Starting phenix.real_space_refine on Fri Dec 8 09:47:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc8_25029/12_2023/7sc8_25029_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc8_25029/12_2023/7sc8_25029.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/7sc8_25029/12_2023/7sc8_25029.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc8_25029/12_2023/7sc8_25029.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc8_25029/12_2023/7sc8_25029_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc8_25029/12_2023/7sc8_25029_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= 0.002 sd= 0.034 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 13209 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "AA GLU 7": "OE1" <-> "OE2" Residue "AA GLU 109": "OE1" <-> "OE2" Residue "AA GLU 131": "OE1" <-> "OE2" Residue "AB GLU 33": "OE1" <-> "OE2" Residue "AB GLU 87": "OE1" <-> "OE2" Residue "AB GLU 106": "OE1" <-> "OE2" Residue "AB GLU 136": "OE1" <-> "OE2" Residue "AC ASP 46": "OD1" <-> "OD2" Residue "AC ASP 77": "OD1" <-> "OD2" Residue "AC GLU 109": "OE1" <-> "OE2" Residue "AC GLU 117": "OE1" <-> "OE2" Residue "AC ASP 123": "OD1" <-> "OD2" Residue "AC GLU 131": "OE1" <-> "OE2" Residue "AC ASP 155": "OD1" <-> "OD2" Residue "AD GLU 17": "OE1" <-> "OE2" Residue "AD GLU 33": "OE1" <-> "OE2" Residue "AE ASP 123": "OD1" <-> "OD2" Residue "AE ASP 155": "OD1" <-> "OD2" Residue "AF GLU 33": "OE1" <-> "OE2" Residue "AF GLU 87": "OE1" <-> "OE2" Residue "AF GLU 106": "OE1" <-> "OE2" Residue "AF GLU 115": "OE1" <-> "OE2" Residue "AF GLU 136": "OE1" <-> "OE2" Residue "AG ASP 116": "OD1" <-> "OD2" Residue "AG GLU 149": "OE1" <-> "OE2" Residue "AH ASP 25": "OD1" <-> "OD2" Residue "AH GLU 62": "OE1" <-> "OE2" Residue "AH ASP 140": "OD1" <-> "OD2" Residue "AH ASP 144": "OD1" <-> "OD2" Residue "AH ASP 152": "OD1" <-> "OD2" Residue "AI ASP 77": "OD1" <-> "OD2" Residue "AI ASP 116": "OD1" <-> "OD2" Residue "AI GLU 117": "OE1" <-> "OE2" Residue "AI TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AJ GLU 62": "OE1" <-> "OE2" Residue "AJ ASP 144": "OD1" <-> "OD2" Residue "AJ GLU 159": "OE1" <-> "OE2" Residue "AK GLU 7": "OE1" <-> "OE2" Residue "AK GLU 23": "OE1" <-> "OE2" Residue "AK GLU 131": "OE1" <-> "OE2" Residue "AK ASP 155": "OD1" <-> "OD2" Residue "AL GLU 33": "OE1" <-> "OE2" Residue "AL ASP 39": "OD1" <-> "OD2" Residue "AL GLU 87": "OE1" <-> "OE2" Residue "AL GLU 136": "OE1" <-> "OE2" Residue "AL ASP 140": "OD1" <-> "OD2" Residue "AM ASP 82": "OD1" <-> "OD2" Residue "AM ASP 116": "OD1" <-> "OD2" Residue "AM ASP 145": "OD1" <-> "OD2" Residue "AN GLU 106": "OE1" <-> "OE2" Residue "AN ASP 107": "OD1" <-> "OD2" Residue "AN ASP 152": "OD1" <-> "OD2" Residue "AO GLU 7": "OE1" <-> "OE2" Residue "AO ASP 46": "OD1" <-> "OD2" Residue "AP GLU 62": "OE1" <-> "OE2" Residue "AP ASP 144": "OD1" <-> "OD2" Residue "AP ASP 165": "OD1" <-> "OD2" Residue "AQ GLU 7": "OE1" <-> "OE2" Residue "AQ GLU 109": "OE1" <-> "OE2" Residue "AQ ASP 116": "OD1" <-> "OD2" Residue "AQ GLU 131": "OE1" <-> "OE2" Residue "AQ ASP 148": "OD1" <-> "OD2" Residue "AR GLU 33": "OE1" <-> "OE2" Residue "AR GLU 87": "OE1" <-> "OE2" Residue "AR GLU 106": "OE1" <-> "OE2" Residue "AR ASP 107": "OD1" <-> "OD2" Residue "AR GLU 115": "OE1" <-> "OE2" Residue "AR GLU 136": "OE1" <-> "OE2" Residue "AR ASP 152": "OD1" <-> "OD2" Residue "AS GLU 7": "OE1" <-> "OE2" Residue "AS ASP 46": "OD1" <-> "OD2" Residue "AS TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AS ASP 116": "OD1" <-> "OD2" Residue "AS GLU 117": "OE1" <-> "OE2" Residue "AS GLU 131": "OE1" <-> "OE2" Residue "AT ASP 25": "OD1" <-> "OD2" Residue "AT GLU 33": "OE1" <-> "OE2" Residue "AT ASP 152": "OD1" <-> "OD2" Residue "AU GLU 7": "OE1" <-> "OE2" Residue "AU GLU 109": "OE1" <-> "OE2" Residue "AU GLU 131": "OE1" <-> "OE2" Residue "AV ASP 3": "OD1" <-> "OD2" Residue "AV ASP 25": "OD1" <-> "OD2" Residue "AV GLU 33": "OE1" <-> "OE2" Residue "AV GLU 87": "OE1" <-> "OE2" Residue "AV ASP 107": "OD1" <-> "OD2" Residue "AW GLU 109": "OE1" <-> "OE2" Residue "AW GLU 131": "OE1" <-> "OE2" Residue "AX ASP 3": "OD1" <-> "OD2" Residue "AX ASP 25": "OD1" <-> "OD2" Residue "AX GLU 62": "OE1" <-> "OE2" Residue "AX GLU 115": "OE1" <-> "OE2" Residue "AX ASP 152": "OD1" <-> "OD2" Residue "AY GLU 109": "OE1" <-> "OE2" Residue "AY ASP 116": "OD1" <-> "OD2" Residue "AY GLU 131": "OE1" <-> "OE2" Residue "AZ GLU 17": "OE1" <-> "OE2" Residue "AZ GLU 62": "OE1" <-> "OE2" Residue "AZ GLU 87": "OE1" <-> "OE2" Residue "AZ GLU 106": "OE1" <-> "OE2" Residue "AZ ASP 144": "OD1" <-> "OD2" Residue "AZ ASP 165": "OD1" <-> "OD2" Residue "BA GLU 109": "OE1" <-> "OE2" Residue "BA ASP 116": "OD1" <-> "OD2" Residue "BA GLU 149": "OE1" <-> "OE2" Residue "BB ASP 25": "OD1" <-> "OD2" Residue "BB GLU 62": "OE1" <-> "OE2" Residue "BB ASP 107": "OD1" <-> "OD2" Residue "BB GLU 115": "OE1" <-> "OE2" Residue "BB ASP 152": "OD1" <-> "OD2" Residue "BC ASP 46": "OD1" <-> "OD2" Residue "BC ASP 155": "OD1" <-> "OD2" Residue "BD GLU 62": "OE1" <-> "OE2" Residue "BD ASP 107": "OD1" <-> "OD2" Residue "BD GLU 136": "OE1" <-> "OE2" Residue "BD ASP 140": "OD1" <-> "OD2" Residue "BE GLU 7": "OE1" <-> "OE2" Residue "BE GLU 117": "OE1" <-> "OE2" Residue "BE ASP 123": "OD1" <-> "OD2" Residue "BF GLU 17": "OE1" <-> "OE2" Residue "BF GLU 87": "OE1" <-> "OE2" Residue "BF GLU 106": "OE1" <-> "OE2" Residue "BF GLU 136": "OE1" <-> "OE2" Residue "BF ASP 140": "OD1" <-> "OD2" Residue "BG GLU 7": "OE1" <-> "OE2" Residue "BG GLU 109": "OE1" <-> "OE2" Residue "BG GLU 149": "OE1" <-> "OE2" Residue "BH GLU 87": "OE1" <-> "OE2" Residue "BH GLU 136": "OE1" <-> "OE2" Residue "BH ASP 140": "OD1" <-> "OD2" Residue "BH ASP 144": "OD1" <-> "OD2" Residue "BI ASP 46": "OD1" <-> "OD2" Residue "BI TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BI ASP 116": "OD1" <-> "OD2" Residue "BI GLU 117": "OE1" <-> "OE2" Residue "BI GLU 131": "OE1" <-> "OE2" Residue "BI ASP 145": "OD1" <-> "OD2" Residue "BI GLU 149": "OE1" <-> "OE2" Residue "BJ GLU 17": "OE1" <-> "OE2" Residue "BJ ASP 25": "OD1" <-> "OD2" Residue "BJ GLU 33": "OE1" <-> "OE2" Residue "BJ GLU 87": "OE1" <-> "OE2" Residue "BJ GLU 136": "OE1" <-> "OE2" Residue "BJ ASP 152": "OD1" <-> "OD2" Residue "BJ ASP 165": "OD1" <-> "OD2" Residue "BK GLU 