Starting phenix.real_space_refine on Mon Mar 11 04:42:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sca_25031/03_2024/7sca_25031_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sca_25031/03_2024/7sca_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_25031/03_2024/7sca_25031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sca_25031/03_2024/7sca_25031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sca_25031/03_2024/7sca_25031_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sca_25031/03_2024/7sca_25031_updated.pdb" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 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. 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 22.39, per 1000 atoms: 0.40 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: 20.51 Conformation dependent library (CDL) restraints added in 7.2 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: 6.53 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: 16.03 Time building geometry restraints manager: 22.11 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: 30987 18.56 - 37.12: 2253 37.12 - 55.68: 427 55.68 - 74.25: 243 74.25 - 92.81: 66 Dihedral angle restraints: 33976 sinusoidal: 14260 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 33973 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 11.620 Check model and map are aligned: 0.640 Set scattering table: 0.370 Process input model: 116.230 Find NCS groups from input model: 3.460 Set up NCS constraints: 0.860 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 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 : 14.951 92.808 21388 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.01 % Allowed : 0.99 % Favored : 98.99 % Rotamer: Outliers : 0.78 % Allowed : 1.70 % Favored : 97.52 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.006 TRPBG 128 HIS 0.018 0.007 HISAK 140 PHE 0.037 0.004 PHEAM 63 TYR 0.055 0.004 TYRBN 75 ARG 0.087 0.003 ARGAX 114 *********************** 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 : 4.655 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. REVERT: AA 79 ARG cc_start: 0.8118 (ttp80) cc_final: 0.7432 (ttp80) REVERT: AD 156 ILE cc_start: 0.8389 (tp) cc_final: 0.8175 (tp) REVERT: AF 15 ARG cc_start: 0.7312 (mtm-85) cc_final: 0.7107 (mtp180) REVERT: AF 17 GLU cc_start: 0.7895 (pt0) cc_final: 0.7678 (pt0) REVERT: AF 39 ASP cc_start: 0.8253 (m-30) cc_final: 0.8029 (m-30) REVERT: AG 42 LYS cc_start: 0.8204 (ttpm) cc_final: 0.7909 (ttpt) REVERT: AJ 30 THR cc_start: 0.8809 (m) cc_final: 0.8581 (m) REVERT: AK 35 ASN cc_start: 0.8199 (m-40) cc_final: 0.7904 (m110) REVERT: AN 79 MET cc_start: 0.9170 (tpp) cc_final: 0.8950 (tpp) REVERT: AT 134 MET cc_start: 0.8980 (mtm) cc_final: 0.8544 (mtp) REVERT: AY 42 LYS cc_start: 0.8192 (tttp) cc_final: 0.7987 (tppt) REVERT: BB 25 ASP cc_start: 0.6704 (m-30) cc_final: 0.6386 (m-30) REVERT: BB 156 ILE cc_start: 0.8227 (mm) cc_final: 0.7878 (mm) REVERT: BD 25 ASP cc_start: 0.7365 (p0) cc_final: 0.7137 (p0) REVERT: BD 30 THR cc_start: 0.8825 (m) cc_final: 0.8592 (m) REVERT: BH 133 LYS cc_start: 0.8553 (mttp) cc_final: 0.8171 (mttp) REVERT: BI 39 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7350 (mm-40) REVERT: BJ 79 MET cc_start: 0.8946 (tpp) cc_final: 0.8708 (tpp) REVERT: BK 42 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8118 (tpt) REVERT: BN 48 ILE cc_start: 0.8555 (mt) cc_final: 0.8226 (mm) outliers start: 41 outliers final: 8 residues processed: 968 average time/residue: 1.7344 time to fit residues: 2035.3016 Evaluate side-chains 870 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 860 time to evaluate : 4.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AJ residue 8 VAL Chi-restraints excluded: chain AM residue 109 GLU Chi-restraints excluded: chain AO residue 120 ARG Chi-restraints excluded: chain AW residue 1 MET Chi-restraints excluded: chain BG residue 14 SER Chi-restraints excluded: chain BI residue 39 GLN Chi-restraints excluded: chain BI residue 42 LYS Chi-restraints excluded: chain BK residue 42 MET Chi-restraints excluded: chain BL residue 29 LEU Chi-restraints excluded: chain BL residue 47 ASP 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: 0.7980 chunk 393 optimal weight: 0.9980 chunk 612 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 AU 47 ASN ** 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 BB 68 GLN BC 49 GLN BC 57 GLN BC 78 GLN ** BD 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 68 GLN BF 132 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: 0.8197 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 55030 Z= 0.161 Angle : 0.574 10.013 74854 Z= 0.279 Chirality : 0.036 0.159 8181 Planarity : 0.004 0.050 9805 Dihedral : 10.174 83.866 10023 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.81 % Allowed : 4.79 % Favored : 94.39 % 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: 2.57 (0.10), residues: 6752 helix: 2.24 (0.07), residues: 5193 sheet: 1.04 (0.56), residues: 55 loop : -0.17 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPBM 146 HIS 0.006 0.002 HISBA 140 PHE 0.013 0.001 PHEBL 91 TYR 0.021 0.001 TYRBN 75 ARG 0.007 0.000 ARGBM 158 *********************** 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 1006 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 963 time to evaluate : 4.640 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. REVERT: AA 79 ARG cc_start: 0.7933 (ttp80) cc_final: 0.7309 (ttp80) REVERT: AD 156 ILE cc_start: 0.8401 (tp) cc_final: 0.8183 (tp) REVERT: AG 120 ARG cc_start: 0.7814 (ttp80) cc_final: 0.7344 (ttp-110) REVERT: AI 79 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7877 (ttt-90) REVERT: AK 35 ASN cc_start: 0.8182 (m-40) cc_final: 0.7972 (m110) REVERT: AL 65 GLN cc_start: 0.7580 (pm20) cc_final: 0.7292 (pp30) REVERT: AN 65 GLN cc_start: 0.7794 (pt0) cc_final: 0.7350 (tp40) REVERT: AN 79 MET cc_start: 0.9147 (tpp) cc_final: 0.8941 (tpp) REVERT: AO 109 GLU cc_start: 0.7786 (tt0) cc_final: 0.7480 (tt0) REVERT: AP 132 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7702 (tm-30) REVERT: AT 134 MET cc_start: 0.8982 (mtm) cc_final: 0.8450 (mtm) REVERT: AU 109 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7293 (tp30) REVERT: AV 79 MET cc_start: 0.8803 (tpp) cc_final: 0.8546 (tpp) REVERT: AX 87 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7417 (tm-30) REVERT: AY 42 LYS cc_start: 0.8203 (tttp) cc_final: 0.7976 (tppt) REVERT: AY 78 GLN cc_start: 0.8543 (tp40) cc_final: 0.8336 (tp-100) REVERT: AY 118 ILE cc_start: 0.8767 (mt) cc_final: 0.8470 (mt) REVERT: AZ 65 GLN cc_start: 0.7887 (pm20) cc_final: 0.7491 (pm20) REVERT: BA 42 LYS cc_start: 0.8081 (ttpp) cc_final: 0.7858 (tttt) REVERT: BA 49 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.7147 (pm20) REVERT: BA 53 ASN cc_start: 0.7367 (m110) cc_final: 0.7105 (m110) REVERT: BB 156 ILE cc_start: 0.8177 (mm) cc_final: 0.7890 (mm) REVERT: BD 114 ARG cc_start: 0.7278 (tpp-160) cc_final: 0.7030 (ttm170) REVERT: BF 159 GLU cc_start: 0.8057 (tt0) cc_final: 0.7848 (tt0) REVERT: BH 133 LYS cc_start: 0.8368 (mttp) cc_final: 0.8122 (mttp) REVERT: BI 79 ARG cc_start: 0.8288 (ttp80) cc_final: 0.8048 (ttp80) REVERT: BJ 134 MET cc_start: 0.8609 (mtm) cc_final: 0.8219 (mtm) REVERT: BK 42 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8042 (tpt) REVERT: BN 48 ILE cc_start: 0.8509 (mt) cc_final: 0.8237 (mp) REVERT: BN 54 ARG cc_start: 0.7960 (mtm110) cc_final: 0.7547 (mtm110) outliers start: 43 outliers final: 16 residues processed: 974 average time/residue: 1.7307 time to fit residues: 2040.7024 Evaluate side-chains 909 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 888 time to evaluate : 4.