Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 23:24:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc9_25030/04_2023/7sc9_25030_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc9_25030/04_2023/7sc9_25030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc9_25030/04_2023/7sc9_25030.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc9_25030/04_2023/7sc9_25030.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc9_25030/04_2023/7sc9_25030_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc9_25030/04_2023/7sc9_25030_trim_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.021 sd= 0.113 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 610 5.16 5 C 74140 2.51 5 N 19818 2.21 5 O 22694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "AE PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AO TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AS TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AV PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BD PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BD TYR 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BD PHE 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BG PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BI TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BM TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BR GLU 22": "OE1" <-> "OE2" Residue "BW TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CG TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CM TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CM PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CM TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CM TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CM PHE 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CM PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CQ TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CR TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CS TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CU TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CW TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CY TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DI PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DK TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DK TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DL TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DL PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DQ TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DU TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DV TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DV TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DY PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EA TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.27s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 117262 Number of models: 1 Model: "" Number of chains: 164 Chain: "AA" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AB" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AC" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AD" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AE" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1254 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 152} Chain: "AF" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AH" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AI" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AJ" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AK" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1322 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain: "AL" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AN" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AO" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AP" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AQ" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AR" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AS" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AU" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AV" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AW" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AX" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "AY" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "AZ" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "BA" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "BB" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "BD" Number of atoms: 6761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 850, 6761 Classifications: {'peptide': 850} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 801} Chain breaks: 1 Chain: "BF" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 277 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 4, 'TRANS': 31} Chain: "BG" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 451 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 51} Chain: "BH" Number of atoms: 2302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2302 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 18, 'TRANS': 281} Chain breaks: 1 Chain: "BI" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "BJ" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "BK" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "BL" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "BM" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1254 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 152} Chain: "BN" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "BP" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "BQ" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "BR" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "BS" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1322 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain: "BT" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "BV" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "BW" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "BX" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "BY" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "BZ" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "CA" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "CC" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "CD" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "CE" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "CF" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "CG" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "CH" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "CJ" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "CK" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "CM" Number of atoms: 6761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 850, 6761 Classifications: {'peptide': 850} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 801} Chain breaks: 1 Chain: "CO" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 277 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 4, 'TRANS': 31} Chain: "CP" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 451 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 51} Chain: "CQ" Number of atoms: 2302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2302 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 18, 'TRANS': 281} Chain breaks: 1 Chain: "CR" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "CS" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "CT" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "CU" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "CV" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "CW" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "CY" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "CZ" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "DA" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "DB" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "DC" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "DD" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "DF" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "DG" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 426 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "DH" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 426 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "DI" Number of atoms: 2280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2280 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 18, 'TRANS': 277} Chain breaks: 1 Chain: "DJ" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "DK" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "DL" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "DM" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "DN" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "DO" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "DQ" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "DR" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "DS" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "DT" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "DU" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1210 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain: "DV" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1206 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Chain: "DX" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "DY" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 426 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "DZ" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 426 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "EA" Number of atoms: 2280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2280 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 18, 'TRANS': 277} Chain breaks: 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AH" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AN" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 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: 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: "BH" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'45D': 1} Classifications: {'undetermined': 