18": "OE1" <-> "OE2" Residue "BK GLU 25": "OE1" <-> "OE2" Residue "BK ASP 41": "OD1" <-> "OD2" Residue "BK GLU 63": "OE1" <-> "OE2" Residue "BK ASP 115": "OD1" <-> "OD2" Residue "BK GLU 168": "OE1" <-> "OE2" Residue "BL GLU 22": "OE1" <-> "OE2" Residue "BL ASP 30": "OD1" <-> "OD2" Residue "BL ASP 47": "OD1" <-> "OD2" Residue "BL GLU 97": "OE1" <-> "OE2" Residue "BM ASP 47": "OD1" <-> "OD2" Residue "BM GLU 80": "OE1" <-> "OE2" Residue "BM TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BM GLU 141": "OE1" <-> "OE2" Residue "BM ASP 145": "OD1" <-> "OD2" Residue "BM GLU 245": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 56784 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: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "AB" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "AC" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "AD" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "AE" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "AF" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "AG" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "AH" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "AI" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "AJ" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "AK" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "AL" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "AM" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "AN" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "AO" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Chain: "AP" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "AQ" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "AR" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "AS" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "AT" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 89 Classifications: {'water': 89} Link IDs: {None: 88} Chain: "AU" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "AV" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "AW" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 87 Classifications: {'water': 87} Link IDs: {None: 86} Chain: "AX" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Chain: "AY" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "AZ" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "BA" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "BB" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "BC" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "BD" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "BE" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "BF" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "BG" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "BH" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "BI" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "BJ" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "BK" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "BL" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "BM" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 123 Classifications: {'water': 123} Link IDs: {None: 122} Chain: "BN" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Time building chain proxies: 22.13, per 1000 atoms: 0.39 Number of scatterers: 56784 At special positions: 0 Unit cell: (127.05, 128.1, 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 13209 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: 20.84 Conformation dependent library (CDL) restraints added in 7.1 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: 372 helices and 3 sheets defined 72.5% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.56 Creating SS restraints... Processing helix chain 'AA' and resid 4 through 14 Processing helix chain 'AA' and resid 21 through 46 removed outlier: 4.316A pdb=" N ASNAA 35 " --> pdb=" O LEUAA 31 " (cutoff:3.500A) removed outlier: 4.961A 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 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 121 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: 3.971A pdb=" N VALAB 8 " --> pdb=" O VALAB 4 " (cutoff:3.500A) Processing helix chain 'AB' and resid 21 through 46 removed outlier: 4.523A pdb=" N ASNAB 35 " --> pdb=" O VALAB 31 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LYSAB 36 " --> pdb=" O ALAAB 32 " (cutoff:3.500A) Processing helix chain 'AB' and resid 48 through 61 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: 4.296A pdb=" N ASNAC 35 " --> pdb=" O LEUAC 31 " (cutoff:3.500A) removed outlier: 5.206A 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 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 144 through 161 Processing helix chain 'AD' and resid 4 through 15 removed outlier: 3.853A 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 46 Processing helix chain 'AD' and resid 48 through 62 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: 4.328A pdb=" N ASNAE 35 " --> pdb=" O LEUAE 31 " (cutoff:3.500A) removed outlier: 4.895A 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 121 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: 4.037A pdb=" N VALAF 8 " --> pdb=" O VALAF 4 " (cutoff:3.500A) Processing helix chain 'AF' and resid 21 through 61 removed outlier: 4.701A pdb=" N ASNAF 35 " --> pdb=" O VALAF 31 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LYSAF 36 " --> pdb=" O ALAAF 32 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N SERAF 49 " --> pdb=" O THRAF 45 " (cutoff:3.500A) removed outlier: 6.342A 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: 4.394A pdb=" N ASNAG 35 " --> pdb=" O LEUAG 31 " (cutoff:3.500A) removed outlier: 5.169A 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: 3.946A pdb=" N VALAH 8 " --> pdb=" O VALAH 4 " (cutoff:3.500A) Processing helix chain 'AH' and resid 21 through 62 removed outlier: 4.983A pdb=" N ASNAH 35 " --> pdb=" O VALAH 31 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LYSAH 36 " --> pdb=" O ALAAH 32 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASNAH 47 " --> pdb=" O ARGAH 43 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N SERAH 49 " --> pdb=" O THRAH 45 " (cutoff:3.500A) removed outlier: 6.353A 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: 4.178A pdb=" N ASNAI 35 " --> pdb=" O