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 50 SER Chi-restraints excluded: chain AB residue 39 ASP Chi-restraints excluded: chain AB residue 86 MET Chi-restraints excluded: chain AG residue 39 GLN Chi-restraints excluded: chain AG residue 50 SER Chi-restraints excluded: chain AI residue 79 ARG Chi-restraints excluded: chain AJ residue 8 VAL Chi-restraints excluded: chain AP residue 132 GLN Chi-restraints excluded: chain AU residue 1 MET Chi-restraints excluded: chain AU residue 15 GLN Chi-restraints excluded: chain AU residue 109 GLU Chi-restraints excluded: chain AX residue 22 SER Chi-restraints excluded: chain BA residue 49 GLN Chi-restraints excluded: chain BD residue 77 ARG Chi-restraints excluded: chain BE residue 10 SER Chi-restraints excluded: chain BF residue 141 ILE Chi-restraints excluded: chain BG residue 116 ASP Chi-restraints excluded: chain BK residue 42 MET Chi-restraints excluded: chain BL residue 29 LEU Chi-restraints excluded: chain BL residue 47 ASP Chi-restraints excluded: chain BM residue 96 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 340 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 509 optimal weight: 8.9990 chunk 416 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 613 optimal weight: 4.9990 chunk 662 optimal weight: 5.9990 chunk 546 optimal weight: 6.9990 chunk 608 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 491 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 AK 47 ASN AL 35 ASN 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 AZ 132 GLN 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 BL 89 ASN BN 14 GLN BN 71 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 55030 Z= 0.262 Angle : 0.631 10.100 74854 Z= 0.311 Chirality : 0.040 0.198 8181 Planarity : 0.004 0.051 9805 Dihedral : 10.330 86.820 10005 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.40 % Allowed : 7.01 % Favored : 91.59 % 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: 2.50 (0.10), residues: 6752 helix: 2.17 (0.07), residues: 5202 sheet: 1.15 (0.58), residues: 50 loop : -0.10 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRPBI 128 HIS 0.009 0.003 HISAK 140 PHE 0.015 0.002 PHEAX 98 TYR 0.023 0.002 TYRBN 75 ARG 0.007 0.001 ARGBM 158 *********************** 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 985 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 911 time to evaluate : 4.672 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. REVERT: AA 79 ARG cc_start: 0.7959 (ttp80) cc_final: 0.7265 (ttp80) REVERT: AB 165 ASP cc_start: 0.8359 (m-30) cc_final: 0.8115 (m-30) REVERT: AC 39 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.7133 (mm110) REVERT: AD 33 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6826 (pp20) REVERT: AE 117 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7439 (pm20) REVERT: AG 42 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7877 (ttpp) REVERT: AG 120 ARG cc_start: 0.7896 (ttp80) cc_final: 0.7433 (ttp-110) REVERT: AJ 30 THR cc_start: 0.8841 (m) cc_final: 0.8628 (m) REVERT: AK 35 ASN cc_start: 0.8217 (m-40) cc_final: 0.8001 (m110) REVERT: AN 65 GLN cc_start: 0.8009 (pt0) cc_final: 0.7504 (tp40) REVERT: AN 79 MET cc_start: 0.9200 (tpp) cc_final: 0.8997 (tpp) REVERT: AP 166 ARG cc_start: 0.8401 (ttm-80) cc_final: 0.8174 (ttt180) REVERT: AQ 1 MET cc_start: 0.7480 (tpp) cc_final: 0.7133 (tpt) REVERT: AR 108 ARG cc_start: 0.7667 (mtt-85) cc_final: 0.7457 (mmt-90) REVERT: AS 7 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7538 (mt-10) REVERT: AT 134 MET cc_start: 0.9037 (mtm) cc_final: 0.8488 (mtm) REVERT: AU 109 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7351 (tp30) REVERT: AW 78 GLN cc_start: 0.8400 (tp40) cc_final: 0.8141 (tp-100) REVERT: AY 42 LYS cc_start: 0.8255 (tttp) cc_final: 0.7958 (tppt) REVERT: AY 109 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7535 (tt0) REVERT: AY 117 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7488 (mt-10) REVERT: AY 118 ILE cc_start: 0.8794 (mt) cc_final: 0.8508 (mt) REVERT: AZ 65 GLN cc_start: 0.7983 (pm20) cc_final: 0.7641 (pm20) REVERT: BB 156 ILE cc_start: 0.8305 (mm) cc_final: 0.8073 (mm) REVERT: BC 117 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: BF 159 GLU cc_start: 0.8154 (tt0) cc_final: 0.7908 (tt0) REVERT: BJ 134 MET cc_start: 0.8678 (mtm) cc_final: 0.8413 (mtm) REVERT: BL 273 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.6976 (mt0) REVERT: BM 50 MET cc_start: 0.8531 (mmt) cc_final: 0.8145 (mmt) REVERT: BN 48 ILE cc_start: 0.8536 (mt) cc_final: 0.8232 (mp) REVERT: BN 64 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7223 (mtm110) REVERT: BN 70 VAL cc_start: 0.8176 (m) cc_final: 0.7947 (p) outliers start: 74 outliers final: 37 residues processed: 933 average time/residue: 1.7480 time to fit residues: 1972.0056 Evaluate side-chains 938 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 890 time to evaluate : 4.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 50 SER Chi-restraints excluded: chain AB residue 86 MET Chi-restraints excluded: chain AC residue 39 GLN Chi-restraints excluded: chain AC residue 42 LYS Chi-restraints excluded: chain AD residue 33 GLU Chi-restraints excluded: chain AE residue 10 SER Chi-restraints excluded: chain AE residue 117 GLU Chi-restraints excluded: chain AG residue 39 GLN Chi-restraints excluded: chain AG residue 42 LYS Chi-restraints excluded: chain AG residue 50 SER Chi-restraints excluded: chain AI residue 79 ARG Chi-restraints excluded: chain AJ residue 8 VAL Chi-restraints excluded: chain AJ residue 22 SER Chi-restraints excluded: chain AJ residue 86 MET Chi-restraints excluded: chain AL residue 22 SER Chi-restraints excluded: chain AM residue 1 MET Chi-restraints excluded: chain AO residue 39 GLN Chi-restraints excluded: chain AP residue 136 GLU Chi-restraints excluded: chain AP residue 156 ILE Chi-restraints excluded: chain AQ residue 117 GLU Chi-restraints excluded: chain AR residue 22 SER Chi-restraints excluded: chain AS residue 7 GLU Chi-restraints excluded: chain AT residue 8 VAL Chi-restraints excluded: chain AU residue 1 MET Chi-restraints excluded: chain AU residue 109 GLU Chi-restraints excluded: chain AW residue 152 SER Chi-restraints excluded: chain AX residue 22 SER Chi-restraints excluded: chain AY residue 109 GLU Chi-restraints excluded: chain AY residue 117 GLU Chi-restraints excluded: chain BB residue 141 ILE Chi-restraints excluded: chain BC residue 117 GLU Chi-restraints excluded: chain BD residue 77 ARG Chi-restraints excluded: chain BE residue 10 SER Chi-restraints excluded: chain BE residue 50 SER Chi-restraints excluded: chain BF residue 1 MET Chi-restraints excluded: chain BF residue 141 ILE Chi-restraints excluded: chain BF residue 144 ASP Chi-restraints excluded: chain BG residue 14 SER Chi-restraints excluded: chain BG residue 116 ASP Chi-restraints excluded: chain BH residue 62 GLU Chi-restraints excluded: chain BK residue 17 VAL Chi-restraints excluded: chain BK residue 155 THR Chi-restraints excluded: chain BL residue 29 LEU Chi-restraints excluded: chain BL residue 47 ASP Chi-restraints excluded: chain BL residue 157 VAL Chi-restraints excluded: chain BL residue 273 GLN Chi-restraints excluded: chain BM residue 96 ILE Chi-restraints excluded: chain BN residue 64 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 605 optimal weight: 9.9990 chunk 461 optimal weight: 0.7980 chunk 318 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 292 optimal weight: 2.9990 chunk 411 optimal weight: 7.9990 chunk 615 optimal weight: 20.0000 chunk 651 optimal weight: 0.0980 chunk 321 optimal weight: 0.6980 chunk 583 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AC 15 GLN AC 78 GLN AE 39 GLN AE 68 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 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 AT 132 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 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 61 ASN BB 65 GLN BC 49 GLN BC 57 GLN BC 78 GLN BD 65 GLN ** BD 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 39 GLN BF 132 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: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 55030 Z= 0.164 Angle : 0.547 10.076 74854 Z= 0.266 Chirality : 0.036 0.155 8181 Planarity : 0.003 0.043 9805 Dihedral : 10.185 86.510 10002 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.38 % Allowed : 8.35 % Favored : 90.27 % 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: 2.70 (0.10), residues: 6752 helix: 2.32 (0.07), residues: 5229 sheet: 1.08 (0.58), residues: 50 loop : -0.11 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPBM 146 HIS 0.006 0.002 HISBA 140 PHE 0.012 0.001 PHEBL 91 TYR 0.013 0.001 TYRAX 92 ARG 0.010 0.000 ARGBM 158 *********************** 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 997 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 924 time to evaluate : 4.761 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. REVERT: AA 79 ARG cc_start: 0.7996 (ttp80) cc_final: 0.7296 (ttp80) REVERT: AA 109 GLU cc_start: 0.8249 (tp30) cc_final: 0.7972 (tp30) REVERT: AB 39 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8107 (m-30) REVERT: AC 39 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.7101 (mm110) REVERT: AD 1 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7385 (ttt) REVERT: AD 86 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7433 (mtp) REVERT: AE 108 ASP cc_start: 0.8460 (m-30) cc_final: 0.8188 (m-30) REVERT: AE 117 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7321 (pm20) REVERT: AG 42 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7861 (ttpp) REVERT: AG 120 ARG cc_start: 0.7917 (ttp80) cc_final: 0.7122 (ttp-110) REVERT: AH 132 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.6733 (mp10) REVERT: AJ 166 ARG cc_start: 0.8269 (ttm-80) cc_final: 0.7804 (ttp-170) REVERT: AM 39 GLN cc_start: 0.7579 (tm-30) cc_final: 0.7282 (tm130) REVERT: AM 109 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7343 (tp30) REVERT: AN 33 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6752 (pp20) REVERT: AN 65 GLN cc_start: 0.7914 (pt0) cc_final: 0.7508 (tp40) REVERT: AN 79 MET cc_start: 0.9166 (tpp) cc_final: 0.8963 (tpp) REVERT: AP 132 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7739 (tm-30) REVERT: AP 135 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7463 (tptm) REVERT: AQ 155 ASP cc_start: 0.8121 (m-30) cc_final: 0.7903 (m-30) REVERT: AR 108 ARG cc_start: 0.7615 (mtt-85) cc_final: 0.7411 (mmt-90) REVERT: AS 7 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7483 (mt-10) REVERT: AT 134 MET cc_start: 0.9001 (mtm) cc_final: 0.8492 (mtm) REVERT: AU 109 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7307 (tp30) REVERT: AY 118 ILE cc_start: 0.8795 (mt) cc_final: 0.8535 (mt) REVERT: AZ 65 GLN cc_start: 0.7958 (pm20) cc_final: 0.7635 (pm20) REVERT: BA 42 LYS cc_start: 0.8139 (ttpp) cc_final: 0.7933 (tttt) REVERT: BA 49 GLN cc_start: 0.7448 (pm20) cc_final: 0.7108 (pm20) REVERT: BA 53 ASN cc_start: 0.7527 (m110) cc_final: 0.7096 (m110) REVERT: BB 25 ASP cc_start: 0.6702 (m-30) cc_final: 0.6494 (m-30) REVERT: BB 156 ILE cc_start: 0.8270 (mm) cc_final: 0.8053 (mm) REVERT: BE 1 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.6144 (mpp) REVERT: BF 159 GLU cc_start: 0.8050 (tt0) cc_final: 0.7829 (tt0) REVERT: BJ 134 MET cc_start: 0.8690 (mtm) cc_final: 0.8433 (mtm) REVERT: BK 42 MET cc_start: 0.8373 (mmm) cc_final: 0.7974 (tpt) REVERT: BL 273 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7026 (mt0) REVERT: BM 258 GLN cc_start: 0.7827 (mt0) cc_final: 0.7560 (mt0) REVERT: BN 48 ILE cc_start: 0.8518 (mt) cc_final: 0.8225 (mp) REVERT: BN 70 VAL cc_start: 0.8097 (m) cc_final: 0.7847 (p) outliers start: 73 outliers final: 28 residues processed: 949 average time/residue: 1.7654 time to fit residues: 2023.0902 Evaluate side-chains 934 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 892 time to evaluate : 4.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 50 SER Chi-restraints excluded: chain AB residue 39 ASP Chi-restraints excluded: chain AB residue 86 MET Chi-restraints excluded: chain AC residue 39 GLN Chi-restraints excluded: chain AD residue 1 MET Chi-restraints excluded: chain AD residue 39 ASP Chi-restraints excluded: chain AD residue 86 MET Chi-restraints excluded: chain AE residue 117 GLU Chi-restraints excluded: chain AG residue 39 GLN Chi-restraints excluded: chain AG residue 42 LYS Chi-restraints excluded: chain AG residue 50 SER Chi-restraints excluded: chain AH residue 132 GLN Chi-restraints excluded: chain AJ residue 8 VAL Chi-restraints excluded: chain AJ residue 22 SER Chi-restraints excluded: chain AJ residue 86 MET Chi-restraints excluded: chain AL residue 17 GLU Chi-restraints excluded: chain AL residue 136 GLU Chi-restraints excluded: chain AM residue 1 MET Chi-restraints excluded: chain AM residue 109 GLU Chi-restraints excluded: chain AP residue 132 GLN Chi-restraints excluded: chain AP residue 135 LYS Chi-restraints excluded: chain AP residue 136 GLU Chi-restraints excluded: chain AP residue 156 ILE Chi-restraints excluded: chain AS residue 7 GLU Chi-restraints excluded: chain AT residue 8 VAL Chi-restraints excluded: chain AU residue 1 MET Chi-restraints excluded: chain AU residue 109 GLU Chi-restraints excluded: chain AW residue 152 SER Chi-restraints excluded: chain AX residue 22 SER Chi-restraints excluded: chain BB residue 141 ILE Chi-restraints excluded: chain BD residue 77 ARG Chi-restraints excluded: chain BE residue 1 MET Chi-restraints excluded: chain BE residue 10 SER Chi-restraints excluded: chain BE residue 50 SER Chi-restraints excluded: chain BG residue 116 ASP Chi-restraints excluded: chain BH residue 135 LYS Chi-restraints excluded: chain BK residue 17 VAL Chi-restraints excluded: chain BL residue 29 LEU Chi-restraints excluded: chain BL residue 47 ASP Chi-restraints excluded: chain BL residue 157 VAL Chi-restraints excluded: chain BL residue 273 GLN Chi-restraints excluded: chain BM residue 96 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 542 optimal weight: 8.9990 chunk 369 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 485 optimal weight: 6.9990 chunk 268 optimal weight: 1.9990 chunk 555 optimal weight: 6.9990 chunk 450 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 332 optimal weight: 4.9990 chunk 584 optimal weight: 5.9990 chunk 164 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 35 ASN AA 78 GLN ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 15 GLN AC 35 ASN AC 78 GLN AE 39 GLN AE 68 GLN AE 78 GLN AF 111 ASN AG 53 ASN ** AH 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 39 GLN AK 47 ASN ** AK 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 70 GLN AL 35 ASN AL 47 ASN AM 39 GLN ** 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 132 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 ** 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 61 ASN BB 35 ASN BB 65 GLN BC 49 GLN BC 78 GLN BD 65 GLN ** BD 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 39 GLN BG 49 GLN BG 53 ASN BI 53 ASN BJ 11 GLN BK 188 GLN BL 89 ASN BM 263 GLN BN 12 ASN ** BN 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 55030 Z= 0.302 Angle : 0.654 9.994 74854 Z= 0.324 Chirality : 0.042 0.218 8181 Planarity : 0.005 0.058 9805 Dihedral : 10.395 87.530 10002 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.76 % Allowed : 8.71 % Favored : 89.53 % 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: 2.42 (0.10), residues: 6752 helix: 2.09 (0.07), residues: 5196 sheet: 0.90 (0.58), residues: 50 loop : -0.06 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRPBM 146 HIS 0.009 0.003 HISAK 140 PHE 0.017 0.002 PHEAX 98 TYR 0.020 0.002 TYRAL 92 ARG 0.007 0.001 ARGBM 158 *********************** 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 984 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 891 time to evaluate : 4.654 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. REVERT: AA 79 ARG cc_start: 0.8176 (ttp80) cc_final: 0.7291 (ttp80) REVERT: AA 109 GLU cc_start: 0.8297 (tp30) cc_final: 0.8045 (tp30) REVERT: AC 1 MET cc_start: 0.7139 (OUTLIER) cc_final: 0.6122 (mpp) REVERT: AC 39 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.7110 (mm110) REVERT: AE 117 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7472 (pm20) REVERT: AF 106 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7331 (mt-10) REVERT: AG 42 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7898 (ttpp) REVERT: AG 120 ARG cc_start: 0.7767 (ttp80) cc_final: 0.7554 (ttp-110) REVERT: AH 132 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.6796 (mp10) REVERT: AI 39 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7457 (tm-30) REVERT: AJ 30 THR cc_start: 0.8869 (m) cc_final: 0.8654 (m) REVERT: AJ 166 ARG cc_start: 0.8315 (ttm-80) cc_final: 0.7650 (ttm-80) REVERT: AM 39 GLN cc_start: 0.7685 (tm130) cc_final: 0.7277 (tm130) REVERT: AM 109 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7353 (tp30) REVERT: AN 65 GLN cc_start: 0.8074 (pt0) cc_final: 0.7507 (tp40) REVERT: AN 79 MET cc_start: 0.9214 (tpp) cc_final: 0.8964 (tpp) REVERT: AP 132 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7786 (tm-30) REVERT: AP 135 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.7485 (tptp) REVERT: AR 134 MET cc_start: 0.8961 (mtm) cc_final: 0.8140 (mtm) REVERT: AT 134 MET cc_start: 0.9018 (mtm) cc_final: 0.8456 (mtm) REVERT: AU 109 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7369 (tp30) REVERT: AV 39 ASP cc_start: 0.8178 (m-30) cc_final: 0.7949 (m-30) REVERT: AY 118 ILE cc_start: 0.8809 (mt) cc_final: 0.8603 (mt) REVERT: AY 137 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8456 (mtpp) REVERT: AZ 17 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7401 (pm20) REVERT: AZ 65 GLN cc_start: 0.7991 (pm20) cc_final: 0.7632 (pm20) REVERT: BA 145 ASP cc_start: 0.8097 (m-30) cc_final: 0.7887 (m-30) REVERT: BB 156 ILE cc_start: 0.8436 (mm) cc_final: 0.8143 (mm) REVERT: BD 30 THR cc_start: 0.8789 (m) cc_final: 0.8561 (m) REVERT: BF 159 GLU cc_start: 0.8165 (tt0) cc_final: 0.7930 (tt0) REVERT: BG 15 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7951 (pm20) REVERT: BI 47 ASN cc_start: 0.7578 (t0) cc_final: 0.7259 (t0) REVERT: BL 273 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7055 (mt0) REVERT: BM 50 MET cc_start: 0.8500 (mmt) cc_final: 0.8118 (mmt) REVERT: BM 258 GLN cc_start: 0.7885 (mt0) cc_final: 0.7631 (mt0) REVERT: BN 64 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7224 (mtm110) outliers start: 93 outliers final: 46 residues processed: 927 average time/residue: 1.7574 time to fit residues: 1964.9824 Evaluate side-chains 937 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 876 time to evaluate : 4.