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BK" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BL" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BM" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BN" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BP" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BQ" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BR" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BS" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BT" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BV" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BW" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BX" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BY" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BZ" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "CC" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "CD" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "CE" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "CF" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "CG" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "CH" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "CM" 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: "CQ" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'45D': 1} Classifications: {'undetermined': 1} Chain: "CR" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "CS" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "CT" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "CU" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "CV" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "CW" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "CY" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "CZ" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "DA" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "DB" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "DC" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "DD" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "DI" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'45D': 1} Classifications: {'undetermined': 1} Chain: "DJ" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "DK" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "DL" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "DM" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "DN" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "DO" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "DQ" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "DR" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "DS" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "DT" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "DU" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "DV" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "EA" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'45D': 1} Classifications: {'undetermined': 1} Time building chain proxies: 43.33, per 1000 atoms: 0.37 Number of scatterers: 117262 At special positions: 0 Unit cell: (210, 223.65, 223.65, 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 610 16.00 O 22694 8.00 N 19818 7.00 C 74140 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=71, symmetry=0 Number of additional bonds: simple=71, symmetry=0 Coordination: Other bonds: Time building additional restraints: 39.22 Conformation dependent library (CDL) restraints added in 12.7 seconds 29512 Ramachandran restraints generated. 14756 Oldfield, 0 Emsley, 14756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 27536 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 758 helices and 18 sheets defined 79.6% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 12.09 Creating SS restraints... Processing helix chain 'AA' and resid 2 through 15 Processing helix chain 'AA' and resid 19 through 47 removed outlier: 4.460A pdb=" N ALAAA 34 " --> pdb=" O VALAA 30 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALAAA 35 " --> pdb=" O THRAA 31 " (cutoff:3.500A) Processing helix chain 'AA' and resid 48 through 63 Proline residue: AA 63 - end of helix Processing helix chain 'AA' and resid 74 through 99 Processing helix chain 'AA' and resid 101 through 108 Processing helix chain 'AA' and resid 111 through 120 Processing helix chain 'AA' and resid 122 through 141 Processing helix chain 'AA' and resid 144 through 161 removed outlier: 3.680A pdb=" N ALAAA 151 " --> pdb=" O ALAAA 147 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYRAA 152 " --> pdb=" O GLUAA 148 " (cutoff:3.500A) Processing helix chain 'AC' and resid 2 through 15 Processing helix chain 'AC' and resid 19 through 47 removed outlier: 4.241A pdb=" N ALAAC 34 " --> pdb=" O VALAC 30 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ALAAC 35 " --> pdb=" O THRAC 31 " (cutoff:3.500A) Processing helix chain 'AC' and resid 48 through 63 Proline residue: AC 63 - end of helix Processing helix chain 'AC' and resid 74 through 99 removed outlier: 4.626A pdb=" N THRAC 78 " --> pdb=" O GLYAC 74 " (cutoff:3.500A) Processing helix chain 'AC' and resid 101 through 108 Processing helix chain 'AC' and resid 111 through 120 Processing helix chain 'AC' and resid 122 through 141 Processing helix chain 'AC' and resid 144 through 161 removed outlier: 4.567A pdb=" N GLUAC 148 " --> pdb=" O ASPAC 144 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALAAC 149 " --> pdb=" O ASPAC 145 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYRAC 152 " --> pdb=" O GLUAC 148 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHEAC 155 " --> pdb=" O ALAAC 151 " (cutoff:3.500A) Processing helix chain 'AH' and resid 2 through 15 Processing helix chain 'AH' and resid 19 through 47 removed outlier: 3.929A pdb=" N ARGAH 25 " --> pdb=" O GLYAH 21 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLYAH 33 " --> pdb=" O PHEAH 29 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ALAAH 34 " --> pdb=" O VALAH 30 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALAAH 35 " --> pdb=" O THRAH 31 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARGAH 36 " --> pdb=" O GLYAH 32 " (cutoff:3.500A) Processing helix chain 'AH' and resid 48 through 63 Proline residue: AH 63 - end of helix Processing helix chain 'AH' and resid 74 through 99 Processing helix chain 'AH' and resid 101 through 108 Processing helix chain 'AH' and resid 111 through 120 Processing helix chain 'AH' and resid 122 through 141 Processing helix chain 'AH' and resid 144 through 161 removed outlier: 3.826A pdb=" N TYRAH 152 " --> pdb=" O GLUAH 148 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 2 through 15 removed outlier: 3.588A pdb=" N GLUAJ 14 " --> pdb=" O ASNAJ 10 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 19 through 47 removed outlier: 4.456A pdb=" N ALAAJ 34 " --> pdb=" O VALAJ 30 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ALAAJ 35 " --> pdb=" O THRAJ 31 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 48 through 63 Proline residue: AJ 63 - end of helix Processing helix chain 'AJ' and resid 74 through 99 Processing helix chain 'AJ' and resid 101 through 108 Processing helix chain 'AJ' and resid 111 through 120 Processing helix chain 'AJ' and resid 122 through 141 removed outlier: 3.543A pdb=" N LEUAJ 140 " --> pdb=" O VALAJ 136 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N METAJ 141 " --> pdb=" O ALAAJ 137 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 144 through 161 removed outlier: 3.508A pdb=" N ALAAJ 151 " --> pdb=" O ALAAJ 147 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TYRAJ 152 " --> pdb=" O GLUAJ 148 " (cutoff:3.500A) Processing helix chain 'AN' and resid 2 through 15 Processing helix chain 'AN' and resid 19 through 47 removed outlier: 5.194A pdb=" N ALAAN 34 " --> pdb=" O VALAN 30 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ALAAN 35 " --> pdb=" O THRAN 31 " (cutoff:3.500A) Processing helix chain 'AN' and resid 48 through 63 removed outlier: 3.938A pdb=" N LYSAN 52 " --> pdb=" O GLUAN 48 " (cutoff:3.500A) Proline residue: AN 63 - end of helix Processing helix chain 'AN' and resid 74 through 99 Processing helix chain 'AN' and resid 101 through 108 removed outlier: 3.591A pdb=" N ILEAN 107 " --> pdb=" O PROAN 103 " (cutoff:3.500A) Processing helix chain 'AN' and resid 111 through 120 removed outlier: 3.760A pdb=" N SERAN 118 " --> pdb=" O GLUAN 114 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEUAN 119 " --> pdb=" O METAN 115 " (cutoff:3.500A) Processing helix chain 'AN' and resid 122 through 141 Processing helix chain 'AN' and resid 144 through 161 removed outlier: 3.889A pdb=" N TYRAN 152 " --> pdb=" O GLUAN 148 " (cutoff:3.500A) Processing helix chain 'AP' and resid 2 through 15 Processing helix chain 'AP' and resid 19 through 47 removed outlier: 5.070A pdb=" N ALAAP 34 " --> pdb=" O VALAP 30 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ALAAP 35 " --> pdb=" O THRAP 31 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARGAP 36 " --> pdb=" O GLYAP 32 " (cutoff:3.500A) Processing helix chain 'AP' and resid 48 through 63 Proline residue: AP 63 - end of helix Processing helix chain 'AP' and resid 74 through 99 Processing helix chain 'AP' and resid 101 through 108 Processing helix chain 'AP' and resid 111 through 120 Processing helix chain 'AP' and resid 122 through 141 Processing helix chain 'AP' and resid 144 through 161 removed outlier: 3.669A pdb=" N ALAAP 151 " --> pdb=" O ALAAP 147 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYRAP 152 " --> pdb=" O GLUAP 148 " (cutoff:3.500A) Processing helix chain 'AR' and resid 2 through 15 Processing helix chain 'AR' and resid 19 through 47 removed outlier: 5.068A pdb=" N ALAAR 34 " --> pdb=" O VALAR 30 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ALAAR 35 " --> pdb=" O THRAR 31 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARGAR 36 " --> pdb=" O GLYAR 32 " (cutoff:3.500A) Processing helix chain 'AR' and resid 48 through 63 Proline residue: AR 63 - end of helix Processing helix chain 'AR' and resid 74 through 99 Processing helix chain 'AR' and resid 101 through 108 Processing helix chain 'AR' and resid 111 through 120 Processing helix chain 'AR' and resid 122 through 141 Processing helix chain 'AR' and resid 144 through 161 removed outlier: 4.044A pdb=" N ALAAR 151 " --> pdb=" O ALAAR 147 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N TYRAR 152 " --> pdb=" O GLUAR 148 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHEAR 153 " --> pdb=" O ALAAR 149 " (cutoff:3.500A) Processing helix chain 'AV' and resid 2 through 15 Processing helix chain 'AV' and resid 19 