LEUAI 31 " (cutoff:3.500A) removed outlier: 5.002A 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 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: 4.272A 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 46 Processing helix chain 'AJ' and resid 48 through 62 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 removed outlier: 3.683A pdb=" N VALAJ 171 " --> pdb=" O ALAAJ 167 " (cutoff:3.500A) Processing helix chain 'AK' and resid 4 through 15 Processing helix chain 'AK' and resid 21 through 46 removed outlier: 4.493A pdb=" N ASNAK 35 " --> pdb=" O LEUAK 31 " (cutoff:3.500A) removed outlier: 5.383A 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: 4.050A 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: 4.485A pdb=" N ASNAM 35 " --> pdb=" O LEUAM 31 " (cutoff:3.500A) removed outlier: 5.128A 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 68 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 14 removed outlier: 3.825A pdb=" N VALAN 8 " --> pdb=" O VALAN 4 " (cutoff:3.500A) Processing helix chain 'AN' and resid 21 through 32 Processing helix chain 'AN' and resid 34 through 46 Processing helix chain 'AN' and resid 48 through 62 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: 4.385A pdb=" N ASNAO 35 " --> pdb=" O LEUAO 31 " (cutoff:3.500A) removed outlier: 5.137A 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: 4.122A 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: 5.162A 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: 4.461A pdb=" N ASNAQ 35 " --> pdb=" O LEUAQ 31 " (cutoff:3.500A) removed outlier: 5.136A 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 67 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: 3.800A 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 46 Processing helix chain 'AR' and resid 48 through 62 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: 4.475A pdb=" N ASNAS 35 " --> pdb=" O LEUAS 31 " (cutoff:3.500A) removed outlier: 5.121A 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: 4.057A 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: 3.577A 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: 4.403A pdb=" N ASNAU 35 " --> pdb=" O LEUAU 31 " (cutoff:3.500A) removed outlier: 5.132A 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: 3.835A 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 103 through 108 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: 3.651A pdb=" N VALAV 171 " --> pdb=" O ALAAV 167 " (cutoff:3.500A) Processing helix chain 'AW' and resid 4 through 14 Processing helix chain 'AW' and resid 21 through 46 removed outlier: 4.612A pdb=" N ASNAW 35 " --> pdb=" O LEUAW 31 " (cutoff:3.500A) removed outlier: 5.282A 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: 3.810A 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 46 Processing helix chain 'AX' and resid 48 through 62 Processing helix chain 'AX' and resid 64 through 67 No H-bonds generated for 'chain 'AX' and resid 64 through 67' 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: 3.693A pdb=" N ASPAX 140 " --> pdb=" O GLUAX 136 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILEAX 141 " --> pdb=" O ALAAX 137 " (cutoff:3.500A) Processing helix chain 'AX' and resid 154 through 171 removed outlier: 3.517A pdb=" N VALAX 171 " --> pdb=" O ALAAX 167 " (cutoff:3.500A) Processing helix chain 'AY' and resid 4 through 14 Processing helix chain 'AY' and resid 21 through 46 removed outlier: 4.472A pdb=" N ASNAY 35 " --> pdb=" O LEUAY 31 " (cutoff:3.500A) removed outlier: 5.057A 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 68 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: 3.967A 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 62 removed outlier: 5.113A pdb=" N SERAZ 49 " --> pdb=" O THRAZ 45 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALAAZ 50 " --> pdb=" O GLYAZ 46 " (cutoff:3.500A) 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 14 Processing helix chain 'BA' and resid 21 through 46 removed outlier: 4.349A pdb=" N ASNBA 35 " --> pdb=" O LEUBA 31 " (cutoff:3.500A) removed outlier: 5.189A 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: 3.897A 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: 4.306A pdb=" N ASNBC 35 " --> pdb=" O LEUBC 31 " (cutoff:3.500A) removed outlier: 4.943A 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: 3.775A pdb=" N VALBD 8 " --> pdb=" O VALBD 4 " (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 66 No H-bonds generated for 'chain 'BD' and resid 64 through 66' 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: 4.331A pdb=" N ASNBE 35 " --> pdb=" O LEUBE 31 " (cutoff:3.500A) removed outlier: 4.995A 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 145 through 161 Processing helix chain 'BF' and resid 4 through 15 removed outlier: 4.020A pdb=" N VALBF 8 " --> pdb=" O VALBF 4 " (cutoff:3.500A) Processing helix chain 'BF' and resid 21 through 62 removed outlier: 4.849A pdb=" N ASNBF 35 " --> pdb=" O VALBF 31 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LYSBF 36 " --> pdb=" O ALABF 32 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N SERBF 49 " --> pdb=" O THRBF 45 " (cutoff:3.500A) removed outlier: 6.350A 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: 4.400A pdb=" N ASNBG 35 " --> pdb=" O LEUBG 31 " (cutoff:3.500A) removed outlier: 4.960A 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 115 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: 4.133A 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: 5.277A pdb=" N SERBH 49 " --> pdb=" O THRBH 45 " (cutoff:3.500A) removed outlier: 6.327A 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 102 through 108 removed outlier: 3.640A pdb=" N ASPBH 107 " --> pdb=" O VALBH 104 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARGBH 108 " --> pdb=" O LEUBH 105 " (cutoff:3.500A) 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: 3.821A 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: 4.305A pdb=" N ASNBI 35 " --> pdb=" O LEUBI 31 " (cutoff:3.500A) removed outlier: 5.046A 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 122 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: 3.590A 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: 3.629A 