Angle : 0.555 10.039 74854 Z= 0.270 Chirality : 0.036 0.153 8181 Planarity : 0.003 0.044 9805 Dihedral : 10.540 88.100 8377 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.10), residues: 6752 helix: 2.29 (0.07), residues: 5201 sheet: 1.00 (0.57), residues: 50 loop : -0.09 (0.16), residues: 1501 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 917 time to evaluate : 4.676 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. outliers start: 67 outliers final: 32 residues processed: 948 average time/residue: 1.6623 time to fit residues: 1913.6568 Evaluate side-chains 913 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 881 time to evaluate : 4.669 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 20 residues processed: 12 average time/residue: 1.0607 time to fit residues: 22.9181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 542 optimal weight: 3.9990 chunk 369 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 485 optimal weight: 2.9990 chunk 268 optimal weight: 0.7980 chunk 555 optimal weight: 6.9990 chunk 450 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 332 optimal weight: 2.9990 chunk 584 optimal weight: 0.3980 chunk 164 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 78 GLN AC 15 GLN AC 35 ASN AC 78 GLN AE 39 GLN AE 78 GLN AF 111 ASN AG 53 ASN ** AH 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 47 ASN ** AK 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 70 GLN AL 35 ASN ** AM 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 68 GLN AN 111 ASN AO 47 ASN AO 78 GLN AQ 15 GLN AQ 39 GLN AQ 68 GLN AR 111 ASN AS 68 GLN ** AU 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 47 ASN AU 78 GLN ** AW 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 78 GLN AW 139 ASN ** AX 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AX 146 ASN AY 39 GLN AY 53 ASN AY 78 GLN AZ 132 GLN BA 49 GLN BA 61 ASN BB 35 ASN BC 49 GLN BC 78 GLN BD 65 GLN BD 72 ASN BE 39 GLN BG 49 GLN BG 53 ASN BI 53 ASN BJ 11 GLN BL 89 ASN BM 8 GLN BM 258 GLN ** BN 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 55030 Z= 0.202 Angle : 0.578 9.994 74854 Z= 0.282 Chirality : 0.037 0.152 8181 Planarity : 0.004 0.046 9805 Dihedral : 10.479 88.382 8377 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.10), residues: 6752 helix: 2.23 (0.07), residues: 5252 sheet: 0.96 (0.57), residues: 50 loop : -0.13 (0.16), residues: 1450 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 891 time to evaluate : 4.962 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. outliers start: 77 outliers final: 37 residues processed: 929 average time/residue: 1.6404 time to fit residues: 1858.8383 Evaluate side-chains 916 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 879 time to evaluate : 4.637 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 22 residues processed: 15 average time/residue: 0.8900 time to fit residues: 24.6844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 219 optimal weight: 3.9990 chunk 586 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 382 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 652 optimal weight: 0.9990 chunk 541 optimal weight: 8.9990 chunk 301 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 342 optimal weight: 0.3980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 78 GLN ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 15 GLN AC 35 ASN AC 39 GLN AE 39 GLN AE 78 GLN AF 111 ASN AG 53 ASN AH 72 ASN AI 47 ASN AK 47 ASN ** AK 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 70 GLN AL 35 ASN ** AM 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 68 GLN AN 111 ASN AO 47 ASN ** AO 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 15 GLN AQ 39 GLN AQ 68 GLN AR 111 ASN AS 68 GLN AT 68 GLN AT 132 GLN ** AU 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 78 GLN ** AW 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 78 GLN ** AX 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AX 146 ASN AY 39 GLN AY 53 ASN AY 78 GLN AZ 132 GLN BA 49 GLN BA 61 ASN BB 35 ASN BC 49 GLN BC 78 GLN BE 39 GLN BF 132 GLN BG 15 GLN BG 49 GLN BG 53 ASN BI 53 ASN BJ 11 GLN BL 89 ASN BM 8 GLN BM 258 GLN BM 263 GLN ** BN 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 55030 Z= 0.203 Angle : 0.576 9.984 74854 Z= 0.282 Chirality : 0.037 0.152 8181 Planarity : 0.004 0.044 9805 Dihedral : 10.490 89.269 8377 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.10), residues: 6752 helix: 2.25 (0.07), residues: 5241 sheet: 0.97 (0.57), residues: 50 loop : -0.05 (0.16), residues: 1461 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 885 time to evaluate : 4.688 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. outliers start: 77 outliers final: 40 residues processed: 921 average time/residue: 1.6223 time to fit residues: 1824.6372 Evaluate side-chains 902 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 862 time to evaluate : 4.692 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 24 residues processed: 16 average time/residue: 0.9913 time to fit residues: 27.5116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 628 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 371 optimal weight: 0.9990 chunk 476 optimal