through 47 removed outlier: 4.813A pdb=" N ALAAV 34 " --> pdb=" O VALAV 30 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ALAAV 35 " --> pdb=" O THRAV 31 " (cutoff:3.500A) Processing helix chain 'AV' and resid 48 through 63 Proline residue: AV 63 - end of helix Processing helix chain 'AV' and resid 74 through 99 Processing helix chain 'AV' and resid 101 through 108 Processing helix chain 'AV' and resid 111 through 120 Processing helix chain 'AV' and resid 122 through 141 Processing helix chain 'AV' and resid 144 through 161 removed outlier: 4.068A pdb=" N GLUAV 148 " --> pdb=" O ASPAV 144 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYRAV 152 " --> pdb=" O GLUAV 148 " (cutoff:3.500A) Processing helix chain 'AX' and resid 2 through 15 Processing helix chain 'AX' and resid 19 through 47 removed outlier: 4.874A pdb=" N ALAAX 34 " --> pdb=" O VALAX 30 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ALAAX 35 " --> pdb=" O THRAX 31 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILEAX 39 " --> pdb=" O ALAAX 35 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALAAX 40 " --> pdb=" O ARGAX 36 " (cutoff:3.500A) Processing helix chain 'AX' and resid 48 through 63 Proline residue: AX 63 - end of helix Processing helix chain 'AX' and resid 74 through 99 Processing helix chain 'AX' and resid 101 through 108 Processing helix chain 'AX' and resid 111 through 120 Processing helix chain 'AX' and resid 122 through 141 Processing helix chain 'AX' and resid 144 through 161 removed outlier: 3.579A pdb=" N ALAAX 151 " --> pdb=" O ALAAX 147 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYRAX 152 " --> pdb=" O GLUAX 148 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 2 through 15 Processing helix chain 'AZ' and resid 19 through 47 removed outlier: 4.349A pdb=" N ALAAZ 34 " --> pdb=" O VALAZ 30 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ALAAZ 35 " --> pdb=" O THRAZ 31 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 48 through 63 Proline residue: AZ 63 - end of helix Processing helix chain 'AZ' and resid 74 through 99 Processing helix chain 'AZ' and resid 101 through 108 Processing helix chain 'AZ' and resid 111 through 120 Processing helix chain 'AZ' and resid 122 through 141 Processing helix chain 'AZ' and resid 144 through 161 removed outlier: 3.620A pdb=" N ALAAZ 151 " --> pdb=" O ALAAZ 147 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TYRAZ 152 " --> pdb=" O GLUAZ 148 " (cutoff:3.500A) Processing helix chain 'BI' and resid 2 through 15 Processing helix chain 'BI' and resid 19 through 47 removed outlier: 4.432A pdb=" N ALABI 34 " --> pdb=" O VALBI 30 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ALABI 35 " --> pdb=" O THRBI 31 " (cutoff:3.500A) Processing helix chain 'BI' and resid 48 through 63 Proline residue: BI 63 - end of helix Processing helix chain 'BI' and resid 74 through 99 Processing helix chain 'BI' and resid 101 through 108 Processing helix chain 'BI' and resid 111 through 120 Processing helix chain 'BI' and resid 122 through 141 Processing helix chain 'BI' and resid 144 through 161 removed outlier: 3.649A pdb=" N ALABI 151 " --> pdb=" O ALABI 147 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYRBI 152 " --> pdb=" O GLUBI 148 " (cutoff:3.500A) Processing helix chain 'BK' and resid 2 through 15 Processing helix chain 'BK' and resid 19 through 47 removed outlier: 4.229A pdb=" N ALABK 34 " --> pdb=" O VALBK 30 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ALABK 35 " --> pdb=" O THRBK 31 " (cutoff:3.500A) Processing helix chain 'BK' and resid 48 through 63 Proline residue: BK 63 - end of helix Processing helix chain 'BK' and resid 74 through 99 removed outlier: 4.590A pdb=" N THRBK 78 " --> pdb=" O GLYBK 74 " (cutoff:3.500A) Processing helix chain 'BK' and resid 101 through 108 Processing helix chain 'BK' and resid 111 through 120 Processing helix chain 'BK' and resid 122 through 141 Processing helix chain 'BK' and resid 144 through 161 removed outlier: 4.538A pdb=" N GLUBK 148 " --> pdb=" O ASPBK 144 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALABK 149 " --> pdb=" O ASPBK 145 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHEBK 155 " --> pdb=" O ALABK 151 " (cutoff:3.500A) Processing helix chain 'BP' and resid 2 through 15 removed outlier: 3.648A pdb=" N ASNBP 10 " --> pdb=" O LYSBP 6 " (cutoff:3.500A) Processing helix chain 'BP' and resid 19 through 47 removed outlier: 4.119A pdb=" N ARGBP 25 " --> pdb=" O GLYBP 21 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLYBP 33 " --> pdb=" O PHEBP 29 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ALABP 34 " --> pdb=" O VALBP 30 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALABP 35 " --> pdb=" O THRBP 31 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ARGBP 36 " --> pdb=" O GLYBP 32 " (cutoff:3.500A) Processing helix chain 'BP' and resid 48 through 63 Proline residue: BP 63 - end of helix Processing helix chain 'BP' and resid 74 through 99 Processing helix chain 'BP' and resid 101 through 108 Processing helix chain 'BP' and resid 111 through 120 Processing helix chain 'BP' and resid 122 through 141 Processing helix chain 'BP' and resid 144 through 161 removed outlier: 3.846A pdb=" N TYRBP 152 " --> pdb=" O GLUBP 148 " (cutoff:3.500A) Processing helix chain 'BR' and resid 2 through 15 removed outlier: 3.601A pdb=" N GLUBR 14 " --> pdb=" O ASNBR 10 " (cutoff:3.500A) Processing helix chain 'BR' and resid 19 through 47 removed outlier: 4.605A pdb=" N ALABR 34 " --> pdb=" O VALBR 30 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ALABR 35 " --> pdb=" O THRBR 31 " (cutoff:3.500A) Processing helix chain 'BR' and resid 48 through 63 Proline residue: BR 63 - end of helix Processing helix chain 'BR' and resid 74 through 99 Processing helix chain 'BR' and resid 101 through 108 Processing helix chain 'BR' and resid 111 through 120 Processing helix chain 'BR' and resid 122 through 141 removed outlier: 3.533A pdb=" N LEUBR 140 " --> pdb=" O VALBR 136 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N METBR 141 " --> pdb=" O ALABR 137 " (cutoff:3.500A) Processing helix chain 'BR' and resid 144 through 161 removed outlier: 3.642A pdb=" N ALABR 151 " --> pdb=" O ALABR 147 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TYRBR 152 " --> pdb=" O GLUBR 148 " (cutoff:3.500A) Processing helix chain 'BV' and resid 2 through 15 Processing helix chain 'BV' and resid 19 through 47 removed outlier: 5.143A pdb=" N ALABV 34 " --> pdb=" O VALBV 30 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ALABV 35 " --> pdb=" O THRBV 31 " (cutoff:3.500A) Processing helix chain 'BV' and resid 48 through 63 removed outlier: 4.386A pdb=" N LYSBV 52 " --> pdb=" O GLUBV 48 " (cutoff:3.500A) Proline residue: BV 63 - end of helix Processing helix chain 'BV' and resid 74 through 99 Processing helix chain 'BV' and resid 101 through 108 removed outlier: 3.713A pdb=" N ILEBV 107 " --> pdb=" O PROBV 103 " (cutoff:3.500A) Processing helix chain 'BV' and resid 111 through 120 removed outlier: 3.511A pdb=" N SERBV 118 " --> pdb=" O GLUBV 114 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEUBV 119 " --> pdb=" O METBV 115 " (cutoff:3.500A) Processing helix chain 'BV' and resid 122 through 141 Processing helix chain 'BV' and resid 144 through 161 removed outlier: 4.008A pdb=" N TYRBV 152 " --> pdb=" O GLUBV 148 " (cutoff:3.500A) Processing helix chain 'BX' and resid 2 through 15 Processing helix chain 'BX' and resid 19 through 47 removed outlier: 4.986A pdb=" N ALABX 34 " --> pdb=" O VALBX 30 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ALABX 35 " --> pdb=" O THRBX 31 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARGBX 36 " --> pdb=" O GLYBX 32 " (cutoff:3.500A) Processing helix chain 'BX' and resid 48 through 63 Proline residue: BX 63 - end of helix Processing helix chain 'BX' and resid 74 through 99 Processing helix chain 'BX' and resid 101 through 108 Processing helix chain 'BX' and resid 111 through 120 Processing helix chain 'BX' and resid 122 through 141 Processing helix chain 'BX' and resid 144 through 161 removed outlier: 3.608A pdb=" N ALABX 151 " --> pdb=" O ALABX 147 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYRBX 152 " --> pdb=" O GLUBX 148 " (cutoff:3.500A) Processing helix chain 'BZ' and resid 2 through 15 Processing helix chain 'BZ' and resid 19 through 47 removed outlier: 5.058A pdb=" N ALABZ 34 " --> pdb=" O VALBZ 30 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ALABZ 35 " --> pdb=" O THRBZ 31 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARGBZ 36 " --> pdb=" O GLYBZ 32 " (cutoff:3.500A) Processing helix chain 'BZ' and resid 48 through 63 Proline residue: BZ 63 - end of helix Processing helix chain 'BZ' and resid 74 through 99 Processing helix chain 'BZ' and resid 101 through 108 Processing helix chain 'BZ' and resid 111 through 120 Processing helix chain 'BZ' and resid 122 through 141 Processing helix chain 'BZ' and resid 144 through 161 removed outlier: 4.010A pdb=" N ALABZ 151 " --> pdb=" O ALABZ 147 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N TYRBZ 152 " --> pdb=" O GLUBZ 148 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHEBZ 153 " --> pdb=" O ALABZ 149 " (cutoff:3.500A) Processing helix chain 'CC' and resid 2 through 15 Processing helix chain 'CC' and resid 19 through 47 removed outlier: 4.430A pdb=" N ALACC 34 " --> pdb=" O VALCC 30 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ALACC 35 " --> pdb=" O THRCC 31 " (cutoff:3.500A) Processing helix chain 'CC' and resid 48 through 63 Proline residue: CC 63 - end of helix Processing helix chain 'CC' and resid 74 through 99 Processing helix chain 'CC' and resid 101 through 108 Processing helix chain 'CC' and resid 111 through 120 Processing helix chain 'CC' and resid 122 through 141 Processing helix chain 'CC' and resid 144 through 161 removed outlier: 3.610A pdb=" N ALACC 151 " --> pdb=" O ALACC 147 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TYRCC 152 " --> pdb=" O GLUCC 148 " (cutoff:3.500A) Processing helix chain 'CE' and resid 2 through 15 Processing helix chain 'CE' and resid 19 through 47 removed outlier: 4.950A pdb=" N ALACE 34 " --> pdb=" O VALCE 30 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ALACE 35 " --> pdb=" O THRCE 31 " (cutoff:3.500A) Processing helix chain 'CE' and resid 48 through 63 Proline