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 71 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: 3.997A pdb=" N ILEBK 127 " --> pdb=" O ILEBK 123 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VALBK 128 " --> pdb=" O ALABK 124 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VALBK 129 " --> pdb=" O TRPBK 125 " (cutoff:3.500A) removed outlier: 4.531A 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: 4.095A pdb=" N PHEBL 168 " --> pdb=" O PHEBL 164 " (cutoff:3.500A) removed outlier: 3.797A 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 205 through 207 No H-bonds generated for 'chain 'BL' and resid 205 through 207' 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: 4.922A pdb=" N ASNBL 269 " --> pdb=" O GLUBL 266 " (cutoff:3.500A) Processing helix chain 'BM' and resid 4 through 10 removed outlier: 4.008A pdb=" N ARGBM 9 " --> pdb=" O VALBM 5 " (cutoff:3.500A) Processing helix chain 'BM' and resid 13 through 17 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 104 Processing helix chain 'BM' and resid 111 through 115 Processing helix chain 'BM' and resid 119 through 134 removed outlier: 8.134A pdb=" N TYRBM 126 " --> pdb=" O HISBM 122 " (cutoff:3.500A) removed outlier: 9.026A pdb=" N GLUBM 127 " --> pdb=" O GLNBM 123 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALABM 128 " --> pdb=" O GLYBM 124 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYRBM 133 " --> pdb=" O GLUBM 129 " (cutoff:3.500A) removed outlier: 3.552A 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: 3.891A pdb=" N SERBM 166 " --> pdb=" O THRBM 162 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHEBM 169 " --> pdb=" O PHEBM 165 " (cutoff:3.500A) removed outlier: 3.877A 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: 5.039A pdb=" N SERBM 254 " --> pdb=" O ASPBM 251 " (cutoff:3.500A) removed outlier: 3.734A 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: 4.534A pdb=" N ASNBN 56 " --> pdb=" O TYRBN 52 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ASPBN 57 " --> pdb=" O ALABN 53 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARGBN 60 " --> pdb=" O ASNBN 56 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'BL' and resid 259 through 264 removed outlier: 3.660A pdb=" N SERBL 284 " --> pdb=" O GLUBL 242 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THRBL 244 " --> pdb=" O VALBL 282 " (cutoff:3.500A) removed outlier: 5.329A 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: 6.418A pdb=" N ILEBM 228 " --> pdb=" O VALBM 267 " (cutoff:3.500A) removed outlier: 5.530A 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: 3.808A pdb=" N ASNBN 71 " --> pdb=" O GLUBN 23 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N SERBN 25 " --> pdb=" O ILEBN 69 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ILEBN 69 " --> pdb=" O SERBN 25 " (cutoff:3.500A) 3427 hydrogen bonds defined for protein. 10140 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: 17.67 Time building geometry restraints manager: 22.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 10171 1.32 - 1.45: 14228 1.45 - 1.57: 30338 1.57 - 1.70: 2 1.70 - 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 1.350 0.163 3.90e-02 6.57e+02 1.76e+01 bond pdb=" CA LYSBA 42 " pdb=" C LYSBA 42 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.27e-02 6.20e+03 1.27e+01 bond pdb=" CB THRBF 6 " pdb=" CG2 THRBF 6 " ideal model delta sigma weight residual 1.521 1.407 0.114 3.30e-02 9.18e+02 1.18e+01 bond pdb=" CB VALBK 17 " pdb=" CG2 VALBK 17 " ideal model delta sigma weight residual 1.521 1.417 0.104 3.30e-02 9.18e+02 9.92e+00 bond pdb=" CGA CYCAT 202 " pdb=" O2A CYCAT 202 " ideal model delta sigma weight residual 1.249 1.309 -0.060 2.00e-02 2.50e+03 8.96e+00 ... (remaining 55025 not shown) Histogram of bond angle deviations from ideal: 93.37 - 103.24: 329 103.24 - 113.11: 28794 113.11 - 122.99: 41833 122.99 - 132.86: 3781 132.86 - 142.74: 117 Bond angle restraints: 74854 Sorted by residual: angle pdb=" C ARGAU 147 " pdb=" CA ARGAU 147 " pdb=" CB ARGAU 147 " ideal model delta sigma weight residual 110.88 96.70 14.18 1.57e+00 4.06e-01 8.15e+01 angle pdb=" N ASPAJ 39 " pdb=" CA ASPAJ 39 " pdb=" CB ASPAJ 39 " ideal model delta sigma weight residual 110.12 120.27 -10.15 1.47e+00 4.63e-01 4.77e+01 angle pdb=" CA GLNAH 11 " pdb=" CB GLNAH 11 " pdb=" CG GLNAH 11 " ideal model delta sigma weight residual 114.10 101.61 12.49 2.00e+00 2.50e-01 3.90e+01 angle pdb=" CA ARGAR 150 " pdb=" CB ARGAR 150 " pdb=" CG ARGAR 150 " ideal model delta sigma weight residual 114.10 126.36 -12.26 2.00e+00 2.50e-01 3.76e+01 angle pdb=" CB METBN 59 " pdb=" CG METBN 59 " pdb=" SD METBN 59 " ideal model delta sigma weight residual 112.70 94.33 18.37 3.00e+00 1.11e-01 3.75e+01 ... (remaining 74849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.12: 31035 18.12 - 36.24: 2192 36.24 - 54.36: 428 54.36 - 72.48: 250 72.48 - 90.59: 71 Dihedral angle restraints: 33976 sinusoidal: 14260 harmonic: 19716 Sorted by residual: dihedral pdb=" C ARGAU 147 " pdb=" N ARGAU 147 " pdb=" CA ARGAU 147 " pdb=" CB ARGAU 147 " ideal model delta harmonic sigma weight residual -122.60 -107.01 -15.59 0 2.50e+00 1.60e-01 3.89e+01 dihedral pdb=" C GLNAM 68 " pdb=" N GLNAM 68 " pdb=" CA GLNAM 68 " pdb=" CB GLNAM 68 " ideal model delta harmonic sigma weight residual -122.60 -135.86 13.26 0 2.50e+00 1.60e-01 2.81e+01 dihedral pdb=" N GLNAM 68 " pdb=" C GLNAM 68 " pdb=" CA GLNAM 68 " pdb=" CB GLNAM 68 " ideal model delta harmonic sigma weight residual 122.80 136.01 -13.21 0 2.50e+00 1.60e-01 2.79e+01 ... (remaining 33973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 8052 0.166 - 0.332: 113 0.332 - 0.499: 12 0.499 - 0.665: 2 0.665 - 0.831: 2 Chirality restraints: 8181 Sorted by residual: chirality pdb=" CG LEUAB 120 " pdb=" CB LEUAB 120 " pdb=" CD1 LEUAB 120 " pdb=" CD2 LEUAB 120 " both_signs ideal model delta sigma weight residual False -2.59 -1.76 -0.83 2.00e-01 2.50e+01 1.73e+01 chirality pdb=" CB THRBF 6 " pdb=" CA THRBF 6 " pdb=" OG1 THRBF 6 " pdb=" CG2 THRBF 6 " both_signs ideal model delta sigma weight residual False 2.55 1.83 0.72 2.00e-01 2.50e+01 1.31e+01 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 -2.03 -0.60 2.00e-01 2.50e+01 8.86e+00 ... (remaining 8178 