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 50 SER Chi-restraints excluded: chain AB residue 86 MET Chi-restraints excluded: chain AC residue 1 MET Chi-restraints excluded: chain AC residue 39 GLN Chi-restraints excluded: chain AC residue 42 LYS Chi-restraints excluded: chain AD residue 39 ASP Chi-restraints excluded: chain AE residue 10 SER Chi-restraints excluded: chain AE residue 117 GLU Chi-restraints excluded: chain AE residue 125 SER Chi-restraints excluded: chain AF residue 106 GLU Chi-restraints excluded: chain AF residue 171 VAL Chi-restraints excluded: chain AG residue 39 GLN Chi-restraints excluded: chain AG residue 42 LYS Chi-restraints excluded: chain AG residue 50 SER Chi-restraints excluded: chain AH residue 132 GLN Chi-restraints excluded: chain AI residue 143 SER Chi-restraints excluded: chain AJ residue 8 VAL Chi-restraints excluded: chain AJ residue 22 SER Chi-restraints excluded: chain AJ residue 86 MET Chi-restraints excluded: chain AL residue 9 VAL Chi-restraints excluded: chain AL residue 22 SER Chi-restraints excluded: chain AL residue 136 GLU Chi-restraints excluded: chain AM residue 1 MET Chi-restraints excluded: chain AM residue 109 GLU Chi-restraints excluded: chain AN residue 6 THR Chi-restraints excluded: chain AO residue 39 GLN Chi-restraints excluded: chain AP residue 132 GLN Chi-restraints excluded: chain AP residue 135 LYS Chi-restraints excluded: chain AP residue 136 GLU Chi-restraints excluded: chain AP residue 156 ILE Chi-restraints excluded: chain AR residue 22 SER Chi-restraints excluded: chain AT residue 8 VAL Chi-restraints excluded: chain AU residue 1 MET Chi-restraints excluded: chain AU residue 109 GLU Chi-restraints excluded: chain AV residue 141 ILE Chi-restraints excluded: chain AW residue 1 MET Chi-restraints excluded: chain AW residue 152 SER Chi-restraints excluded: chain AX residue 22 SER Chi-restraints excluded: chain AY residue 125 SER Chi-restraints excluded: chain AY residue 137 LYS Chi-restraints excluded: chain AZ residue 17 GLU Chi-restraints excluded: chain BD residue 65 GLN Chi-restraints excluded: chain BD residue 77 ARG Chi-restraints excluded: chain BE residue 10 SER Chi-restraints excluded: chain BE residue 50 SER Chi-restraints excluded: chain BF residue 1 MET Chi-restraints excluded: chain BF residue 141 ILE Chi-restraints excluded: chain BG residue 14 SER Chi-restraints excluded: chain BG residue 15 GLN Chi-restraints excluded: chain BG residue 116 ASP Chi-restraints excluded: chain BH residue 135 LYS Chi-restraints excluded: chain BK residue 17 VAL Chi-restraints excluded: chain BK residue 155 THR Chi-restraints excluded: chain BL residue 29 LEU Chi-restraints excluded: chain BL residue 47 ASP Chi-restraints excluded: chain BL residue 157 VAL Chi-restraints excluded: chain BL residue 161 THR Chi-restraints excluded: chain BL residue 273 GLN Chi-restraints excluded: chain BM residue 28 THR Chi-restraints excluded: chain BM residue 96 ILE Chi-restraints excluded: chain BN residue 64 ARG 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: 0.9980 chunk 128 optimal weight: 10.0000 chunk 382 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 652 optimal weight: 0.9980 chunk 541 optimal weight: 7.9990 chunk 301 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 342 optimal weight: 0.9980 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 39 GLN AF 111 ASN AG 53 ASN ** AH 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 47 ASN AJ 143 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** BA 61 ASN BB 35 ASN BC 49 GLN BC 78 GLN BD 72 ASN BE 39 GLN BG 53 ASN BI 53 ASN BJ 11 GLN BL 89 ASN BM 8 GLN BM 263 GLN ** BN 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 55030 Z= 0.228 Angle : 0.599 10.026 74854 Z= 0.294 Chirality : 0.038 0.185 8181 Planarity : 0.004 0.048 9805 Dihedral : 10.373 88.069 10002 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.72 % Allowed : 9.41 % Favored : 88.86 % 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: 2.52 (0.10), residues: 6752 helix: 2.17 (0.07), residues: 5202 sheet: 0.85 (0.57), residues: 50 loop : -0.07 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRPBM 146 HIS 0.007 0.003 HISBE 140 PHE 0.016 0.002 PHEAZ 164 TYR 0.016 0.002 TYRAX 92 ARG 0.007 0.001 ARGBA 120 *********************** 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 980 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 889 time to evaluate : 4.689 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. REVERT: AA 79 ARG cc_start: 0.8144 (ttp80) cc_final: 0.7300 (ttp80) REVERT: AA 109 GLU cc_start: 0.8309 (tp30) cc_final: 0.8075 (tp30) REVERT: AC 39 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.7097 (mm110) REVERT: AE 117 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7488 (pm20) REVERT: AF 106 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7306 (mt-10) REVERT: AG 42 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7861 (ttpp) REVERT: AG 120 ARG cc_start: 0.7836 (ttp80) cc_final: 0.7448 (ttp-110) REVERT: AH 132 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.6783 (mp10) REVERT: AI 39 GLN cc_start: 0.7995 (tm-30) cc_final: 0.7511 (tm-30) REVERT: AJ 30 THR cc_start: 0.8845 (m) cc_final: 0.8632 (m) REVERT: AJ 166 ARG cc_start: 0.8264 (ttm-80) cc_final: 0.7697 (ttm-80) REVERT: AM 39 GLN cc_start: 0.7609 (tm130) cc_final: 0.7235 (tm130) REVERT: AM 109 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7358 (tp30) REVERT: AN 65 GLN cc_start: 0.8012 (pt0) cc_final: 0.7548 (tp40) REVERT: AN 79 MET cc_start: 0.9208 (tpp) cc_final: 0.8997 (tpp) REVERT: AP 132 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7770 (tm-30) REVERT: AP 135 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7492 (tptp) REVERT: AQ 155 ASP cc_start: 0.8155 (m-30) cc_final: 0.7882 (m-30) REVERT: AR 134 MET cc_start: 0.8962 (mtm) cc_final: 0.8223 (mtm) REVERT: AT 134 MET cc_start: 0.9018 (mtm) cc_final: 0.8493 (mtm) REVERT: AU 109 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7346 (tp30) REVERT: AV 39 ASP cc_start: 0.8133 (m-30) cc_final: 0.7932 (m-30) REVERT: AY 118 ILE cc_start: 0.8806 (mt) cc_final: 0.8539 (mt) REVERT: AZ 17 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7341 (pm20) REVERT: AZ 65 GLN cc_start: 0.7973 (pm20) cc_final: 0.7605 (pm20) REVERT: BA 145 ASP cc_start: 0.8120 (m-30) cc_final: 0.7899 (m-30) REVERT: BB 25 ASP cc_start: 0.6691 (m-30) cc_final: 0.6450 (m-30) REVERT: BB 156 ILE cc_start: 0.8371 (mm) cc_final: 0.8090 (mm) REVERT: BF 159 GLU cc_start: 0.8092 (tt0) cc_final: 0.7858 (tt0) REVERT: BG 15 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7876 (pm20) REVERT: BI 47 ASN cc_start: 0.7554 (t0) cc_final: 0.7217 (t0) REVERT: BL 273 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7048 (mt0) REVERT: BM 50 MET cc_start: 0.8497 (mmt) cc_final: 0.8145 (mmt) REVERT: BM 258 GLN cc_start: 0.7859 (mt0) cc_final: 0.7599 (mt0) REVERT: BN 48 ILE cc_start: 0.8526 (mt) cc_final: 0.8222 (mp) outliers start: 91 outliers final: 48 residues processed: 927 average time/residue: 1.7412 time to fit residues: 1951.0717 Evaluate side-chains 934 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 874 time to evaluate : 4.