residue: CE 63 - end of helix Processing helix chain 'CE' and resid 74 through 99 Processing helix chain 'CE' and resid 101 through 108 Processing helix chain 'CE' and resid 111 through 120 Processing helix chain 'CE' and resid 122 through 141 Processing helix chain 'CE' and resid 144 through 161 removed outlier: 4.063A pdb=" N GLUCE 148 " --> pdb=" O ASPCE 144 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYRCE 152 " --> pdb=" O GLUCE 148 " (cutoff:3.500A) Processing helix chain 'CG' and resid 2 through 15 Processing helix chain 'CG' and resid 19 through 47 removed outlier: 4.968A pdb=" N ALACG 34 " --> pdb=" O VALCG 30 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ALACG 35 " --> pdb=" O THRCG 31 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILECG 39 " --> pdb=" O ALACG 35 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALACG 40 " --> pdb=" O ARGCG 36 " (cutoff:3.500A) Processing helix chain 'CG' and resid 48 through 63 Proline residue: CG 63 - end of helix Processing helix chain 'CG' and resid 74 through 99 Processing helix chain 'CG' and resid 101 through 108 Processing helix chain 'CG' and resid 111 through 120 Processing helix chain 'CG' and resid 122 through 141 Processing helix chain 'CG' and resid 144 through 161 removed outlier: 4.199A pdb=" N TYRCG 152 " --> pdb=" O GLUCG 148 " (cutoff:3.500A) Processing helix chain 'CR' and resid 2 through 15 Processing helix chain 'CR' and resid 19 through 47 removed outlier: 5.062A pdb=" N ALACR 34 " --> pdb=" O VALCR 30 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ALACR 35 " --> pdb=" O THRCR 31 " (cutoff:3.500A) Processing helix chain 'CR' and resid 48 through 63 Proline residue: CR 63 - end of helix Processing helix chain 'CR' and resid 74 through 99 removed outlier: 3.863A pdb=" N CYSCR 81 " --> pdb=" O METCR 77 " (cutoff:3.500A) Processing helix chain 'CR' and resid 101 through 108 Processing helix chain 'CR' and resid 111 through 120 Processing helix chain 'CR' and resid 122 through 141 Processing helix chain 'CR' and resid 144 through 161 removed outlier: 4.206A pdb=" N GLUCR 148 " --> pdb=" O ASPCR 144 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYRCR 152 " --> pdb=" O GLUCR 148 " (cutoff:3.500A) Processing helix chain 'CT' and resid 2 through 15 Processing helix chain 'CT' and resid 19 through 47 removed outlier: 4.208A pdb=" N ARGCT 25 " --> pdb=" O GLYCT 21 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ALACT 34 " --> pdb=" O VALCT 30 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALACT 35 " --> pdb=" O THRCT 31 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARGCT 36 " --> pdb=" O GLYCT 32 " (cutoff:3.500A) Processing helix chain 'CT' and resid 48 through 63 Proline residue: CT 63 - end of helix Processing helix chain 'CT' and resid 74 through 99 removed outlier: 6.324A pdb=" N THRCT 78 " --> pdb=" O GLYCT 74 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALACT 79 " --> pdb=" O GLUCT 75 " (cutoff:3.500A) Processing helix chain 'CT' and resid 101 through 108 Processing helix chain 'CT' and resid 111 through 120 Processing helix chain 'CT' and resid 122 through 141 Processing helix chain 'CT' and resid 144 through 161 removed outlier: 4.047A pdb=" N TYRCT 152 " --> pdb=" O GLUCT 148 " (cutoff:3.500A) Processing helix chain 'CV' and resid 2 through 15 Processing helix chain 'CV' and resid 19 through 47 removed outlier: 4.667A pdb=" N ALACV 34 " --> pdb=" O VALCV 30 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ALACV 35 " --> pdb=" O THRCV 31 " (cutoff:3.500A) Processing helix chain 'CV' and resid 48 through 63 Proline residue: CV 63 - end of helix Processing helix chain 'CV' and resid 74 through 99 Processing helix chain 'CV' and resid 101 through 108 Processing helix chain 'CV' and resid 111 through 120 Processing helix chain 'CV' and resid 122 through 141 Processing helix chain 'CV' and resid 144 through 161 removed outlier: 3.747A pdb=" N ALACV 151 " --> pdb=" O ALACV 147 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYRCV 152 " --> pdb=" O GLUCV 148 " (cutoff:3.500A) Processing helix chain 'DA' and resid 2 through 15 Processing helix chain 'DA' and resid 19 through 47 removed outlier: 5.098A pdb=" N ALADA 34 " --> pdb=" O VALDA 30 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ALADA 35 " --> pdb=" O THRDA 31 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARGDA 36 " --> pdb=" O GLYDA 32 " (cutoff:3.500A) Processing helix chain 'DA' and resid 48 through 63 Proline residue: DA 63 - end of helix Processing helix chain 'DA' and resid 74 through 99 Processing helix chain 'DA' and resid 101 through 108 Processing helix chain 'DA' and resid 111 through 120 removed outlier: 3.766A pdb=" N GLYDA 120 " --> pdb=" O TYRDA 116 " (cutoff:3.500A) Processing helix chain 'DA' and resid 122 through 141 Processing helix chain 'DA' and resid 144 through 161 removed outlier: 4.183A pdb=" N TYRDA 152 " --> pdb=" O GLUDA 148 " (cutoff:3.500A) Processing helix chain 'DC' and resid 2 through 15 Processing helix chain 'DC' and resid 19 through 47 removed outlier: 4.379A pdb=" N ALADC 34 " --> pdb=" O VALDC 30 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ALADC 35 " --> pdb=" O THRDC 31 " (cutoff:3.500A) Processing helix chain 'DC' and resid 48 through 63 Proline residue: DC 63 - end of helix Processing helix chain 'DC' and resid 74 through 99 Processing helix chain 'DC' and resid 101 through 108 Processing helix chain 'DC' and resid 111 through 120 Processing helix chain 'DC' and resid 122 through 141 Processing helix chain 'DC' and resid 144 through 161 removed outlier: 4.047A pdb=" N TYRDC 152 " --> pdb=" O GLUDC 148 " (cutoff:3.500A) Processing helix chain 'DJ' and resid 2 through 15 Processing helix chain 'DJ' and resid 19 through 47 removed outlier: 5.072A pdb=" N ALADJ 34 " --> pdb=" O VALDJ 30 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ALADJ 35 " --> pdb=" O THRDJ 31 " (cutoff:3.500A) Processing helix chain 'DJ' and resid 48 through 63 Proline residue: DJ 63 - end of helix Processing helix chain 'DJ' and resid 74 through 99 Processing helix chain 'DJ' and resid 101 through 108 Processing helix chain 'DJ' and resid 111 through 120 Processing helix chain 'DJ' and resid 122 through 141 Processing helix chain 'DJ' and resid 144 through 161 removed outlier: 4.087A pdb=" N GLUDJ 148 " --> pdb=" O ASPDJ 144 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYRDJ 152 " --> pdb=" O GLUDJ 148 " (cutoff:3.500A) Processing helix chain 'DN' and resid 2 through 15 Processing helix chain 'DN' and resid 19 through 47 removed outlier: 4.572A pdb=" N ALADN 34 " --> pdb=" O VALDN 30 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ALADN 35 " --> pdb=" O THRDN 31 " (cutoff:3.500A) Processing helix chain 'DN' and resid 48 through 63 Proline residue: DN 63 - end of helix Processing helix chain 'DN' and resid 74 through 99 Processing helix chain 'DN' and resid 101 through 108 Processing helix chain 'DN' and resid 111 through 120 Processing helix chain 'DN' and resid 122 through 141 Processing helix chain 'DN' and resid 144 through 161 removed outlier: 3.685A pdb=" N ALADN 151 " --> pdb=" O ALADN 147 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYRDN 152 " --> pdb=" O GLUDN 148 " (cutoff:3.500A) Processing helix chain 'DQ' and resid 2 through 15 Processing helix chain 'DQ' and resid 19 through 47 removed outlier: 5.338A pdb=" N ALADQ 34 " --> pdb=" O VALDQ 30 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ALADQ 35 " --> pdb=" O THRDQ 31 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARGDQ 36 " --> pdb=" O GLYDQ 32 " (cutoff:3.500A) Processing helix chain 'DQ' and resid 48 through 63 Proline residue: DQ 63 - end of helix Processing helix chain 'DQ' and resid 74 through 99 Processing helix chain 'DQ' and resid 101 through 108 Processing helix chain 'DQ' and resid 111 through 120 Processing helix chain 'DQ' and resid 122 through 141 Processing helix chain 'DQ' and resid 144 through 161 removed outlier: 3.638A pdb=" N GLUDQ 148 " --> pdb=" O ASPDQ 144 " (cutoff:3.500A) Processing helix chain 'DS' and resid 2 through 15 Processing helix chain 'DS' and resid 19 through 47 removed outlier: 5.170A pdb=" N ALADS 34 " --> pdb=" O VALDS 30 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ALADS 35 " --> pdb=" O THRDS 31 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARGDS 36 " --> pdb=" O GLYDS 32 " (cutoff:3.500A) Processing helix chain 'DS' and resid 48 through 63 Proline residue: DS 63 - end of helix Processing helix chain 'DS' and resid 74 through 99 Processing helix chain 'DS' and resid 101 through 108 Processing helix chain 'DS' and resid 111 through 120 Processing helix chain 'DS' and resid 122 through 141 Processing helix chain 'DS' and resid 144 through 161 removed outlier: 4.090A pdb=" N TYRDS 152 " --> pdb=" O GLUDS 148 " (cutoff:3.500A) Processing helix chain 'DU' and resid 2 through 15 Processing helix chain 'DU' and resid 19 through 47 removed outlier: 4.385A pdb=" N ALADU 34 " --> pdb=" O VALDU 30 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ALADU 35 " --> pdb=" O THRDU 31 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SERDU 46 " --> pdb=" O THRDU 42 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARGDU 47 " --> pdb=" O LEUDU 43 " (cutoff:3.500A) Processing helix chain 'DU' and resid 48 through 63 Proline residue: DU 63 - end of helix Processing helix chain 'DU' and resid 74 through 99 Processing helix chain 'DU' and resid 101 through 108 Processing helix chain 'DU' and resid 111 through 120 Processing helix chain 'DU' and resid 122 through 141 Processing helix chain 'DU' and resid 144 through 161 removed outlier: 4.041A pdb=" N TYRDU 152 " --> pdb=" O GLUDU 148 " (cutoff:3.500A) Processing helix chain 'CY' and resid 2 through 15 removed outlier: 3.779A pdb=" N GLUCY 14 " --> pdb=" O ASNCY 10 " (cutoff:3.500A) Processing helix chain 'CY' and resid 19 through 33 Processing helix chain 'CY' and resid 34 through 47 removed outlier: 4.200A pdb=" N SERCY 46 " --> pdb=" O THRCY 42 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARGCY 47 " --> pdb=" O LEUCY 43 " (cutoff:3.500A) Processing helix chain 'CY' and resid 48 through 63 removed outlier: 3.634A pdb=" N GLNCY 60 " --> pdb=" O ASPCY 56 " (cutoff:3.500A) Proline residue: CY 63 - end of helix Processing helix chain 'CY' and resid 74 through 99 