not shown) Planarity restraints: 9805 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB CYCAX 201 " -0.093 2.00e-02 2.50e+03 1.97e-01 8.72e+02 pdb=" OB CYCAX 201 " 0.196 2.00e-02 2.50e+03 pdb=" C1B CYCAX 201 " -0.037 2.00e-02 2.50e+03 pdb=" C2B CYCAX 201 " 0.128 2.00e-02 2.50e+03 pdb=" C3B CYCAX 201 " 0.153 2.00e-02 2.50e+03 pdb=" C4B CYCAX 201 " 0.032 2.00e-02 2.50e+03 pdb=" CAB CYCAX 201 " -0.412 2.00e-02 2.50e+03 pdb=" CHB CYCAX 201 " -0.195 2.00e-02 2.50e+03 pdb=" CMB CYCAX 201 " 0.227 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A CYCAT 202 " -0.049 2.00e-02 2.50e+03 1.54e-01 5.35e+02 pdb=" C2A CYCAT 202 " 0.029 2.00e-02 2.50e+03 pdb=" C3A CYCAT 202 " -0.057 2.00e-02 2.50e+03 pdb=" C4A CYCAT 202 " 0.035 2.00e-02 2.50e+03 pdb=" CAA CYCAT 202 " 0.281 2.00e-02 2.50e+03 pdb=" CHA CYCAT 202 " -0.141 2.00e-02 2.50e+03 pdb=" CHB CYCAT 202 " 0.197 2.00e-02 2.50e+03 pdb=" CMA CYCAT 202 " -0.260 2.00e-02 2.50e+03 pdb=" NA CYCAT 202 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CYCAB 201 " 0.021 2.00e-02 2.50e+03 1.50e-01 5.04e+02 pdb=" OB CYCAB 201 " -0.079 2.00e-02 2.50e+03 pdb=" C1B CYCAB 201 " 0.030 2.00e-02 2.50e+03 pdb=" C2B CYCAB 201 " -0.087 2.00e-02 2.50e+03 pdb=" C3B CYCAB 201 " -0.142 2.00e-02 2.50e+03 pdb=" C4B CYCAB 201 " -0.076 2.00e-02 2.50e+03 pdb=" CAB CYCAB 201 " 0.318 2.00e-02 2.50e+03 pdb=" CHB CYCAB 201 " 0.179 2.00e-02 2.50e+03 pdb=" CMB CYCAB 201 " -0.164 2.00e-02 2.50e+03 ... (remaining 9802 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 2391 2.66 - 3.22: 58139 3.22 - 3.78: 115047 3.78 - 4.34: 148155 4.34 - 4.90: 228698 Nonbonded interactions: 552430 Sorted by model distance: nonbonded pdb=" OE2 GLUBA 109 " pdb=" OG SERBK 39 " model vdw 2.102 2.440 nonbonded pdb=" OD2 ASPAI 108 " pdb=" O HOHAI 301 " model vdw 2.111 2.440 nonbonded pdb=" OD1 ASNBA 47 " pdb=" OG SERBA 50 " model vdw 2.172 2.440 nonbonded pdb=" OG1 THRAI 104 " pdb=" O HOHAI 301 " model vdw 2.179 2.440 nonbonded pdb=" O HISBM 117 " pdb=" O HOHBM 301 " model vdw 2.181 2.440 ... (remaining 552425 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 10.940 Check model and map are aligned: 0.620 Set scattering table: 0.370 Process input model: 116.750 Find NCS groups from input model: 3.350 Set up NCS constraints: 0.820 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:9.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 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 : 0.008 0.163 55030 Z= 0.556 Angle : 1.117 18.370 74854 Z= 0.580 Chirality : 0.065 0.831 8181 Planarity : 0.012 0.197 9805 Dihedral : 14.646 90.594 21388 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.38 % Allowed : 1.95 % Favored : 97.67 % Cbeta Deviations : 0.16 % 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: 2.13 (0.10), residues: 6752 helix: 1.92 (0.07), residues: 5197 sheet: 0.95 (0.53), residues: 55 loop : -0.30 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRPAW 128 HIS 0.019 0.006 HISBL 117 PHE 0.035 0.004 PHEBE 122 TYR 0.053 0.004 TYRBN 75 ARG 0.026 0.002 ARGBJ 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 1274 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1254 time to evaluate : 4.453 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. outliers start: 20 outliers final: 6 residues processed: 1267 average time/residue: 1.3703 time to fit residues: 2216.3320 Evaluate side-chains 1131 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1125 time to evaluate : 4.349 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 2 residues processed: 4 average time/residue: 1.9055 time to fit residues: 15.0505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 569 optimal weight: 0.9990 chunk 510 optimal weight: 0.6980 chunk 283 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 344 optimal weight: 0.9990 chunk 272 optimal weight: 0.6980 chunk 528 optimal weight: 0.7980 chunk 204 optimal weight: 1.9990 chunk 321 optimal weight: 0.9980 chunk 393 optimal weight: 0.9980 chunk 612 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 49 GLN AA 78 GLN ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AF 54 ASN ** AF 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AH 132 GLN AI 15 GLN AI 78 GLN AM 25 GLN AM 39 GLN AO 47 ASN AO 49 GLN AO 61 ASN AP 146 ASN AR 35 ASN AT 63 GLN AU 25 GLN AU 78 GLN AW 15 GLN AW 68 GLN AX 47 ASN AX 132 GLN ** AY 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 139 ASN BA 61 ASN BA 78 GLN ** BA 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 15 GLN BC 49 GLN BD 65 GLN BD 68 GLN ** BD 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 139 ASN BF 54 ASN BG 15 GLN BJ 132 GLN BK 13 GLN BK 72 ASN BK 143 ASN BK 163 ASN BL 181 GLN BL 195 GLN BL 267 GLN BM 52 GLN BM 159 ASN BM 170 GLN BM 220 ASN BM 252 ASN BM 258 GLN ** BM 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.1219 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= 0.217 Angle : 0.576 10.897 74854 Z= 0.275 Chirality : 0.037 0.215 8181 Planarity : 0.004 0.053 9805 Dihedral : 9.816 84.443 9997 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.40 % Allowed : 8.77 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.10), residues: 6752 helix: 2.24 (0.07), residues: 5229 sheet: 0.89 (0.52), residues: 55 loop : -0.31 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPAC 128 HIS 0.006 0.002 HISAS 140 PHE 0.013 0.001 PHEBB 164 TYR 0.020 0.001 TYRBK 134 ARG 0.008 0.001 ARGBB 15 *********************** 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 1219 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 1145 time to evaluate : 4.