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 50 SER Chi-restraints excluded: chain AB residue 86 MET Chi-restraints excluded: chain AC residue 39 GLN Chi-restraints excluded: chain AC residue 42 LYS Chi-restraints excluded: chain AC residue 127 SER Chi-restraints excluded: chain AD residue 39 ASP Chi-restraints excluded: chain AE residue 10 SER Chi-restraints excluded: chain AE residue 117 GLU Chi-restraints excluded: chain AE residue 118 ILE Chi-restraints excluded: chain AF residue 106 GLU Chi-restraints excluded: chain AF residue 127 VAL Chi-restraints excluded: chain AF residue 136 GLU Chi-restraints excluded: chain AF residue 171 VAL Chi-restraints excluded: chain AG residue 39 GLN Chi-restraints excluded: chain AG residue 42 LYS Chi-restraints excluded: chain AG residue 50 SER Chi-restraints excluded: chain AH residue 132 GLN Chi-restraints excluded: chain AI residue 62 LYS Chi-restraints excluded: chain AJ residue 8 VAL Chi-restraints excluded: chain AJ residue 22 SER Chi-restraints excluded: chain AJ residue 86 MET Chi-restraints excluded: chain AL residue 22 SER Chi-restraints excluded: chain AL residue 136 GLU Chi-restraints excluded: chain AM residue 1 MET Chi-restraints excluded: chain AM residue 109 GLU Chi-restraints excluded: chain AN residue 6 THR Chi-restraints excluded: chain AP residue 132 GLN Chi-restraints excluded: chain AP residue 135 LYS Chi-restraints excluded: chain AP residue 136 GLU Chi-restraints excluded: chain AP residue 156 ILE Chi-restraints excluded: chain AR residue 22 SER Chi-restraints excluded: chain AS residue 116 ASP Chi-restraints excluded: chain AT residue 8 VAL Chi-restraints excluded: chain AU residue 1 MET Chi-restraints excluded: chain AU residue 3 THR Chi-restraints excluded: chain AU residue 109 GLU Chi-restraints excluded: chain AV residue 141 ILE Chi-restraints excluded: chain AW residue 1 MET Chi-restraints excluded: chain AW residue 152 SER Chi-restraints excluded: chain AX residue 22 SER Chi-restraints excluded: chain AY residue 1 MET Chi-restraints excluded: chain AZ residue 17 GLU Chi-restraints excluded: chain BB residue 141 ILE Chi-restraints excluded: chain BD residue 77 ARG Chi-restraints excluded: chain BE residue 10 SER Chi-restraints excluded: chain BE residue 50 SER Chi-restraints excluded: chain BF residue 1 MET Chi-restraints excluded: chain BF residue 141 ILE Chi-restraints excluded: chain BG residue 14 SER Chi-restraints excluded: chain BG residue 15 GLN Chi-restraints excluded: chain BG residue 116 ASP Chi-restraints excluded: chain BH residue 135 LYS Chi-restraints excluded: chain BK residue 17 VAL Chi-restraints excluded: chain BL residue 29 LEU Chi-restraints excluded: chain BL residue 47 ASP Chi-restraints excluded: chain BL residue 157 VAL Chi-restraints excluded: chain BL residue 161 THR Chi-restraints excluded: chain BL residue 273 GLN Chi-restraints excluded: chain BM residue 28 THR Chi-restraints excluded: chain BM residue 96 ILE 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: 0.0060 chunk 371 optimal weight: 0.8980 chunk 476 optimal weight: 5.9990 chunk 368 optimal weight: 10.0000 chunk 548 optimal weight: 3.9990 chunk 364 optimal weight: 1.9990 chunk 649 optimal weight: 4.9990 chunk 406 optimal weight: 0.4980 chunk 396 optimal weight: 9.9990 chunk 299 optimal weight: 1.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 15 GLN AC 35 ASN AF 111 ASN AG 53 ASN AH 72 ASN AK 49 GLN AK 70 GLN AL 35 ASN ** 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 71 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 55030 Z= 0.165 Angle : 0.546 10.036 74854 Z= 0.266 Chirality : 0.036 0.149 8181 Planarity : 0.003 0.042 9805 Dihedral : 10.209 87.093 10002 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.50 % Allowed : 9.89 % Favored : 88.62 % 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: 2.73 (0.10), residues: 6752 helix: 2.33 (0.07), residues: 5235 sheet: 0.91 (0.57), residues: 50 loop : -0.05 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPBM 146 HIS 0.006 0.002 HISBI 140 PHE 0.013 0.001 PHEBL 91 TYR 0.014 0.001 TYRBG 90 ARG 0.008 0.000 ARGBA 120 *********************** 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 988 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 909 time to evaluate : 4.710 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. REVERT: AA 79 ARG cc_start: 0.8066 (ttp80) cc_final: 0.7335 (ttp80) REVERT: AA 109 GLU cc_start: 0.8293 (tp30) cc_final: 0.8075 (tp30) REVERT: AC 39 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.7136 (mm110) REVERT: AD 74 TYR cc_start: 0.8481 (t80) cc_final: 0.8263 (t80) REVERT: AE 117 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7371 (pm20) REVERT: AG 42 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7860 (ttpp) REVERT: AG 120 ARG cc_start: 0.7752 (ttp80) cc_final: 0.7339 (ttp-110) REVERT: AH 132 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7059 (mp10) REVERT: AI 39 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7435 (tm-30) REVERT: AJ 166 ARG cc_start: 0.8250 (ttm-80) cc_final: 0.7824 (ttp-170) REVERT: AM 109 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7348 (tp30) REVERT: AN 33 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6898 (pp20) REVERT: AN 65 GLN cc_start: 0.7913 (pt0) cc_final: 0.7486 (tp40) REVERT: AP 132 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: AP 135 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7432 (tptp) REVERT: AQ 155 ASP cc_start: 0.8110 (m-30) cc_final: 0.7816 (m-30) REVERT: AT 134 MET cc_start: 0.8979 (mtm) cc_final: 0.8327 (mtm) REVERT: AU 109 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7317 (tp30) REVERT: AY 118 ILE cc_start: 0.8794 (mt) cc_final: 0.8516 (mt) REVERT: AZ 65 GLN cc_start: 0.7949 (pm20) cc_final: 0.7579 (pm20) REVERT: BA 145 ASP cc_start: 0.8081 (m-30) cc_final: 0.7871 (m-30) REVERT: BB 25 ASP cc_start: 0.6728 (m-30) cc_final: 0.6505 (m-30) REVERT: BB 156 ILE cc_start: 0.8224 (mm) cc_final: 0.8016 (mm) REVERT: BC 68 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.6829 (mt0) REVERT: BC 117 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7243 (mt-10) REVERT: BE 147 ARG cc_start: 0.7921 (tmm-80) cc_final: 0.7696 (ttp-170) REVERT: BF 159 GLU cc_start: 0.8054 (tt0) cc_final: 0.7826 (tt0) REVERT: BG 15 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7901 (pm20) REVERT: BK 42 MET cc_start: 0.8206 (mmm) cc_final: 0.7930 (tpt) REVERT: BL 273 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7056 (mt0) REVERT: BM 258 GLN cc_start: 0.7823 (mt0) cc_final: 0.7551 (mt0) REVERT: BN 48 ILE cc_start: 0.8517 (mt) cc_final: 0.8230 (mp) outliers start: 79 outliers final: 45 residues processed: 941 average time/residue: 1.7572 time to fit residues: 2000.5483 Evaluate side-chains 935 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 878 time to evaluate : 4.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 50 SER Chi-restraints excluded: chain AB residue 86 MET Chi-restraints excluded: chain AC residue 39 GLN Chi-restraints excluded: chain AC residue 42 LYS Chi-restraints excluded: chain AC residue 127 SER Chi-restraints excluded: chain AD residue 39 ASP Chi-restraints excluded: chain AE residue 117 GLU Chi-restraints excluded: chain AE residue 125 SER Chi-restraints excluded: chain AF residue 136 GLU Chi-restraints excluded: chain AG residue 39 GLN Chi-restraints excluded: chain AG residue 42 LYS Chi-restraints excluded: chain AG residue 50 SER Chi-restraints excluded: chain AH residue 132 GLN Chi-restraints excluded: chain AI residue 62 LYS Chi-restraints excluded: chain AJ residue 8 VAL Chi-restraints excluded: chain AJ residue 22 SER Chi-restraints excluded: chain AJ residue 86 MET Chi-restraints excluded: chain AL residue 22 SER Chi-restraints excluded: chain AL residue 136 GLU Chi-restraints excluded: chain AM residue 1 MET Chi-restraints excluded: chain AM residue 109 GLU Chi-restraints excluded: chain AN residue 6 THR Chi-restraints excluded: chain AP residue 132 GLN Chi-restraints excluded: chain AP residue 135 LYS Chi-restraints excluded: chain AP residue 136 GLU Chi-restraints excluded: chain AP residue 156 ILE Chi-restraints excluded: chain AR residue 22 SER Chi-restraints excluded: chain AT residue 8 VAL Chi-restraints excluded: chain AU residue 1 MET Chi-restraints excluded: chain AU residue 3 THR Chi-restraints excluded: chain AU residue 109 GLU Chi-restraints excluded: chain AV residue 141 ILE Chi-restraints excluded: chain AW residue 152 SER Chi-restraints excluded: chain AX residue 22 SER Chi-restraints excluded: chain AY residue 1 MET Chi-restraints excluded: chain BB residue 141 ILE Chi-restraints