Processing helix chain 'CY' and resid 101 through 108 Processing helix chain 'CY' and resid 111 through 120 Processing helix chain 'CY' and resid 122 through 141 Processing helix chain 'CY' and resid 143 through 161 removed outlier: 3.891A pdb=" N TYRCY 152 " --> pdb=" O GLUCY 148 " (cutoff:3.500A) Processing helix chain 'DL' and resid 2 through 15 removed outlier: 3.808A pdb=" N GLUDL 14 " --> pdb=" O ASNDL 10 " (cutoff:3.500A) Processing helix chain 'DL' and resid 19 through 33 removed outlier: 4.196A pdb=" N ARGDL 25 " --> pdb=" O GLYDL 21 " (cutoff:3.500A) Processing helix chain 'DL' and resid 34 through 47 Processing helix chain 'DL' and resid 48 through 63 Proline residue: DL 63 - end of helix Processing helix chain 'DL' and resid 74 through 99 removed outlier: 6.342A pdb=" N THRDL 78 " --> pdb=" O GLYDL 74 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALADL 79 " --> pdb=" O GLUDL 75 " (cutoff:3.500A) Processing helix chain 'DL' and resid 101 through 108 Processing helix chain 'DL' and resid 111 through 120 Processing helix chain 'DL' and resid 122 through 141 Processing helix chain 'DL' and resid 143 through 161 removed outlier: 4.077A pdb=" N TYRDL 152 " --> pdb=" O GLUDL 148 " (cutoff:3.500A) Processing helix chain 'AB' and resid 3 through 16 removed outlier: 3.828A pdb=" N GLNAB 15 " --> pdb=" O SERAB 11 " (cutoff:3.500A) Processing helix chain 'AB' and resid 21 through 48 removed outlier: 4.741A pdb=" N LYSAB 26 " --> pdb=" O ALAAB 22 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLUAB 35 " --> pdb=" O PHEAB 31 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LEUAB 36 " --> pdb=" O ALAAB 32 " (cutoff:3.500A) Processing helix chain 'AB' and resid 49 through 59 Processing helix chain 'AB' and resid 63 through 68 Proline residue: AB 68 - end of helix Processing helix chain 'AB' and resid 74 through 99 Processing helix chain 'AB' and resid 101 through 107 Processing helix chain 'AB' and resid 111 through 120 Processing helix chain 'AB' and resid 122 through 142 Processing helix chain 'AB' and resid 143 through 161 removed outlier: 3.772A pdb=" N TYRAB 152 " --> pdb=" O GLUAB 148 " (cutoff:3.500A) Processing helix chain 'AD' and resid 3 through 16 removed outlier: 3.871A pdb=" N GLNAD 15 " --> pdb=" O SERAD 11 " (cutoff:3.500A) Processing helix chain 'AD' and resid 21 through 48 removed outlier: 4.256A pdb=" N GLUAD 35 " --> pdb=" O PHEAD 31 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEUAD 36 " --> pdb=" O ALAAD 32 " (cutoff:3.500A) Processing helix chain 'AD' and resid 49 through 59 Processing helix chain 'AD' and resid 63 through 68 Proline residue: AD 68 - end of helix Processing helix chain 'AD' and resid 74 through 99 Processing helix chain 'AD' and resid 101 through 107 removed outlier: 3.882A pdb=" N ASPAD 105 " --> pdb=" O ALAAD 101 " (cutoff:3.500A) Processing helix chain 'AD' and resid 111 through 120 Processing helix chain 'AD' and resid 122 through 142 Processing helix chain 'AD' and resid 143 through 161 removed outlier: 3.656A pdb=" N GLUAD 148 " --> pdb=" O ASPAD 144 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYRAD 152 " --> pdb=" O GLUAD 148 " (cutoff:3.500A) Processing helix chain 'AF' and resid 3 through 16 removed outlier: 3.736A pdb=" N VALAF 8 " --> pdb=" O ALAAF 4 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILEAF 9 " --> pdb=" O ILEAF 5 " (cutoff:3.500A) Processing helix chain 'AF' and resid 21 through 48 removed outlier: 4.741A pdb=" N LYSAF 26 " --> pdb=" O ALAAF 22 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLUAF 35 " --> pdb=" O PHEAF 31 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEUAF 36 " --> pdb=" O ALAAF 32 " (cutoff:3.500A) Processing helix chain 'AF' and resid 49 through 59 Processing helix chain 'AF' and resid 63 through 68 Proline residue: AF 68 - end of helix Processing helix chain 'AF' and resid 74 through 99 Processing helix chain 'AF' and resid 101 through 107 Processing helix chain 'AF' and resid 111 through 120 Processing helix chain 'AF' and resid 122 through 142 Processing helix chain 'AF' and resid 143 through 161 removed outlier: 3.997A pdb=" N GLUAF 148 " --> pdb=" O ASPAF 144 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYRAF 152 " --> pdb=" O GLUAF 148 " (cutoff:3.500A) Processing helix chain 'AI' and resid 3 through 16 removed outlier: 3.911A pdb=" N GLNAI 15 " --> pdb=" O SERAI 11 " (cutoff:3.500A) Processing helix chain 'AI' and resid 21 through 48 removed outlier: 4.432A pdb=" N GLUAI 35 " --> pdb=" O PHEAI 31 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEUAI 36 " --> pdb=" O ALAAI 32 " (cutoff:3.500A) Processing helix chain 'AI' and resid 49 through 59 Processing helix chain 'AI' and resid 63 through 68 removed outlier: 3.820A pdb=" N ARGAI 67 " --> pdb=" O SERAI 63 " (cutoff:3.500A) Proline residue: AI 68 - end of helix No H-bonds generated for 'chain 'AI' and resid 63 through 68' Processing helix chain 'AI' and resid 74 through 99 Processing helix chain 'AI' and resid 101 through 107 removed outlier: 3.744A pdb=" N ASPAI 105 " --> pdb=" O ALAAI 101 " (cutoff:3.500A) Processing helix chain 'AI' and resid 111 through 120 Processing helix chain 'AI' and resid 122 through 142 Processing helix chain 'AI' and resid 143 through 161 removed outlier: 3.613A pdb=" N GLUAI 148 " --> pdb=" O ASPAI 144 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYRAI 152 " --> pdb=" O GLUAI 148 " (cutoff:3.500A) Processing helix chain 'AL' and resid 3 through 16 Processing helix chain 'AL' and resid 21 through 48 removed outlier: 4.393A pdb=" N ASPAL 25 " --> pdb=" O GLYAL 21 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLUAL 35 " --> pdb=" O PHEAL 31 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEUAL 36 " --> pdb=" O ALAAL 32 " (cutoff:3.500A) Processing helix chain 'AL' and resid 49 through 59 Processing helix chain 'AL' and resid 63 through 68 Proline residue: AL 68 - end of helix Processing helix chain 'AL' and resid 74 through 99 Processing helix chain 'AL' and resid 101 through 107 Processing helix chain 'AL' and resid 111 through 120 Processing helix chain 'AL' and resid 122 through 142 Processing helix chain 'AL' and resid 143 through 161 removed outlier: 4.315A pdb=" N TYRAL 152 " --> pdb=" O GLUAL 148 " (cutoff:3.500A) Processing helix chain 'AO' and resid 3 through 16 removed outlier: 3.761A pdb=" N GLNAO 15 " --> pdb=" O SERAO 11 " (cutoff:3.500A) Processing helix chain 'AO' and resid 21 through 48 removed outlier: 3.988A pdb=" N GLUAO 35 " --> pdb=" O PHEAO 31 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEUAO 36 " --> pdb=" O ALAAO 32 " (cutoff:3.500A) Processing helix chain 'AO' and resid 49 through 59 Processing helix chain 'AO' and resid 63 through 68 Proline residue: AO 68 - end of helix Processing helix chain 'AO' and resid 74 through 99 Processing helix chain 'AO' and resid 101 through 107 Processing helix chain 'AO' and resid 111 through 120 Processing helix chain 'AO' and resid 122 through 142 Processing helix chain 'AO' and resid 143 through 161 removed outlier: 3.807A pdb=" N TYRAO 152 " --> pdb=" O GLUAO 148 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 3 through 16 removed outlier: 3.672A pdb=" N GLNAQ 15 " --> pdb=" O SERAQ 11 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 21 through 48 removed outlier: 4.355A pdb=" N GLUAQ 35 " --> pdb=" O PHEAQ 31 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEUAQ 36 " --> pdb=" O ALAAQ 32 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 49 through 59 Processing helix chain 'AQ' and resid 63 through 68 Proline residue: AQ 68 - end of helix Processing helix chain 'AQ' and resid 74 through 99 Processing helix chain 'AQ' and resid 101 through 107 Processing helix chain 'AQ' and resid 111 through 120 Processing helix chain 'AQ' and resid 122 through 142 Processing helix chain 'AQ' and resid 143 through 161 Processing helix chain 'AS' and resid 3 through 16 Processing helix chain 'AS' and resid 21 through 48 removed outlier: 4.503A pdb=" N GLUAS 35 " --> pdb=" O PHEAS 31 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEUAS 36 " --> pdb=" O ALAAS 32 " (cutoff:3.500A) Processing helix chain 'AS' and resid 49 through 59 Processing helix chain 'AS' and resid 63 through 68 Proline residue: AS 68 - end of helix Processing helix chain 'AS' and resid 74 through 99 Processing helix chain 'AS' and resid 101 through 107 removed outlier: 3.648A pdb=" N ASPAS 105 " --> pdb=" O ALAAS 101 " (cutoff:3.500A) Processing helix chain 'AS' and resid 111 through 120 Processing helix chain 'AS' and resid 122 through 142 removed outlier: 3.713A pdb=" N GLUAS 135 " --> pdb=" O GLNAS 131 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEUAS 140 " --> pdb=" O VALAS 136 " (cutoff:3.500A) Processing helix chain 'AS' and resid 143 through 161 Processing helix chain 'AU' and resid 3 through 16 removed outlier: 3.748A pdb=" N GLNAU 15 " --> pdb=" O SERAU 11 " (cutoff:3.500A) Processing helix chain 'AU' and resid 21 through 48 removed outlier: 4.531A pdb=" N GLUAU 35 " --> pdb=" O PHEAU 31 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEUAU 36 " --> pdb=" O ALAAU 32 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASNAU 47 " --> pdb=" O VALAU 43 " (cutoff:3.500A) Processing helix chain 'AU' and resid 49 through 59 removed outlier: 3.793A pdb=" N ALAAU 57 " --> pdb=" O LYSAU 53 " (cutoff:3.500A) Processing helix chain 'AU' and resid 63 through 68 Proline residue: AU 68 - end of helix Processing helix chain 'AU' and resid 74 through 99 Processing helix chain 'AU' and resid 101 through 107 Processing helix chain 'AU' and resid 111 through 120 Processing helix chain 'AU' and resid 122 through 142 removed outlier: 3.615A pdb=" N VALAU 136 " --> pdb=" O ALAAU 132 " (cutoff:3.500A) Processing helix chain 'AU' and resid 143 through 161 Processing helix chain 'AW' and resid 3 through 16 removed outlier: 3.686A pdb=" N GLNAW 15 " --> pdb=" O SERAW 11 " (cutoff:3.500A) Processing helix chain 'AW' and resid 21 through 48 removed outlier: 3.622A pdb=" N LYSAW 26 " --> pdb=" O ALAAW 22 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLUAW 35 " --> pdb=" O PHEAW 31 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LEUAW 36 " --> pdb=" O ALAAW 32 " (cutoff:3.500A) Processing helix chain 'AW' and resid 49 through 59 Processing helix chain 'AW' and resid 63 through 68 Proline