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. outliers start: 74 outliers final: 37 residues processed: 1169 average time/residue: 1.3972 time to fit residues: 2086.0605 Evaluate side-chains 1158 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1121 time to evaluate : 4.478 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 15 residues processed: 25 average time/residue: 0.6456 time to fit residues: 31.7544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 340 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 509 optimal weight: 5.9990 chunk 416 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 613 optimal weight: 0.9980 chunk 662 optimal weight: 2.9990 chunk 546 optimal weight: 0.7980 chunk 608 optimal weight: 0.6980 chunk 209 optimal weight: 0.9980 chunk 491 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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** AD 132 GLN AF 54 ASN ** AF 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 151 ASN AI 15 GLN AK 68 GLN AL 63 GLN AM 25 GLN AQ 15 GLN AT 63 GLN AU 25 GLN AW 15 GLN AY 139 ASN BA 61 ASN BC 15 GLN ** BD 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 35 ASN BF 54 ASN BK 13 GLN BK 74 GLN BL 181 GLN BM 52 GLN BM 90 ASN BM 170 GLN ** BM 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 258 GLN ** BM 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 55030 Z= 0.256 Angle : 0.557 10.783 74854 Z= 0.265 Chirality : 0.038 0.194 8181 Planarity : 0.004 0.062 9805 Dihedral : 9.714 89.721 9997 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.69 % Allowed : 10.91 % Favored : 87.41 % 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: 2.67 (0.10), residues: 6752 helix: 2.33 (0.07), residues: 5229 sheet: 0.75 (0.54), residues: 53 loop : -0.27 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPBM 146 HIS 0.008 0.003 HISBA 140 PHE 0.012 0.002 PHEBF 98 TYR 0.023 0.001 TYRBN 75 ARG 0.010 0.001 ARGAV 15 *********************** 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 1237 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1148 time to evaluate : 4.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. outliers start: 89 outliers final: 38 residues processed: 1179 average time/residue: 1.4066 time to fit residues: 2115.5032 Evaluate side-chains 1173 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 1135 time to evaluate : 4.384 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 15 residues processed: 25 average time/residue: 0.6237 time to fit residues: 31.0740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 605 optimal weight: 2.9990 chunk 461 optimal weight: 0.9980 chunk 318 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 292 optimal weight: 2.9990 chunk 411 optimal weight: 1.9990 chunk 615 optimal weight: 0.5980 chunk 651 optimal weight: 1.9990 chunk 321 optimal weight: 1.9990 chunk 583 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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** AD 111 ASN AF 11 GLN AF 54 ASN ** AF 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 15 GLN ** AK 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 63 GLN AM 25 GLN AR 35 ASN AT 47 ASN AT 63 GLN AU 25 GLN AW 15 GLN AX 47 ASN AY 25 GLN BA 53 ASN BA 61 ASN BC 15 GLN BC 78 GLN ** BD 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 35 ASN BF 54 ASN BG 15 GLN BK 13 GLN BL 92 GLN BL 181 GLN BL 195 GLN BM 52 GLN ** BM 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 111 GLN BM 157 GLN BM 159 ASN BM 170 GLN ** BM 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 258 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 55030 Z= 0.238 Angle : 0.536 10.575 74854 Z= 0.254 Chirality : 0.037 0.202 8181 Planarity : 0.004 0.047 9805 Dihedral : 9.680 89.803 9997 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.74 % Allowed : 12.08 % Favored : 86.17 % 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: 2.72 (0.10), residues: 6752 helix: 2.36 (0.07), residues: 5231 sheet: 0.70 (0.55), residues: 53 loop : -0.24 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPBM 146 HIS 0.006 0.002 HISAS 140 PHE 0.010 0.001 PHEBL 265 TYR 0.024 0.001 TYRBN 75 ARG 0.008 0.000 ARGAR 15 *********************** 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 1228 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1136 time to evaluate : 4.505 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. outliers start: 92 outliers final: 49 residues processed: 1164 average time/residue: 1.3997 time to fit residues: 2085.0694 Evaluate side-chains 1159 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1110 time to evaluate : 4.380 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 20 residues processed: 31 average time/residue: 0.7717 time to fit residues: 41.6651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 542 optimal weight: 5.9990 chunk 369 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 485 optimal weight: 3.9990 chunk 268 optimal weight: 2.9990 chunk 555 optimal weight: 2.9990 chunk 450 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 332 optimal weight: 0.9980 chunk 584 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** AF 54 ASN ** AF 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 15 GLN AL 63 GLN AR 35 ASN AT 63 GLN AV 47 ASN AW 15 GLN BA 61 ASN BC 15 GLN ** BD 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 35 ASN BF 54 ASN BG 15 GLN BI 15 GLN BI 73 ASN BK 13 GLN BK 163 ASN BL 92 GLN ** BL 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BL 176 ASN BL 181 GLN BM 52 GLN BM 92 GLN BM 111 GLN BM 157 GLN BM 159 ASN BM 170 GLN BM 220 ASN ** BM 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 55030 Z= 0.243 Angle : 0.535 10.553 74854 Z= 0.253 Chirality : 0.037 0.225 8181 Planarity : 0.004 0.050 9805 Dihedral : 9.634 89.879 9997 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.57 % Allowed : 12.95 % Favored : 85.47 % 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: 2.77 (0.10), residues: 6752 helix: 2.39 (0.07), residues: 5231 sheet: 0.73 (0.55), residues: 53 loop : -0.18 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPBM 146 HIS 0.006 0.002 HISAS 140 PHE 0.013 0.001 PHEAD 98 TYR 0.023 0.001 TYRBN 75 ARG 0.009 0.000 ARGAF 15 *********************** 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 1200 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1117 time to evaluate : 4.586 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. outliers start: 83 outliers final: 45 residues processed: 1151 average time/residue: 1.4431 time to fit residues: 2114.1217 Evaluate side-chains 1148 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1103 time to evaluate : 4.349 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 22 residues processed: 25 average time/residue: 0.7574 time to fit residues: 34.4177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 219 optimal weight: 1.9990 chunk 586 