excluded: chain BC residue 68 GLN Chi-restraints excluded: chain BC residue 117 GLU Chi-restraints excluded: chain BD residue 65 GLN Chi-restraints excluded: chain BD residue 77 ARG Chi-restraints excluded: chain BE residue 10 SER Chi-restraints excluded: chain BE residue 50 SER Chi-restraints excluded: chain BF residue 8 VAL Chi-restraints excluded: chain BG residue 14 SER Chi-restraints excluded: chain BG residue 15 GLN Chi-restraints excluded: chain BG residue 116 ASP Chi-restraints excluded: chain BH residue 135 LYS Chi-restraints excluded: chain BJ residue 77 ARG Chi-restraints excluded: chain BK residue 17 VAL Chi-restraints excluded: chain BL residue 17 GLU Chi-restraints excluded: chain BL residue 29 LEU Chi-restraints excluded: chain BL residue 47 ASP Chi-restraints excluded: chain BL residue 157 VAL Chi-restraints excluded: chain BL residue 161 THR Chi-restraints excluded: chain BL residue 273 GLN Chi-restraints excluded: chain BM residue 28 THR Chi-restraints excluded: chain BM residue 96 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 401 optimal weight: 6.9990 chunk 259 optimal weight: 0.2980 chunk 387 optimal weight: 0.6980 chunk 195 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 125 optimal weight: 7.9990 chunk 413 optimal weight: 1.9990 chunk 442 optimal weight: 7.9990 chunk 321 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 510 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 AE 78 GLN AF 111 ASN AG 53 ASN 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** AO 78 GLN AQ 15 GLN AQ 39 GLN AQ 68 GLN AR 111 ASN AS 39 GLN AS 68 GLN AT 68 GLN AT 132 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 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 49 GLN BG 53 ASN BI 53 ASN BJ 11 GLN BL 89 ASN ** BL 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 8 GLN ** BM 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 55030 Z= 0.244 Angle : 0.610 9.965 74854 Z= 0.300 Chirality : 0.039 0.187 8181 Planarity : 0.004 0.053 9805 Dihedral : 10.297 87.967 10002 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.65 % Allowed : 10.11 % Favored : 88.24 % 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: 2.61 (0.10), residues: 6752 helix: 2.24 (0.07), residues: 5202 sheet: 0.90 (0.57), residues: 50 loop : -0.02 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRPBM 146 HIS 0.007 0.003 HISAK 140 PHE 0.016 0.002 PHEAZ 164 TYR 0.018 0.002 TYRBA 90 ARG 0.009 0.001 ARGBM 158 *********************** 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 970 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 883 time to evaluate : 4.762 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. REVERT: AA 79 ARG cc_start: 0.8133 (ttp80) cc_final: 0.7309 (ttp80) REVERT: AC 39 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.7112 (mm110) REVERT: AD 25 ASP cc_start: 0.7542 (m-30) cc_final: 0.7293 (m-30) REVERT: AE 117 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7503 (pm20) REVERT: AG 42 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7847 (ttpp) REVERT: AG 120 ARG cc_start: 0.7800 (ttp80) cc_final: 0.7380 (ttp-110) REVERT: AH 132 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7080 (mp10) REVERT: AI 39 GLN cc_start: 0.7865 (tm-30) cc_final: 0.7419 (tm-30) REVERT: AJ 30 THR cc_start: 0.8793 (m) cc_final: 0.8582 (m) REVERT: AJ 166 ARG cc_start: 0.8255 (ttm-80) cc_final: 0.7698 (ttm-80) REVERT: AM 109 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7370 (tp30) REVERT: AN 65 GLN cc_start: 0.7981 (pt0) cc_final: 0.7514 (tp40) REVERT: AP 132 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7771 (tm-30) REVERT: AP 135 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.7496 (tptp) REVERT: AT 134 MET cc_start: 0.9003 (mtm) cc_final: 0.8490 (mtm) REVERT: AU 109 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7354 (tp30) REVERT: AV 39 ASP cc_start: 0.8141 (m-30) cc_final: 0.7935 (m-30) REVERT: AV 106 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7081 (pm20) REVERT: AY 118 ILE cc_start: 0.8795 (mt) cc_final: 0.8521 (mt) REVERT: AY 137 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8454 (mtpp) REVERT: AZ 17 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7336 (pm20) REVERT: AZ 65 GLN cc_start: 0.7965 (pm20) cc_final: 0.7589 (pm20) REVERT: BA 145 ASP cc_start: 0.8122 (m-30) cc_final: 0.7897 (m-30) REVERT: BB 156 ILE cc_start: 0.8292 (mm) cc_final: 0.8073 (mm) REVERT: BC 68 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.6851 (mt0) REVERT: BC 117 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7251 (mt-10) REVERT: BE 147 ARG cc_start: 0.7927 (tmm-80) cc_final: 0.7677 (ttp-170) REVERT: BF 159 GLU cc_start: 0.8101 (tt0) cc_final: 0.7872 (tt0) REVERT: BG 15 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7955 (pm20) REVERT: BI 47 ASN cc_start: 0.7563 (t0) cc_final: 0.7307 (t0) REVERT: BL 273 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7120 (mt0) REVERT: BM 50 MET cc_start: 0.8501 (mmp) cc_final: 0.8247 (mmt) REVERT: BM 258 GLN cc_start: 0.7878 (mt0) cc_final: 0.7633 (mt0) outliers start: 87 outliers final: 51 residues processed: 921 average time/residue: 1.7666 time to fit residues: 1968.4111 Evaluate side-chains 933 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 867 time to evaluate : 4.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 50 SER Chi-restraints excluded: chain AB residue 86 MET Chi-restraints excluded: chain AC residue 39 GLN Chi-restraints excluded: chain AC residue 42 LYS Chi-restraints excluded: chain AC residue 125 SER Chi-restraints excluded: chain AC residue 127 SER Chi-restraints excluded: chain AD residue 39 ASP Chi-restraints excluded: chain AE residue 10 SER Chi-restraints excluded: chain AE residue 95 VAL Chi-restraints excluded: chain AE residue 117 GLU Chi-restraints excluded: chain AE residue 118 ILE Chi-restraints excluded: chain AE residue 125 SER Chi-restraints excluded: chain AF residue 127 VAL Chi-restraints excluded: chain AF residue 136 GLU Chi-restraints excluded: chain AF residue 171 VAL Chi-restraints excluded: chain AG residue 39 GLN Chi-restraints excluded: chain AG residue 42 LYS Chi-restraints excluded: chain AG residue 50 SER Chi-restraints excluded: chain AH residue 132 GLN Chi-restraints excluded: chain AI residue 62 LYS Chi-restraints excluded: chain AJ residue 8 VAL Chi-restraints excluded: chain AJ residue 22 SER Chi-restraints excluded: chain AJ residue 86 MET Chi-restraints excluded: chain AK residue 1 MET Chi-restraints excluded: chain AL residue 9 VAL Chi-restraints excluded: chain AL residue 22 SER Chi-restraints excluded: chain AL residue 136 GLU Chi-restraints excluded: chain AM residue 1 MET Chi-restraints excluded: chain AM residue 109 GLU Chi-restraints excluded: chain AN residue 6 THR Chi-restraints excluded: chain AN residue 9 VAL Chi-restraints excluded: chain AP residue 132 GLN Chi-restraints excluded: chain AP residue 135 LYS Chi-restraints excluded: chain AP residue 136 GLU Chi-restraints excluded: chain AP residue 156 ILE Chi-restraints excluded: chain AR residue 22 SER Chi-restraints excluded: chain AT residue 8 VAL Chi-restraints excluded: chain AU residue 1 MET Chi-restraints excluded: chain AU residue 3 THR Chi-restraints excluded: chain AU residue 109 GLU Chi-restraints excluded: chain AV residue 106 GLU Chi-restraints excluded: chain AV residue 141 ILE Chi-restraints excluded: chain AW residue 152 SER Chi-restraints excluded: chain AX residue 22 SER Chi-restraints excluded: chain AY residue 137 LYS Chi-restraints excluded: chain AZ residue 17 GLU Chi-restraints excluded: chain BB residue 141 ILE Chi-restraints excluded: chain BC residue 68 GLN Chi-restraints excluded: chain BC residue 117 GLU Chi-restraints excluded: chain BD residue 77 ARG Chi-restraints excluded: chain BE residue 10 SER Chi-restraints excluded: chain BE residue 50 SER Chi-restraints excluded: chain BF residue 141 ILE Chi-restraints excluded: chain BG residue 14 SER Chi-restraints excluded: chain BG residue 15 GLN Chi-restraints excluded: chain BG residue 116 ASP Chi-restraints excluded: chain BK residue 17 VAL Chi-restraints excluded: chain BK residue 155 THR Chi-restraints excluded: chain BL residue 29 LEU Chi-restraints excluded: chain BL residue 47 ASP Chi-restraints excluded: chain BL residue 157 VAL Chi-restraints excluded: chain BL residue 161 THR Chi-restraints excluded: chain BL residue 162 VAL Chi-restraints excluded: chain BL residue 273 GLN Chi-restraints excluded: chain BM residue 28 THR Chi-restraints excluded: chain BM residue 96 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 590 optimal weight: 3.9990 chunk 622 optimal weight: 0.5980 chunk 567 optimal weight: 6.9990 chunk 605 optimal weight: 2.9990 chunk 364 optimal weight: 5.9990 chunk 263 optimal weight: 3.9990 chunk 475 optimal weight: 3.9990 chunk 185 optimal weight: 0.8980 chunk 547 optimal weight: 5.9990 chunk 572 optimal weight: 0.7980 chunk 603 optimal weight: 10.