residue: AW 68 - end of helix Processing helix chain 'AW' and resid 74 through 99 Processing helix chain 'AW' and resid 101 through 107 Processing helix chain 'AW' and resid 111 through 120 removed outlier: 3.650A pdb=" N THRAW 115 " --> pdb=" O GLYAW 111 " (cutoff:3.500A) Processing helix chain 'AW' and resid 122 through 142 Processing helix chain 'AW' and resid 143 through 161 removed outlier: 3.725A pdb=" N TYRAW 152 " --> pdb=" O GLUAW 148 " (cutoff:3.500A) Processing helix chain 'AY' and resid 3 through 16 removed outlier: 3.743A pdb=" N GLNAY 15 " --> pdb=" O SERAY 11 " (cutoff:3.500A) Processing helix chain 'AY' and resid 21 through 48 removed outlier: 4.208A pdb=" N GLUAY 35 " --> pdb=" O PHEAY 31 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LEUAY 36 " --> pdb=" O ALAAY 32 " (cutoff:3.500A) Processing helix chain 'AY' and resid 49 through 59 Processing helix chain 'AY' and resid 63 through 68 Proline residue: AY 68 - end of helix Processing helix chain 'AY' and resid 74 through 99 Processing helix chain 'AY' and resid 101 through 107 Processing helix chain 'AY' and resid 111 through 120 Processing helix chain 'AY' and resid 122 through 142 Processing helix chain 'AY' and resid 143 through 161 removed outlier: 4.192A pdb=" N GLUAY 148 " --> pdb=" O ASPAY 144 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 3 through 16 removed outlier: 3.864A pdb=" N GLNBJ 15 " --> pdb=" O SERBJ 11 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 21 through 48 removed outlier: 5.001A pdb=" N LYSBJ 26 " --> pdb=" O ALABJ 22 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEUBJ 27 " --> pdb=" O ALABJ 23 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLUBJ 35 " --> pdb=" O PHEBJ 31 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEUBJ 36 " --> pdb=" O ALABJ 32 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 49 through 59 Processing helix chain 'BJ' and resid 63 through 68 Proline residue: BJ 68 - end of helix Processing helix chain 'BJ' and resid 74 through 99 Processing helix chain 'BJ' and resid 101 through 107 Processing helix chain 'BJ' and resid 111 through 120 Processing helix chain 'BJ' and resid 122 through 142 Processing helix chain 'BJ' and resid 143 through 161 removed outlier: 3.773A pdb=" N TYRBJ 152 " --> pdb=" O GLUBJ 148 " (cutoff:3.500A) Processing helix chain 'BL' and resid 3 through 16 removed outlier: 3.978A pdb=" N GLNBL 15 " --> pdb=" O SERBL 11 " (cutoff:3.500A) Processing helix chain 'BL' and resid 21 through 48 removed outlier: 4.395A pdb=" N GLUBL 35 " --> pdb=" O PHEBL 31 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEUBL 36 " --> pdb=" O ALABL 32 " (cutoff:3.500A) Processing helix chain 'BL' and resid 49 through 59 Processing helix chain 'BL' and resid 63 through 68 Proline residue: BL 68 - end of helix Processing helix chain 'BL' and resid 74 through 99 Processing helix chain 'BL' and resid 101 through 107 removed outlier: 3.993A pdb=" N ASPBL 105 " --> pdb=" O ALABL 101 " (cutoff:3.500A) Processing helix chain 'BL' and resid 111 through 120 Processing helix chain 'BL' and resid 122 through 142 Processing helix chain 'BL' and resid 143 through 161 removed outlier: 3.650A pdb=" N GLUBL 148 " --> pdb=" O ASPBL 144 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYRBL 152 " --> pdb=" O GLUBL 148 " (cutoff:3.500A) Processing helix chain 'BN' and resid 3 through 16 removed outlier: 3.825A pdb=" N VALBN 8 " --> pdb=" O ALABN 4 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILEBN 9 " --> pdb=" O ILEBN 5 " (cutoff:3.500A) Processing helix chain 'BN' and resid 21 through 48 removed outlier: 4.675A pdb=" N LYSBN 26 " --> pdb=" O ALABN 22 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLUBN 35 " --> pdb=" O PHEBN 31 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N LEUBN 36 " --> pdb=" O ALABN 32 " (cutoff:3.500A) Processing helix chain 'BN' and resid 49 through 59 Processing helix chain 'BN' and resid 63 through 68 Proline residue: BN 68 - end of helix Processing helix chain 'BN' and resid 74 through 99 Processing helix chain 'BN' and resid 101 through 107 Processing helix chain 'BN' and resid 111 through 120 Processing helix chain 'BN' and resid 122 through 142 Processing helix chain 'BN' and resid 143 through 161 removed outlier: 3.748A pdb=" N GLUBN 148 " --> pdb=" O ASPBN 144 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYRBN 152 " --> pdb=" O GLUBN 148 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 3 through 16 removed outlier: 3.876A pdb=" N GLNBQ 15 " --> pdb=" O SERBQ 11 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 21 through 48 removed outlier: 3.668A pdb=" N LYSBQ 26 " --> pdb=" O ALABQ 22 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLUBQ 35 " --> pdb=" O PHEBQ 31 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LEUBQ 36 " --> pdb=" O ALABQ 32 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 49 through 59 Processing helix chain 'BQ' and resid 63 through 68 removed outlier: 3.937A pdb=" N ARGBQ 67 " --> pdb=" O SERBQ 63 " (cutoff:3.500A) Proline residue: BQ 68 - end of helix No H-bonds generated for 'chain 'BQ' and resid 63 through 68' Processing helix chain 'BQ' and resid 74 through 99 Processing helix chain 'BQ' and resid 101 through 107 removed outlier: 3.636A pdb=" N ASPBQ 105 " --> pdb=" O ALABQ 101 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 111 through 120 Processing helix chain 'BQ' and resid 122 through 142 Processing helix chain 'BQ' and resid 143 through 161 removed outlier: 3.613A pdb=" N TYRBQ 152 " --> pdb=" O GLUBQ 148 " (cutoff:3.500A) Processing helix chain 'BT' and resid 3 through 16 Processing helix chain 'BT' and resid 21 through 48 removed outlier: 4.136A pdb=" N ASPBT 25 " --> pdb=" O GLYBT 21 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLUBT 35 " --> pdb=" O PHEBT 31 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LEUBT 36 " --> pdb=" O ALABT 32 " (cutoff:3.500A) Processing helix chain 'BT' and resid 49 through 59 Processing helix chain 'BT' and resid 63 through 68 Proline residue: BT 68 - end of helix Processing helix chain 'BT' and resid 74 through 99 Processing helix chain 'BT' and resid 101 through 107 Processing helix chain 'BT' and resid 111 through 120 Processing helix chain 'BT' and resid 122 through 142 Processing helix chain 'BT' and resid 143 through 161 removed outlier: 4.210A pdb=" N TYRBT 152 " --> pdb=" O GLUBT 148 " (cutoff:3.500A) Processing helix chain 'BW' and resid 3 through 16 removed outlier: 3.669A pdb=" N GLNBW 15 " --> pdb=" O SERBW 11 " (cutoff:3.500A) Processing helix chain 'BW' and resid 21 through 48 removed outlier: 4.122A pdb=" N GLUBW 35 " --> pdb=" O PHEBW 31 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEUBW 36 " --> pdb=" O ALABW 32 " (cutoff:3.500A) Processing helix chain 'BW' and resid 49 through 59 Processing helix chain 'BW' and resid 63 through 68 Proline residue: BW 68 - end of helix Processing helix chain 'BW' and resid 74 through 99 Processing helix chain 'BW' and resid 101 through 107 Processing helix chain 'BW' and resid 111 through 120 Processing helix chain 'BW' and resid 122 through 142 Processing helix chain 'BW' and resid 143 through 161 removed outlier: 3.842A pdb=" N TYRBW 152 " --> pdb=" O GLUBW 148 " (cutoff:3.500A) Processing helix chain 'BY' and resid 3 through 16 removed outlier: 3.690A pdb=" N GLNBY 15 " --> pdb=" O SERBY 11 " (cutoff:3.500A) Processing helix chain 'BY' and resid 21 through 48 removed outlier: 4.369A pdb=" N GLUBY 35 " --> pdb=" O PHEBY 31 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEUBY 36 " --> pdb=" O ALABY 32 " (cutoff:3.500A) Processing helix chain 'BY' and resid 49 through 59 Processing helix chain 'BY' and resid 63 through 68 Proline residue: BY 68 - end of helix Processing helix chain 'BY' and resid 74 through 99 Processing helix chain 'BY' and resid 101 through 107 Processing helix chain 'BY' and resid 111 through 120 Processing helix chain 'BY' and resid 122 through 142 Processing helix chain 'BY' and resid 143 through 161 removed outlier: 3.582A pdb=" N TYRBY 152 " --> pdb=" O GLUBY 148 " (cutoff:3.500A) Processing helix chain 'CA' and resid 3 through 16 Processing helix chain 'CA' and resid 21 through 48 removed outlier: 4.679A pdb=" N GLUCA 35 " --> pdb=" O PHECA 31 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEUCA 36 " --> pdb=" O ALACA 32 " (cutoff:3.500A) Processing helix chain 'CA' and resid 49 through 59 Processing helix chain 'CA' and resid 63 through 68 Proline residue: CA 68 - end of helix Processing helix chain 'CA' and resid 74 through 99 Processing helix chain 'CA' and resid 101 through 107 removed outlier: 3.627A pdb=" N ASPCA 105 " --> pdb=" O ALACA 101 " (cutoff:3.500A) Processing helix chain 'CA' and resid 111 through 120 Processing helix chain 'CA' and resid 122 through 142 removed outlier: 3.553A pdb=" N GLUCA 135 " --> pdb=" O GLNCA 131 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEUCA 140 " --> pdb=" O VALCA 136 " (cutoff:3.500A) Processing helix chain 'CA' and resid 143 through 161 Processing helix chain 'CD' and resid 3 through 16 removed outlier: 3.779A pdb=" N GLNCD 15 " --> pdb=" O SERCD 11 " (cutoff:3.500A) Processing helix chain 'CD' and resid 21 through 48 removed outlier: 4.550A pdb=" N GLUCD 35 " --> pdb=" O PHECD 31 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LEUCD 36 " --> pdb=" O ALACD 32 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASNCD 47 " --> pdb=" O VALCD 43 " (cutoff:3.500A) Processing helix chain 'CD' and resid 49 through 59 removed outlier: 3.844A pdb=" N ALACD 57 " --> pdb=" O LYSCD 53 " (cutoff:3.500A) Processing helix chain 'CD' and resid 63 through 68 Proline residue: CD 68 - end of helix Processing helix chain 'CD' and resid 74 through 99 Processing helix chain 'CD' and resid 101 through 107 Processing helix chain 'CD' and resid 111 through 120 removed outlier: 4.010A pdb=" N THRCD 115 " --> pdb=" O GLYCD 111 " (cutoff:3.500A) Processing helix chain 'CD' and resid 122 through 142 Processing helix chain 'CD' and resid 143 through 161 Processing helix chain 'CF' and resid 3 through 16 removed outlier: 3.633A pdb=" N GLNCF 15 " --> pdb=" O SERCF 11 " (cutoff:3.500A) Processing helix chain 'CF' and resid 21 through 48 removed outlier: 4.609A pdb=" N GLUCF 35 " --> pdb=" O PHECF 31 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LEUCF 