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 382 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 652 optimal weight: 2.9990 chunk 541 optimal weight: 0.6980 chunk 301 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 342 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 15 GLN ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AD 68 GLN AF 72 ASN AI 15 GLN AL 63 GLN AM 25 GLN AR 35 ASN AS 15 GLN AW 15 GLN BA 61 ASN BC 15 GLN ** BD 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 139 ASN BF 35 ASN BI 15 GLN BI 73 ASN BK 13 GLN BL 92 GLN BL 176 ASN BL 181 GLN BL 234 GLN ** BL 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 52 GLN BM 90 ASN ** BM 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 111 GLN BM 157 GLN BM 170 GLN BM 220 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 55030 Z= 0.256 Angle : 0.538 10.558 74854 Z= 0.255 Chirality : 0.037 0.240 8181 Planarity : 0.004 0.052 9805 Dihedral : 9.569 88.513 9997 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.67 % Allowed : 13.14 % Favored : 85.19 % 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: 2.75 (0.10), residues: 6752 helix: 2.37 (0.07), residues: 5252 sheet: 0.66 (0.59), residues: 49 loop : -0.19 (0.16), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPBM 146 HIS 0.007 0.002 HISAI 140 PHE 0.013 0.001 PHEAS 122 TYR 0.024 0.001 TYRBN 75 ARG 0.011 0.000 ARGAF 15 *********************** 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 1211 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1123 time to evaluate : 5.333 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. outliers start: 88 outliers final: 55 residues processed: 1156 average time/residue: 1.4632 time to fit residues: 2146.9216 Evaluate side-chains 1177 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1122 time to evaluate : 4.410 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 25 residues processed: 33 average time/residue: 0.7066 time to fit residues: 42.0199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 628 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 371 optimal weight: 0.5980 chunk 476 optimal weight: 5.9990 chunk 368 optimal weight: 0.9990 chunk 548 optimal weight: 1.9990 chunk 364 optimal weight: 0.7980 chunk 649 optimal weight: 2.9990 chunk 406 optimal weight: 1.9990 chunk 396 optimal weight: 2.9990 chunk 299 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** AE 57 GLN AF 72 ASN AI 15 GLN AI 139 ASN AL 63 GLN ** AV 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 15 GLN BA 61 ASN ** BC 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 139 ASN BF 35 ASN BG 15 GLN BI 73 ASN BK 13 GLN BK 92 ASN BK 185 HIS BL 92 GLN BL 176 ASN BL 181 GLN ** BL 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 52 GLN BM 90 ASN BM 92 GLN BM 111 GLN BM 157 GLN BM 220 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 55030 Z= 0.215 Angle : 0.524 10.515 74854 Z= 0.248 Chirality : 0.036 0.191 8181 Planarity : 0.004 0.046 9805 Dihedral : 9.559 88.981 9997 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.46 % Allowed : 13.77 % Favored : 84.77 % 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: 2.82 (0.10), residues: 6752 helix: 2.45 (0.07), residues: 5230 sheet: 0.69 (0.60), residues: 49 loop : -0.26 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPBM 146 HIS 0.006 0.002 HISAS 140 PHE 0.011 0.001 PHEAD 98 TYR 0.021 0.001 TYRBN 75 ARG 0.010 0.000 ARGAF 15 *********************** 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 1208 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1131 time to evaluate : 4.472 Fit side-chains TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. outliers start: 77 outliers final: 48 residues processed: 1164 average time/residue: 1.4450 time to fit residues: 2140.6034 Evaluate side-chains 1168 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1120 time to evaluate : 4.373 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 28 residues processed: 23 average time/residue: 0.7388 time to fit residues: 31.8403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 401 optimal weight: 0.9990 chunk 259 optimal weight: 1.9990 chunk 387 optimal weight: 0.6980 chunk 195 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 413 optimal weight: 0.9990 chunk 442 optimal weight: 2.9990 chunk 321 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 510 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 35 ASN AA 139 ASN ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AF 72 ASN AG 151 ASN AI 15 GLN AL 63 GLN AM 25 GLN AM 68 GLN ** AV 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 15 GLN BA 61 ASN ** BC 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 139 ASN BF 35 ASN BG 35 ASN BG 139 ASN BH 146 ASN BI 73 ASN BK 13 GLN BL 92 GLN BL 176 ASN BL 181 GLN BM 52 GLN BM 90 ASN BM 92 GLN BM 111 GLN BM 157 GLN BM 170 GLN BM 220 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 55030 Z= 0.224 Angle : 0.527 10.460 74854 Z= 0.251 Chirality : 0.036 0.194 8181 Planarity : 0.004 0.046 9805 Dihedral : 9.506 88.706 9997 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.50 % Allowed : 14.02 % Favored : 84.49 % 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: 2.86 (0.10), residues: 6752 helix: 2.44 (0.07), residues: 5232 sheet: 0.63 (0.60), residues: 49 loop : -0.11 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPBM 146 HIS 0.006 0.002 HISAS 140 PHE 0.012 0.001 PHEAD 98 TYR 0.021 0.001 TYRBN 75 ARG 0.010 0.000 ARGAF 77 *********************** 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 1198 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1119 time to evaluate : 4.655 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. outliers start: 79 outliers final: 49 residues processed: 1152 average time/residue: 1.4687 time to fit residues: 2153.6984 Evaluate side-chains 1150 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1101 time to evaluate : 4.370 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 30 residues processed: 22 average time/residue: 0.8776 time to fit residues: 34.0346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 590 optimal weight: 0.9980 chunk 622 optimal weight: 1.9990 chunk 567 optimal weight: 0.9990 chunk 605 optimal