weight: 7.9990 chunk 368 optimal weight: 6.9990 chunk 548 optimal weight: 9.9990 chunk 364 optimal weight: 1.9990 chunk 649 optimal weight: 5.9990 chunk 406 optimal weight: 0.8980 chunk 396 optimal weight: 10.0000 chunk 299 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 78 GLN ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 15 GLN AC 35 ASN AC 78 GLN AE 68 GLN AE 78 GLN AG 53 ASN AI 39 GLN AI 47 ASN AJ 143 ASN ** AK 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 70 GLN AL 35 ASN ** AM 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 68 GLN AN 111 ASN AO 47 ASN ** AO 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 78 GLN AQ 15 GLN AQ 39 GLN AQ 68 GLN AR 111 ASN AS 68 GLN AT 68 GLN AT 132 GLN ** AU 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 78 GLN ** AW 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 78 GLN ** AX 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AX 146 ASN AY 39 GLN AY 47 ASN AY 53 ASN AY 78 GLN AZ 132 GLN BA 49 GLN BA 61 ASN BC 49 GLN BC 78 GLN BD 65 GLN BE 39 GLN BF 132 GLN BG 53 ASN BI 53 ASN BJ 11 GLN BL 89 ASN BM 8 GLN BM 258 GLN BM 263 GLN BN 12 ASN ** BN 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 55030 Z= 0.256 Angle : 0.620 9.971 74854 Z= 0.306 Chirality : 0.040 0.169 8181 Planarity : 0.004 0.055 9805 Dihedral : 10.508 88.370 8377 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.10), residues: 6752 helix: 2.18 (0.07), residues: 5202 sheet: 0.92 (0.57), residues: 50 loop : -0.03 (0.16), residues: 1500 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 878 time to evaluate : 4.872 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. outliers start: 78 outliers final: 42 residues processed: 918 average time/residue: 1.6421 time to fit residues: 1844.9102 Evaluate side-chains 905 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 863 time to evaluate : 4.721 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 27 residues processed: 15 average time/residue: 0.9126 time to fit residues: 25.2008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 401 optimal weight: 2.9990 chunk 259 optimal weight: 0.3980 chunk 387 optimal weight: 2.9990 chunk 195 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 413 optimal weight: 2.9990 chunk 442 optimal weight: 5.9990 chunk 321 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 510 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 78 GLN ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 15 GLN AC 35 ASN AC 39 GLN AC 78 GLN AE 68 GLN AF 111 ASN AG 15 GLN AG 53 ASN AI 39 GLN AI 47 ASN ** AK 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 70 GLN AL 35 ASN ** AM 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 68 GLN AN 111 ASN AO 47 ASN ** AO 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 15 GLN AQ 39 GLN AQ 68 GLN AR 111 ASN AS 68 GLN AT 68 GLN AT 132 GLN ** AU 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 78 GLN ** AW 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 78 GLN ** AX 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AX 146 ASN AY 39 GLN AY 47 ASN AY 53 ASN AY 78 GLN AZ 132 GLN BA 49 GLN BA 61 ASN BC 49 GLN BC 78 GLN BE 39 GLN BF 132 GLN BG 53 ASN BI 53 ASN BJ 11 GLN BL 89 ASN BM 8 GLN BM 258 GLN ** BM 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 71 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 55030 Z= 0.230 Angle : 0.602 9.982 74854 Z= 0.296 Chirality : 0.039 0.159 8181 Planarity : 0.004 0.050 9805 Dihedral : 10.525 88.742 8377 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.10), residues: 6752 helix: 2.20 (0.07), residues: 5208 sheet: 0.93 (0.56), residues: 50 loop : -0.04 (0.16), residues: 1494 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 875 time to evaluate : 4.737 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. outliers start: 74 outliers final: 47 residues processed: 920 average time/residue: 1.6784 time to fit residues: 1885.1810 Evaluate side-chains 917 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 870 time to evaluate : 4.740 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 34 residues processed: 13 average time/residue: 0.9464 time to fit residues: 23.1012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 590 optimal weight: 2.9990 chunk 622 optimal weight: 0.6980 chunk 567 optimal weight: 0.9980 chunk 605 optimal weight: 8.9990 chunk 364 optimal weight: 5.9990 chunk 263 optimal weight: 5.9990 chunk 475 optimal weight: 10.0000 chunk 185 optimal weight: 9.9990 chunk 547 optimal weight: 0.9990 chunk 572 optimal weight: 1.9990 chunk 603 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 78 GLN ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 15 GLN AC 35 ASN AC 78 GLN AE 68 GLN AF 111 ASN AG 53 ASN AI 39 GLN ** AK 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 70 GLN AL 35 ASN ** AM 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 68 GLN AN 111 ASN AO 47 ASN ** AO 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 78 GLN AQ 15 GLN AQ 39 GLN AQ 68 GLN AR 111 ASN AS 68 GLN AT 68 GLN ** AU 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 78 GLN ** AW 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 78 GLN ** AX 