36 " --> pdb=" O ALACF 32 " (cutoff:3.500A) Processing helix chain 'CF' and resid 49 through 59 Processing helix chain 'CF' and resid 63 through 68 Proline residue: CF 68 - end of helix Processing helix chain 'CF' and resid 74 through 99 Processing helix chain 'CF' and resid 101 through 107 Processing helix chain 'CF' and resid 111 through 120 removed outlier: 3.502A pdb=" N THRCF 115 " --> pdb=" O GLYCF 111 " (cutoff:3.500A) Processing helix chain 'CF' and resid 122 through 142 Processing helix chain 'CF' and resid 143 through 161 removed outlier: 3.885A pdb=" N TYRCF 152 " --> pdb=" O GLUCF 148 " (cutoff:3.500A) Processing helix chain 'CH' and resid 3 through 16 removed outlier: 3.883A pdb=" N GLNCH 15 " --> pdb=" O SERCH 11 " (cutoff:3.500A) Processing helix chain 'CH' and resid 21 through 48 removed outlier: 4.251A pdb=" N GLUCH 35 " --> pdb=" O PHECH 31 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LEUCH 36 " --> pdb=" O ALACH 32 " (cutoff:3.500A) Processing helix chain 'CH' and resid 49 through 59 Processing helix chain 'CH' and resid 63 through 68 Proline residue: CH 68 - end of helix Processing helix chain 'CH' and resid 74 through 99 Processing helix chain 'CH' and resid 101 through 107 Processing helix chain 'CH' and resid 111 through 120 Processing helix chain 'CH' and resid 122 through 142 Processing helix chain 'CH' and resid 143 through 161 removed outlier: 4.113A pdb=" N GLUCH 148 " --> pdb=" O ASPCH 144 " (cutoff:3.500A) Processing helix chain 'CS' and resid 3 through 16 removed outlier: 3.921A pdb=" N GLNCS 15 " --> pdb=" O SERCS 11 " (cutoff:3.500A) Processing helix chain 'CS' and resid 21 through 48 removed outlier: 4.123A pdb=" N GLUCS 35 " --> pdb=" O PHECS 31 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEUCS 36 " --> pdb=" O ALACS 32 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARGCS 39 " --> pdb=" O GLUCS 35 " (cutoff:3.500A) Processing helix chain 'CS' and resid 49 through 59 Processing helix chain 'CS' and resid 63 through 68 Proline residue: CS 68 - end of helix Processing helix chain 'CS' and resid 74 through 99 Processing helix chain 'CS' and resid 101 through 107 Processing helix chain 'CS' and resid 111 through 120 Processing helix chain 'CS' and resid 122 through 142 Processing helix chain 'CS' and resid 143 through 161 Processing helix chain 'CU' and resid 3 through 16 removed outlier: 3.941A pdb=" N GLNCU 15 " --> pdb=" O SERCU 11 " (cutoff:3.500A) Processing helix chain 'CU' and resid 21 through 48 removed outlier: 4.137A pdb=" N GLUCU 35 " --> pdb=" O PHECU 31 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEUCU 36 " --> pdb=" O ALACU 32 " (cutoff:3.500A) Processing helix chain 'CU' and resid 49 through 59 Processing helix chain 'CU' and resid 63 through 68 Proline residue: CU 68 - end of helix Processing helix chain 'CU' and resid 74 through 99 Processing helix chain 'CU' and resid 101 through 107 removed outlier: 4.090A pdb=" N ASPCU 105 " --> pdb=" O ALACU 101 " (cutoff:3.500A) Processing helix chain 'CU' and resid 111 through 120 Processing helix chain 'CU' and resid 122 through 142 Processing helix chain 'CU' and resid 143 through 161 removed outlier: 3.691A pdb=" N TYRCU 152 " --> pdb=" O GLUCU 148 " (cutoff:3.500A) Processing helix chain 'CW' and resid 3 through 16 removed outlier: 4.315A pdb=" N GLNCW 15 " --> pdb=" O SERCW 11 " (cutoff:3.500A) Processing helix chain 'CW' and resid 21 through 48 removed outlier: 4.463A pdb=" N GLUCW 35 " --> pdb=" O PHECW 31 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEUCW 36 " --> pdb=" O ALACW 32 " (cutoff:3.500A) Processing helix chain 'CW' and resid 49 through 59 Processing helix chain 'CW' and resid 63 through 68 removed outlier: 3.540A pdb=" N ARGCW 67 " --> pdb=" O SERCW 63 " (cutoff:3.500A) Proline residue: CW 68 - end of helix No H-bonds generated for 'chain 'CW' and resid 63 through 68' Processing helix chain 'CW' and resid 74 through 99 Processing helix chain 'CW' and resid 101 through 107 Processing helix chain 'CW' and resid 111 through 120 removed outlier: 3.906A pdb=" N THRCW 115 " --> pdb=" O GLYCW 111 " (cutoff:3.500A) Processing helix chain 'CW' and resid 122 through 142 removed outlier: 3.629A pdb=" N GLNCW 128 " --> pdb=" O SERCW 124 " (cutoff:3.500A) Processing helix chain 'CW' and resid 143 through 161 removed outlier: 3.957A pdb=" N GLUCW 148 " --> pdb=" O ASPCW 144 " (cutoff:3.500A) Processing helix chain 'CZ' and resid 3 through 16 removed outlier: 3.870A pdb=" N GLNCZ 15 " --> pdb=" O SERCZ 11 " (cutoff:3.500A) Processing helix chain 'CZ' and resid 21 through 48 removed outlier: 4.557A pdb=" N GLUCZ 35 " --> pdb=" O PHECZ 31 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LEUCZ 36 " --> pdb=" O ALACZ 32 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARGCZ 37 " --> pdb=" O SERCZ 33 " (cutoff:3.500A) Processing helix chain 'CZ' and resid 49 through 59 Processing helix chain 'CZ' and resid 63 through 68 Proline residue: CZ 68 - end of helix Processing helix chain 'CZ' and resid 74 through 99 Processing helix chain 'CZ' and resid 101 through 107 Processing helix chain 'CZ' and resid 111 through 120 Processing helix chain 'CZ' and resid 122 through 142 Processing helix chain 'CZ' and resid 143 through 161 Processing helix chain 'DB' and resid 3 through 16 removed outlier: 3.722A pdb=" N VALDB 8 " --> pdb=" O ALADB 4 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLNDB 15 " --> pdb=" O SERDB 11 " (cutoff:3.500A) Processing helix chain 'DB' and resid 21 through 48 removed outlier: 4.202A pdb=" N GLUDB 35 " --> pdb=" O PHEDB 31 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEUDB 36 " --> pdb=" O ALADB 32 " (cutoff:3.500A) Processing helix chain 'DB' and resid 49 through 59 Processing helix chain 'DB' and resid 63 through 68 Proline residue: DB 68 - end of helix Processing helix chain 'DB' and resid 74 through 99 removed outlier: 3.697A pdb=" N TYRDB 78 " --> pdb=" O THRDB 74 " (cutoff:3.500A) Processing helix chain 'DB' and resid 101 through 107 removed outlier: 3.902A pdb=" N ASPDB 105 " --> pdb=" O ALADB 101 " (cutoff:3.500A) Processing helix chain 'DB' and resid 111 through 120 Processing helix chain 'DB' and resid 122 through 142 Processing helix chain 'DB' and resid 143 through 161 Processing helix chain 'DD' and resid 3 through 16 Processing helix chain 'DD' and resid 21 through 48 removed outlier: 4.348A pdb=" N GLUDD 35 " --> pdb=" O PHEDD 31 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEUDD 36 " --> pdb=" O ALADD 32 " (cutoff:3.500A) Processing helix chain 'DD' and resid 49 through 59 Processing helix chain 'DD' and resid 63 through 68 Proline residue: DD 68 - end of helix Processing helix chain 'DD' and resid 74 through 99 Processing helix chain 'DD' and resid 101 through 107 Processing helix chain 'DD' and resid 111 through 120 Processing helix chain 'DD' and resid 122 through 142 Processing helix chain 'DD' and resid 143 through 161 removed outlier: 3.722A pdb=" N TYRDD 152 " --> pdb=" O GLUDD 148 " (cutoff:3.500A) Processing helix chain 'DK' and resid 3 through 16 removed outlier: 3.936A pdb=" N VALDK 8 " --> pdb=" O ALADK 4 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLNDK 15 " --> pdb=" O SERDK 11 " (cutoff:3.500A) Processing helix chain 'DK' and resid 21 through 48 removed outlier: 4.437A pdb=" N GLUDK 35 " --> pdb=" O PHEDK 31 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEUDK 36 " --> pdb=" O ALADK 32 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASNDK 47 " --> pdb=" O VALDK 43 " (cutoff:3.500A) Processing helix chain 'DK' and resid 49 through 59 Processing helix chain 'DK' and resid 63 through 68 Proline residue: DK 68 - end of helix Processing helix chain 'DK' and resid 74 through 99 Processing helix chain 'DK' and resid 101 through 107 Processing helix chain 'DK' and resid 111 through 120 Processing helix chain 'DK' and resid 122 through 142 Processing helix chain 'DK' and resid 143 through 161 removed outlier: 3.683A pdb=" N TYRDK 152 " --> pdb=" O GLUDK 148 " (cutoff:3.500A) Processing helix chain 'DM' and resid 3 through 16 removed outlier: 4.413A pdb=" N GLNDM 15 " --> pdb=" O SERDM 11 " (cutoff:3.500A) Processing helix chain 'DM' and resid 21 through 48 removed outlier: 4.081A pdb=" N GLUDM 35 " --> pdb=" O PHEDM 31 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEUDM 36 " --> pdb=" O ALADM 32 " (cutoff:3.500A) Processing helix chain 'DM' and resid 49 through 59 Processing helix chain 'DM' and resid 63 through 68 Proline residue: DM 68 - end of helix Processing helix chain 'DM' and resid 74 through 99 Processing helix chain 'DM' and resid 101 through 107 removed outlier: 4.297A pdb=" N ASPDM 105 " --> pdb=" O ALADM 101 " (cutoff:3.500A) Processing helix chain 'DM' and resid 111 through 120 Processing helix chain 'DM' and resid 122 through 142 Processing helix chain 'DM' and resid 143 through 161 removed outlier: 3.560A pdb=" N TYRDM 152 " --> pdb=" O GLUDM 148 " (cutoff:3.500A) Processing helix chain 'DO' and resid 3 through 16 removed outlier: 3.946A pdb=" N GLNDO 15 " --> pdb=" O SERDO 11 " (cutoff:3.500A) Processing helix chain 'DO' and resid 21 through 48 removed outlier: 4.372A pdb=" N GLUDO 35 " --> pdb=" O PHEDO 31 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEUDO 36 " --> pdb=" O ALADO 32 " (cutoff:3.500A) Processing helix chain 'DO' and resid 49 through 59 Processing helix chain 'DO' and resid 63 through 68 Proline residue: DO 68 - end of helix Processing helix chain 'DO' and resid 74 through 99 Processing helix chain 'DO' and resid 101 through 107 Processing helix chain 'DO' and resid 111 through 120 Processing helix chain 'DO' and resid 122 through 142 Processing helix chain 'DO' and resid 143 through 161 removed outlier: 3.815A pdb=" N GLUDO 148 " --> pdb=" O ASPDO 144 " (cutoff:3.500A) Processing helix chain 'DR' and resid 3 through 16 removed outlier: 3.777A pdb=" N GLNDR 15 " --> pdb=" O SERDR 11 " (cutoff:3.500A) Processing helix chain 'DR' and resid 21 through 48 removed outlier: 4.479A pdb=" N LYSDR 26 " --> pdb=" O ALADR 22 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLUDR 35 " --> pdb=" O PHEDR 31 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEUDR 36 " --> pdb=" O ALADR 32 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARGDR 37 " --> pdb=" O SERDR 33 " (cutoff:3.500A) Processing helix chain 'DR' and resid 49 