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 15 GLN AC 35 ASN AC 78 GLN AF 111 ASN AG 53 ASN ** 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 49 GLN 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 49 GLN BG 53 ASN BI 53 ASN BJ 11 GLN BL 89 ASN BM 8 GLN BN 71 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 55030 Z= 0.218 Angle : 0.593 10.000 74854 Z= 0.291 Chirality : 0.038 0.175 8181 Planarity : 0.004 0.048 9805 Dihedral : 10.298 87.544 10002 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.52 % Allowed : 10.47 % Favored : 88.01 % 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: 2.62 (0.10), residues: 6752 helix: 2.24 (0.07), residues: 5208 sheet: 0.93 (0.56), residues: 50 loop : -0.03 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRPBM 146 HIS 0.006 0.002 HISBE 140 PHE 0.015 0.002 PHEAZ 164 TYR 0.021 0.002 TYRBG 90 ARG 0.010 0.001 ARGAN 114 *********************** 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 964 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 884 time to evaluate : 4.652 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. REVERT: AA 79 ARG cc_start: 0.8123 (ttp80) cc_final: 0.7315 (ttp80) REVERT: AC 39 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.7130 (mm110) REVERT: AD 25 ASP cc_start: 0.7538 (m-30) cc_final: 0.7291 (m-30) REVERT: AD 74 TYR cc_start: 0.8515 (t80) cc_final: 0.8298 (t80) REVERT: AE 117 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7462 (pm20) REVERT: AG 42 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7844 (ttpp) REVERT: AG 120 ARG cc_start: 0.7880 (ttp80) cc_final: 0.7228 (ttp-110) REVERT: AH 132 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.6767 (mp10) REVERT: AI 39 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7409 (tm-30) REVERT: AJ 30 THR cc_start: 0.8788 (m) cc_final: 0.8579 (m) REVERT: AJ 166 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.7703 (ttm-80) REVERT: AM 109 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7370 (tp30) REVERT: AN 65 GLN cc_start: 0.7963 (pt0) cc_final: 0.7506 (tp40) REVERT: AP 132 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7758 (tm-30) REVERT: AP 135 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7489 (tptp) REVERT: AQ 155 ASP cc_start: 0.8137 (m-30) cc_final: 0.7809 (m-30) REVERT: AR 134 MET cc_start: 0.8957 (mtm) cc_final: 0.8157 (mtm) REVERT: AS 2 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.6783 (tmtm) REVERT: AT 134 MET cc_start: 0.9006 (mtm) cc_final: 0.8511 (mtm) REVERT: AU 109 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7348 (tp30) REVERT: AV 106 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7083 (pm20) REVERT: AY 118 ILE cc_start: 0.8795 (mt) cc_final: 0.8528 (mt) REVERT: AY 137 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8489 (mtpp) REVERT: AZ 65 GLN cc_start: 0.7958 (pm20) cc_final: 0.7576 (pm20) REVERT: BA 145 ASP cc_start: 0.8118 (m-30) cc_final: 0.7893 (m-30) REVERT: BB 1 MET cc_start: 0.7787 (ptp) cc_final: 0.7526 (ttm) REVERT: BB 156 ILE cc_start: 0.8285 (mm) cc_final: 0.8069 (mm) REVERT: BC 68 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.6848 (mt0) REVERT: BE 147 ARG cc_start: 0.7925 (tmm-80) cc_final: 0.7685 (ttp-170) REVERT: BF 159 GLU cc_start: 0.8092 (tt0) cc_final: 0.7854 (tt0) REVERT: BG 15 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7931 (pm20) REVERT: BH 166 ARG cc_start: 0.8093 (ttm-80) cc_final: 0.7845 (ttm-80) REVERT: BI 47 ASN cc_start: 0.7563 (t0) cc_final: 0.7301 (t0) REVERT: BJ 77 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.6332 (tmm160) REVERT: BL 273 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7117 (mt0) REVERT: BM 50 MET cc_start: 0.8498 (mmp) cc_final: 0.8256 (mmt) REVERT: BM 258 GLN cc_start: 0.7869 (mt0) cc_final: 0.7638 (mt0) outliers start: 80 outliers final: 52 residues processed: 920 average time/residue: 1.7913 time to fit residues: 1987.7718 Evaluate side-chains 951 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 884 time to evaluate : 4.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 50 SER Chi-restraints excluded: chain AB residue 86 MET Chi-restraints excluded: chain AC residue 39 GLN Chi-restraints excluded: chain AC residue 42 LYS Chi-restraints excluded: chain AC residue 125 SER Chi-restraints excluded: chain AC residue 127 SER Chi-restraints excluded: chain AD residue 39 ASP Chi-restraints excluded: chain AE residue 95 VAL Chi-restraints excluded: chain AE residue 117 GLU Chi-restraints excluded: chain AE residue 118 ILE Chi-restraints excluded: chain AE residue 125 SER Chi-restraints excluded: chain AF residue 133 LYS Chi-restraints excluded: chain AF residue 136 GLU Chi-restraints excluded: chain AF residue 171 VAL Chi-restraints excluded: chain AG residue 39 GLN Chi-restraints excluded: chain AG residue 42 LYS Chi-restraints excluded: chain AG residue 50 SER Chi-restraints excluded: chain AH residue 132 GLN Chi-restraints excluded: chain AI residue 62 LYS Chi-restraints excluded: chain AJ residue 8 VAL Chi-restraints excluded: chain AJ residue 22 SER Chi-restraints excluded: chain AJ residue 86 MET Chi-restraints excluded: chain AJ residue 141 ILE Chi-restraints excluded: chain AK residue 1 MET Chi-restraints excluded: chain AL residue 9 VAL Chi-restraints excluded: chain AL residue 22 SER Chi-restraints excluded: chain AL residue 136 GLU Chi-restraints excluded: chain AM residue 1 MET Chi-restraints excluded: chain AM residue 109 GLU Chi-restraints excluded: chain AN residue 6 THR Chi-restraints excluded: chain AN residue 9 VAL Chi-restraints excluded: chain AP residue 132 GLN Chi-restraints excluded: chain AP residue 135 LYS Chi-restraints excluded: chain AP residue 136 GLU Chi-restraints excluded: chain AP residue 156 ILE Chi-restraints excluded: chain AR residue 22 SER Chi-restraints excluded: chain AS residue 2 LYS Chi-restraints excluded: chain AS residue 116 ASP Chi-restraints excluded: chain AT residue 8 VAL Chi-restraints excluded: chain AU residue 1 MET Chi-restraints excluded: chain AU residue 3 THR Chi-restraints excluded: chain AU residue 109 GLU Chi-restraints excluded: chain AV residue 106 GLU Chi-restraints excluded: chain AV residue 141 ILE Chi-restraints excluded: chain AW residue 152 SER Chi-restraints excluded: chain AX residue 22 SER Chi-restraints excluded: chain AY residue 7 GLU Chi-restraints excluded: chain AY residue 137 LYS Chi-restraints excluded: chain BB residue 141 ILE Chi-restraints excluded: chain BC residue 68 GLN Chi-restraints excluded: chain BD residue 77 ARG Chi-restraints excluded: chain BE residue 10 SER Chi-restraints excluded: chain BE residue 50 SER Chi-restraints excluded: chain BG residue 14 SER Chi-restraints excluded: chain BG residue 15 GLN Chi-restraints excluded: chain BG residue 116 ASP Chi-restraints excluded: chain BJ residue 77 ARG Chi-restraints excluded: chain BK residue 17 VAL Chi-restraints excluded: chain BL residue 17 GLU Chi-restraints excluded: chain BL residue 29 LEU Chi-restraints excluded: chain BL residue 47 ASP Chi-restraints excluded: chain BL residue 157 VAL Chi-restraints excluded: chain BL residue 161 THR Chi-restraints excluded: chain BL residue 162 VAL Chi-restraints excluded: chain BL residue 273 GLN Chi-restraints excluded: chain BM residue 28 THR Chi-restraints excluded: chain BM residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 397 optimal weight: 2.9990 chunk 640 optimal weight: 8.9990 chunk 390 optimal weight: 6.9990 chunk 303 optimal weight: 3.9990 chunk 445 optimal weight: 6.9990 chunk 671 optimal weight: 0.9980 chunk 618 optimal weight: 20.0000 chunk 534 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 413 optimal weight: 0.9990 chunk 327 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 15 GLN AC 35 ASN AF 111 ASN AG 53 ASN ** 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** 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 49 GLN BG 53 ASN BI 53 ASN BJ 11 GLN BL 89 ASN ** BL 