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AX 146 ASN AY 39 GLN AY 47 ASN AY 53 ASN AY 78 GLN AZ 132 GLN BA 49 GLN BA 61 ASN BC 49 GLN BC 78 GLN BE 39 GLN BF 132 GLN BG 15 GLN BG 53 ASN BI 53 ASN BJ 11 GLN BL 89 ASN BM 8 GLN BM 258 GLN ** BM 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 55030 Z= 0.197 Angle : 0.579 9.989 74854 Z= 0.285 Chirality : 0.037 0.162 8181 Planarity : 0.004 0.044 9805 Dihedral : 10.507 87.945 8377 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.10), residues: 6752 helix: 2.24 (0.07), residues: 5241 sheet: 0.96 (0.56), residues: 50 loop : -0.05 (0.16), residues: 1461 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 892 time to evaluate : 4.712 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. outliers start: 52 outliers final: 43 residues processed: 929 average time/residue: 1.6447 time to fit residues: 1867.4954 Evaluate side-chains 913 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 870 time to evaluate : 4.662 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 34 residues processed: 9 average time/residue: 1.1580 time to fit residues: 19.6833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 397 optimal weight: 0.9990 chunk 640 optimal weight: 10.0000 chunk 390 optimal weight: 10.0000 chunk 303 optimal weight: 3.9990 chunk 445 optimal weight: 7.9990 chunk 671 optimal weight: 0.8980 chunk 618 optimal weight: 0.8980 chunk 534 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 413 optimal weight: 6.9990 chunk 327 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 78 GLN ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 15 GLN AC 35 ASN AC 39 GLN AE 68 GLN AF 111 ASN AG 53 ASN AI 39 GLN ** AK 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 70 GLN AL 35 ASN ** AL 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 68 GLN AN 111 ASN AO 47 ASN ** AO 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 15 GLN AQ 39 GLN AQ 68 GLN AR 111 ASN AS 68 GLN AT 68 GLN ** AU 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 78 GLN ** AW 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AX 146 ASN AY 39 GLN AY 47 ASN AY 53 ASN AY 78 GLN AZ 132 GLN BA 49 GLN BA 61 ASN BC 49 GLN BC 78 GLN BE 39 GLN BF 132 GLN BG 53 ASN BI 53 ASN BJ 11 GLN BL 89 ASN BM 8 GLN BM 258 GLN ** BM 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 71 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 55030 Z= 0.198 Angle : 0.582 9.958 74854 Z= 0.286 Chirality : 0.037 0.163 8181 Planarity : 0.004 0.044 9805 Dihedral : 10.492 88.185 8377 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.10), residues: 6752 helix: 2.25 (0.07), residues: 5241 sheet: 0.95 (0.56), residues: 50 loop : -0.04 (0.16), residues: 1461 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 927 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 876 time to evaluate : 4.737 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. outliers start: 51 outliers final: 41 residues processed: 913 average time/residue: 1.6553 time to fit residues: 1851.4427 Evaluate side-chains 914 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 873 time to evaluate : 4.701 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 35 residues processed: 6 average time/residue: 1.1188 time to fit residues: 14.9122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 424 optimal weight: 0.9990 chunk 569 optimal weight: 9.9990 chunk 163 optimal weight: 20.0000 chunk 493 optimal weight: 0.9980 chunk 78 optimal weight: 0.1980 chunk 148 optimal weight: 4.9990 chunk 535 optimal weight: 0.0040 chunk 224 optimal weight: 0.9990 chunk 549 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 78 GLN AC 15 GLN AC 35 ASN ** AC 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 78 GLN AE 68 GLN AF 111 ASN AG 53 ASN AI 39 GLN AK 49 GLN AK 70 GLN AL 35 ASN AL 65 GLN AL 132 GLN ** AM 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 68 GLN AN 111 ASN AO 47 ASN AQ 15 GLN AQ 39 GLN AQ 68 GLN AR 111 ASN AS 39 GLN AS 68 GLN AT 68 GLN ** AU 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 78 GLN ** AW 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AX 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AX 146 ASN AY 39 GLN AY 47 ASN AY 53 ASN AY 78 GLN AZ 68 GLN AZ 132 GLN BA 49 GLN BA 61 ASN BC 49 GLN BC 78 GLN BE 39 GLN BF 132 GLN BG 49 GLN BG 53 ASN BI 53 ASN BJ 11 GLN BL 89 ASN BM 8 GLN BM 258 GLN ** BM 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 71 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.137266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.124335 restraints weight = 57483.491| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 0.71 r_work: 0.3432 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 55030 Z= 0.141 Angle : 0.525 9.980 74854 Z= 0.257 Chirality : 0.035 0.174 8181 Planarity : 0.003 0.042 9805 Dihedral : 10.455 87.532 8377 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.10), residues: 6752 helix: 2.45 (0.07), residues: 5233 sheet: 1.13 (0.58), residues: 50 loop : 0.02 (0.16), residues: 1469 =============================================================================== Job complete usr+sys time: 23854.25 seconds wall clock time: 412 minutes 24.14 seconds (24744.14 seconds total)