weight: 2.9990 chunk 364 optimal weight: 3.9990 chunk 263 optimal weight: 0.9990 chunk 475 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 547 optimal weight: 1.9990 chunk 572 optimal weight: 3.9990 chunk 603 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 15 GLN AA 35 ASN ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AF 72 ASN AF 132 GLN AF 146 ASN AI 15 GLN AL 63 GLN ** AV 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 15 GLN BA 61 ASN ** BC 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 139 ASN BF 35 ASN BG 15 GLN BG 139 ASN BI 73 ASN BK 13 GLN BK 92 ASN BL 92 GLN BL 181 GLN ** BL 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 52 GLN BM 90 ASN BM 92 GLN BM 111 GLN BM 157 GLN BM 170 GLN BM 220 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 55030 Z= 0.306 Angle : 0.560 10.512 74854 Z= 0.266 Chirality : 0.039 0.191 8181 Planarity : 0.004 0.047 9805 Dihedral : 9.493 89.536 9997 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.42 % Allowed : 14.20 % Favored : 84.38 % 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: 2.71 (0.10), residues: 6752 helix: 2.34 (0.07), residues: 5252 sheet: 0.62 (0.60), residues: 49 loop : -0.20 (0.16), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRPBK 60 HIS 0.007 0.003 HISAI 140 PHE 0.013 0.002 PHEAD 98 TYR 0.028 0.001 TYRBN 75 ARG 0.011 0.000 ARGBD 43 *********************** 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 1197 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1122 time to evaluate : 4.452 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. outliers start: 75 outliers final: 51 residues processed: 1154 average time/residue: 1.4597 time to fit residues: 2145.0295 Evaluate side-chains 1165 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1114 time to evaluate : 4.414 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 28 residues processed: 26 average time/residue: 0.6846 time to fit residues: 33.7608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 397 optimal weight: 0.6980 chunk 640 optimal weight: 1.9990 chunk 390 optimal weight: 2.9990 chunk 303 optimal weight: 0.0870 chunk 445 optimal weight: 2.9990 chunk 671 optimal weight: 0.0030 chunk 618 optimal weight: 1.9990 chunk 534 optimal weight: 0.9980 chunk 55 optimal weight: 0.0970 chunk 413 optimal weight: 0.8980 chunk 327 optimal weight: 0.0040 overall best weight: 0.1778 ------------------------------------------------------------------------------- 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** AF 72 ASN AF 146 ASN AI 15 GLN AL 63 GLN AM 25 GLN AN 65 GLN AU 68 GLN ** AV 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 15 GLN BA 61 ASN ** BC 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 72 ASN BE 139 ASN BF 35 ASN BG 15 GLN BG 139 ASN BI 73 ASN BK 13 GLN BL 176 ASN BL 181 GLN BL 195 GLN ** BL 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 52 GLN BM 90 ASN BM 92 GLN ** BM 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BM 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 220 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 55030 Z= 0.127 Angle : 0.491 10.263 74854 Z= 0.236 Chirality : 0.034 0.212 8181 Planarity : 0.003 0.044 9805 Dihedral : 9.568 89.047 9997 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.83 % Allowed : 15.34 % Favored : 83.83 % 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: 3.07 (0.10), residues: 6752 helix: 2.64 (0.07), residues: 5192 sheet: 0.72 (0.61), residues: 49 loop : -0.15 (0.16), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPBK 60 HIS 0.005 0.001 HISAU 140 PHE 0.010 0.001 PHEBH 60 TYR 0.014 0.001 TYRBF 95 ARG 0.009 0.000 ARGAF 77 ********************** 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 1175 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1131 time to evaluate : 4.736 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. outliers start: 44 outliers final: 29 residues processed: 1162 average time/residue: 1.4589 time to fit residues: 2161.1502 Evaluate side-chains 1139 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1110 time to evaluate : 4.385 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 26 residues processed: 6 average time/residue: 0.6717 time to fit residues: 12.3380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 424 optimal weight: 1.9990 chunk 569 optimal weight: 0.6980 chunk 163 optimal weight: 2.9990 chunk 493 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 535 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 chunk 549 optimal weight: 3.9990 chunk 67 optimal weight: 0.3980 chunk 98 optimal weight: 0.5980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 35 ASN ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AF 72 ASN AI 15 GLN AL 63 GLN ** AV 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 15 GLN BC 15 GLN BD 35 ASN BG 15 GLN BI 73 ASN BK 13 GLN BL 92 GLN ** BL 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BL 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 52 GLN BM 90 ASN BM 92 GLN ** BM 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BM 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BM 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 170 GLN BM 220 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.126145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.120196 restraints weight = 69505.533| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.01 r_work: 0.3716 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2278 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= 0.262 Angle : 0.542 10.405 74854 Z= 0.259 Chirality : 0.037 0.189 8181 Planarity : 0.004 0.053 9805 Dihedral : 9.402 89.066 9997 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.83 % Allowed : 15.53 % Favored : 83.64 % 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: 2.92 (0.10), residues: 6752 helix: 2.50 (0.07), residues: 5215 sheet: 0.66 (0.60), residues: 49 loop : -0.13 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRPBK 60 HIS 0.007 0.003 HISBA 140 PHE 0.014 0.001 PHEAD 98 TYR 0.023 0.001 TYRBN 75 ARG 0.011 0.000 ARGAP 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27266.27 seconds wall clock time: 471 minutes 20.53 seconds (28280.53 seconds total)