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 8 GLN ** BM 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 71 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1302 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= 0.199 Angle : 0.580 9.982 74854 Z= 0.285 Chirality : 0.037 0.162 8181 Planarity : 0.004 0.044 9805 Dihedral : 10.254 87.168 10002 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.42 % Allowed : 10.70 % Favored : 87.88 % 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: 2.65 (0.10), residues: 6752 helix: 2.25 (0.07), residues: 5241 sheet: 0.97 (0.55), residues: 50 loop : -0.03 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPBM 146 HIS 0.006 0.002 HISBE 140 PHE 0.013 0.002 PHEAZ 164 TYR 0.021 0.001 TYRBG 90 ARG 0.009 0.000 ARGBA 120 ********************** 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 961 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 886 time to evaluate : 4.733 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. REVERT: AA 79 ARG cc_start: 0.8128 (ttp80) cc_final: 0.7346 (ttp80) REVERT: AC 39 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.7129 (mm110) REVERT: AD 1 MET cc_start: 0.7822 (ttt) cc_final: 0.7540 (ttt) REVERT: AD 74 TYR cc_start: 0.8506 (t80) cc_final: 0.8290 (t80) REVERT: AG 42 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7856 (ttpp) REVERT: AH 132 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7068 (mp10) REVERT: AI 39 GLN cc_start: 0.7853 (tm-30) cc_final: 0.7373 (tm-30) REVERT: AJ 166 ARG cc_start: 0.8219 (ttm-80) cc_final: 0.7700 (ttm-80) REVERT: AL 65 GLN cc_start: 0.7691 (pm20) cc_final: 0.7465 (pp30) REVERT: AM 109 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7364 (tp30) REVERT: AN 65 GLN cc_start: 0.7950 (pt0) cc_final: 0.7495 (tp40) REVERT: AP 132 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7754 (tm-30) REVERT: AP 135 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7488 (tptp) REVERT: AS 2 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.6790 (tmtm) REVERT: AT 134 MET cc_start: 0.9001 (mtm) cc_final: 0.8520 (mtm) REVERT: AU 109 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7344 (tp30) REVERT: AV 106 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7099 (pm20) REVERT: AY 137 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8492 (mtpp) REVERT: AZ 17 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7250 (pm20) REVERT: AZ 65 GLN cc_start: 0.7950 (pm20) cc_final: 0.7572 (pm20) REVERT: BA 145 ASP cc_start: 0.8093 (m-30) cc_final: 0.7872 (m-30) REVERT: BB 1 MET cc_start: 0.7809 (ptp) cc_final: 0.7575 (ttm) REVERT: BB 156 ILE cc_start: 0.8275 (mm) cc_final: 0.8063 (mm) REVERT: BC 68 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.6849 (mt0) REVERT: BE 147 ARG cc_start: 0.7961 (tmm-80) cc_final: 0.7730 (ttp-170) REVERT: BF 159 GLU cc_start: 0.8077 (tt0) cc_final: 0.7842 (tt0) REVERT: BG 15 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7935 (pm20) REVERT: BH 166 ARG cc_start: 0.8061 (ttm-80) cc_final: 0.7856 (ttm-80) REVERT: BI 47 ASN cc_start: 0.7543 (t0) cc_final: 0.7222 (t0) REVERT: BL 273 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7123 (mt0) REVERT: BM 50 MET cc_start: 0.8503 (mmp) cc_final: 0.8262 (mmt) REVERT: BM 258 GLN cc_start: 0.7828 (mt0) cc_final: 0.7588 (mt0) outliers start: 75 outliers final: 52 residues processed: 921 average time/residue: 1.7361 time to fit residues: 1934.2166 Evaluate side-chains 936 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 870 time to evaluate : 4.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 50 SER Chi-restraints excluded: chain AB residue 86 MET Chi-restraints excluded: chain AC residue 39 GLN Chi-restraints excluded: chain AC residue 42 LYS Chi-restraints excluded: chain AC residue 125 SER Chi-restraints excluded: chain AC residue 127 SER Chi-restraints excluded: chain AD residue 39 ASP Chi-restraints excluded: chain AE residue 95 VAL Chi-restraints excluded: chain AE residue 118 ILE Chi-restraints excluded: chain AE residue 125 SER Chi-restraints excluded: chain AF residue 133 LYS Chi-restraints excluded: chain AF residue 136 GLU Chi-restraints excluded: chain AF residue 171 VAL Chi-restraints excluded: chain AG residue 39 GLN Chi-restraints excluded: chain AG residue 42 LYS Chi-restraints excluded: chain AG residue 50 SER Chi-restraints excluded: chain AH residue 132 GLN Chi-restraints excluded: chain AI residue 62 LYS Chi-restraints excluded: chain AJ residue 8 VAL Chi-restraints excluded: chain AJ residue 22 SER Chi-restraints excluded: chain AJ residue 86 MET Chi-restraints excluded: chain AJ residue 141 ILE Chi-restraints excluded: chain AK residue 1 MET Chi-restraints excluded: chain AL residue 9 VAL Chi-restraints excluded: chain AL residue 22 SER Chi-restraints excluded: chain AL residue 136 GLU Chi-restraints excluded: chain AM residue 1 MET Chi-restraints excluded: chain AM residue 109 GLU Chi-restraints excluded: chain AN residue 6 THR Chi-restraints excluded: chain AP residue 132 GLN Chi-restraints excluded: chain AP residue 135 LYS Chi-restraints excluded: chain AP residue 136 GLU Chi-restraints excluded: chain AP residue 156 ILE Chi-restraints excluded: chain AR residue 22 SER Chi-restraints excluded: chain AS residue 2 LYS Chi-restraints excluded: chain AS residue 116 ASP Chi-restraints excluded: chain AT residue 8 VAL Chi-restraints excluded: chain AU residue 1 MET Chi-restraints excluded: chain AU residue 3 THR Chi-restraints excluded: chain AU residue 109 GLU Chi-restraints excluded: chain AV residue 106 GLU Chi-restraints excluded: chain AV residue 141 ILE Chi-restraints excluded: chain AW residue 152 SER Chi-restraints excluded: chain AX residue 22 SER Chi-restraints excluded: chain AY residue 137 LYS Chi-restraints excluded: chain AZ residue 17 GLU Chi-restraints excluded: chain BB residue 141 ILE Chi-restraints excluded: chain BC residue 68 GLN Chi-restraints excluded: chain BD residue 77 ARG Chi-restraints excluded: chain BE residue 10 SER Chi-restraints excluded: chain BE residue 50 SER Chi-restraints excluded: chain BG residue 14 SER Chi-restraints excluded: chain BG residue 15 GLN Chi-restraints excluded: chain BG residue 116 ASP Chi-restraints excluded: chain BH residue 135 LYS Chi-restraints excluded: chain BK residue 17 VAL Chi-restraints excluded: chain BK residue 155 THR Chi-restraints excluded: chain BL residue 17 GLU Chi-restraints excluded: chain BL residue 29 LEU Chi-restraints excluded: chain BL residue 47 ASP Chi-restraints excluded: chain BL residue 157 VAL Chi-restraints excluded: chain BL residue 161 THR Chi-restraints excluded: chain BL residue 162 VAL Chi-restraints excluded: chain BL residue 273 GLN Chi-restraints excluded: chain BM residue 28 THR Chi-restraints excluded: chain BM residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 424 optimal weight: 1.9990 chunk 569 optimal weight: 9.9990 chunk 163 optimal weight: 20.0000 chunk 493 optimal weight: 10.0000 chunk 78 optimal weight: 0.2980 chunk 148 optimal weight: 3.9990 chunk 535 optimal weight: 7.9990 chunk 224 optimal weight: 0.9990 chunk 549 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.2588 ------------------------------------------------------------------------------- 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 AF 111 ASN AG 53 ASN AK 49 GLN 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 68 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 ** BL 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 8 GLN ** BM 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.135142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.122014 restraints weight = 57438.981| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 0.71 r_work: 0.3396 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 55030 Z= 0.179 Angle : 0.565 9.959 74854 Z= 0.277 Chirality : 0.037 0.150 8181 Planarity : 0.004 0.045 9805 Dihedral : 10.199 86.815 10002 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.27 % Allowed : 10.98 % Favored : 87.75 % 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: 2.73 (0.10), residues: 6752 helix: 2.31 (0.07), residues: 5235 sheet: 1.05 (0.57), residues: 50 loop : -0.01 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPBM 146 HIS 0.006 0.002 HISBE 140 PHE 0.014 0.002 PHEAX 164 TYR 0.023 0.001 TYRBG 90 ARG 0.010 0.000 ARGAN 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25379.42 seconds wall clock time: 438 minutes 58.94 seconds (26338.94 seconds total)