through 59 Processing helix chain 'DR' and resid 63 through 68 Proline residue: DR 68 - end of helix Processing helix chain 'DR' and resid 74 through 99 Processing helix chain 'DR' and resid 101 through 107 removed outlier: 3.659A pdb=" N ASPDR 105 " --> pdb=" O ALADR 101 " (cutoff:3.500A) Processing helix chain 'DR' and resid 111 through 120 Processing helix chain 'DR' and resid 122 through 142 Processing helix chain 'DR' and resid 143 through 161 Processing helix chain 'DT' and resid 3 through 16 removed outlier: 4.224A pdb=" N GLNDT 15 " --> pdb=" O SERDT 11 " (cutoff:3.500A) Processing helix chain 'DT' and resid 21 through 48 removed outlier: 4.201A pdb=" N GLUDT 35 " --> pdb=" O PHEDT 31 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEUDT 36 " --> pdb=" O ALADT 32 " (cutoff:3.500A) Processing helix chain 'DT' and resid 49 through 59 Processing helix chain 'DT' and resid 63 through 68 Proline residue: DT 68 - end of helix Processing helix chain 'DT' and resid 74 through 99 removed outlier: 3.654A pdb=" N TYRDT 78 " --> pdb=" O THRDT 74 " (cutoff:3.500A) Processing helix chain 'DT' and resid 101 through 107 removed outlier: 4.079A pdb=" N ASPDT 105 " --> pdb=" O ALADT 101 " (cutoff:3.500A) Processing helix chain 'DT' and resid 111 through 120 Processing helix chain 'DT' and resid 122 through 142 Processing helix chain 'DT' and resid 143 through 161 removed outlier: 3.805A pdb=" N GLUDT 148 " --> pdb=" O ASPDT 144 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N METDT 149 " --> pdb=" O ALADT 145 " (cutoff:3.500A) Processing helix chain 'DV' and resid 3 through 16 Processing helix chain 'DV' and resid 21 through 48 removed outlier: 4.302A pdb=" N GLUDV 35 " --> pdb=" O PHEDV 31 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEUDV 36 " --> pdb=" O ALADV 32 " (cutoff:3.500A) Processing helix chain 'DV' and resid 49 through 59 removed outlier: 4.452A pdb=" N LYSDV 53 " --> pdb=" O ALADV 49 " (cutoff:3.500A) Processing helix chain 'DV' and resid 63 through 68 removed outlier: 3.721A pdb=" N ARGDV 67 " --> pdb=" O SERDV 63 " (cutoff:3.500A) Proline residue: DV 68 - end of helix No H-bonds generated for 'chain 'DV' and resid 63 through 68' Processing helix chain 'DV' and resid 74 through 99 Processing helix chain 'DV' and resid 101 through 107 Processing helix chain 'DV' and resid 111 through 120 Processing helix chain 'DV' and resid 122 through 142 Processing helix chain 'DV' and resid 143 through 161 Processing helix chain 'AE' and resid 2 through 15 Processing helix chain 'AE' and resid 19 through 47 removed outlier: 4.861A pdb=" N ALAAE 34 " --> pdb=" O LEUAE 30 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLNAE 35 " --> pdb=" O THRAE 31 " (cutoff:3.500A) Processing helix chain 'AE' and resid 48 through 63 Proline residue: AE 63 - end of helix Processing helix chain 'AE' and resid 74 through 99 Processing helix chain 'AE' and resid 101 through 108 Processing helix chain 'AE' and resid 111 through 120 removed outlier: 3.821A pdb=" N LEUAE 119 " --> pdb=" O METAE 115 " (cutoff:3.500A) Processing helix chain 'AE' and resid 122 through 142 removed outlier: 4.879A pdb=" N SERAE 142 " --> pdb=" O LEUAE 138 " (cutoff:3.500A) Processing helix chain 'AE' and resid 143 through 161 Proline residue: AE 151 - end of helix Processing helix chain 'BM' and resid 2 through 15 Processing helix chain 'BM' and resid 19 through 47 removed outlier: 4.881A pdb=" N ALABM 34 " --> pdb=" O LEUBM 30 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLNBM 35 " --> pdb=" O THRBM 31 " (cutoff:3.500A) Processing helix chain 'BM' and resid 48 through 63 Proline residue: BM 63 - end of helix Processing helix chain 'BM' and resid 74 through 99 Processing helix chain 'BM' and resid 101 through 108 Processing helix chain 'BM' and resid 111 through 120 removed outlier: 3.750A pdb=" N LEUBM 119 " --> pdb=" O METBM 115 " (cutoff:3.500A) Processing helix chain 'BM' and resid 122 through 142 removed outlier: 4.895A pdb=" N SERBM 142 " --> pdb=" O LEUBM 138 " (cutoff:3.500A) Processing helix chain 'BM' and resid 143 through 161 Proline residue: BM 151 - end of helix Processing helix chain 'AK' and resid 3 through 16 removed outlier: 3.655A pdb=" N THRAK 15 " --> pdb=" O ASNAK 11 " (cutoff:3.500A) Processing helix chain 'AK' and resid 20 through 48 removed outlier: 4.540A pdb=" N SERAK 35 " --> pdb=" O PHEAK 31 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALAAK 36 " --> pdb=" O GLUAK 32 " (cutoff:3.500A) Processing helix chain 'AK' and resid 49 through 64 removed outlier: 4.333A pdb=" N GLUAK 61 " --> pdb=" O ALAAK 57 " (cutoff:3.500A) Proline residue: AK 64 - end of helix Processing helix chain 'AK' and resid 75 through 100 Processing helix chain 'AK' and resid 101 through 109 removed outlier: 4.658A pdb=" N LEUAK 105 " --> pdb=" O ASPAK 101 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARGAK 108 " --> pdb=" O VALAK 104 " (cutoff:3.500A) Processing helix chain 'AK' and resid 112 through 121 Processing helix chain 'AK' and resid 123 through 146 removed outlier: 4.419A pdb=" N THRAK 127 " --> pdb=" O PROAK 123 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VALAK 128 " --> pdb=" O ILEAK 124 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SERAK 146 " --> pdb=" O ALAAK 142 " (cutoff:3.500A) Processing helix chain 'AK' and resid 150 through 165 removed outlier: 4.581A pdb=" N ALAAK 154 " --> pdb=" O THRAK 150 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SERAK 155 " --> pdb=" O ASPAK 151 " (cutoff:3.500A) Proline residue: AK 156 - end of helix Processing helix chain 'BS' and resid 3 through 16 removed outlier: 3.747A pdb=" N THRBS 15 " --> pdb=" O ASNBS 11 " (cutoff:3.500A) Processing helix chain 'BS' and resid 20 through 48 removed outlier: 4.613A pdb=" N SERBS 35 " --> pdb=" O PHEBS 31 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ALABS 36 " --> pdb=" O GLUBS 32 " (cutoff:3.500A) Processing helix chain 'BS' and resid 49 through 64 removed outlier: 5.006A pdb=" N GLUBS 61 " --> pdb=" O ALABS 57 " (cutoff:3.500A) Proline residue: BS 64 - end of helix Processing helix chain 'BS' and resid 75 through 100 Processing helix chain 'BS' and resid 101 through 109 removed outlier: 4.868A pdb=" N LEUBS 105 " --> pdb=" O ASPBS 101 " (cutoff:3.500A) Processing helix chain 'BS' and resid 112 through 121 Processing helix chain 'BS' and resid 123 through 146 removed outlier: 4.179A pdb=" N THRBS 127 " --> pdb=" O PROBS 123 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VALBS 128 " --> pdb=" O ILEBS 124 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SERBS 146 " --> pdb=" O ALABS 142 " (cutoff:3.500A) Processing helix chain 'BS' and resid 150 through 165 removed outlier: 4.432A pdb=" N ALABS 154 " --> pdb=" O THRBS 150 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SERBS 155 " --> pdb=" O ASPBS 151 " (cutoff:3.500A) Proline residue: BS 156 - end of helix Processing helix chain 'BA' and resid 14 through 19 Processing helix chain 'BA' and resid 32 through 47 removed outlier: 4.249A pdb=" N PHEBA 37 " --> pdb=" O TYRBA 33 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ARGBA 38 " --> pdb=" O ASPBA 34 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 14 through 19 Processing helix chain 'CJ' and resid 32 through 47 removed outlier: 4.160A pdb=" N PHECJ 37 " --> pdb=" O TYRCJ 33 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ARGCJ 38 " --> pdb=" O ASPCJ 34 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLYCJ 47 " --> pdb=" O ILECJ 43 " (cutoff:3.500A) Processing helix chain 'BB' and resid 21 through 26 Processing helix chain 'BB' and resid 32 through 47 removed outlier: 4.452A pdb=" N PHEBB 37 " --> pdb=" O TYRBB 33 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ARGBB 38 " --> pdb=" O ASPBB 34 " (cutoff:3.500A) Processing helix chain 'CK' and resid 21 through 26 Processing helix chain 'CK' and resid 32 through 47 removed outlier: 4.429A pdb=" N PHECK 37 " --> pdb=" O TYRCK 33 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ARGCK 38 " --> pdb=" O ASPCK 34 " (cutoff:3.500A) Processing helix chain 'DF' and resid 21 through 26 Processing helix chain 'DF' and resid 32 through 47 removed outlier: 4.314A pdb=" N PHEDF 37 " --> pdb=" O TYRDF 33 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ARGDF 38 " --> pdb=" O ASPDF 34 " (cutoff:3.500A) Processing helix chain 'DX' and resid 21 through 26 Processing helix chain 'DX' and resid 32 through 47 removed outlier: 4.211A pdb=" N PHEDX 37 " --> pdb=" O TYRDX 33 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ARGDX 38 " --> pdb=" O ASPDX 34 " (cutoff:3.500A) Processing helix chain 'BD' and resid 19 through 32 Processing helix chain 'BD' and resid 36 through 61 removed outlier: 4.079A pdb=" N ALABD 51 " --> pdb=" O PHEBD 47 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEUBD 52 " --> pdb=" O GLNBD 48 " (cutoff:3.500A) Processing helix chain 'BD' and resid 63 through 76 Processing helix chain 'BD' and resid 80 through 85 removed outlier: 5.069A pdb=" N TYRBD 84 " --> pdb=" O SERBD 80 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEUBD 85 " --> pdb=" O PROBD 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'BD' and resid 80 through 85' Processing helix chain 'BD' and resid 140 through 145 Processing helix chain 'BD' and resid 146 through 170 removed outlier: 3.540A pdb=" N SERBD 157 " --> pdb=" O LEUBD 153 " (cutoff:3.500A) Processing helix chain 'BD' and resid 172 through 188 removed outlier: 5.086A pdb=" N GLYBD 181 " --> pdb=" O VALBD 177 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEUBD 182 " --> pdb=" O ASNBD 178 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYSBD 183 " --> pdb=" O THRBD 179 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLUBD 184 " --> pdb=" O ARGBD 180 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VALBD 185 " --> pdb=" O GLYBD 181 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASNBD 188 " --> pdb=" O GLUBD 184 " (cutoff:3.500A) Processing helix chain 'BD' and resid 191 through 211 Processing helix chain 'BD' and resid 213 through 234 removed outlier: 5.386A pdb=" N ILEBD 219 " --> pdb=" O GLNBD 215 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VALBD 220 " --> pdb=" O ALABD 216 " (cutoff:3.500A) Proline residue: BD 234 - end of helix Processing helix chain 'BD' and resid 254 through 262 removed outlier: 3.598A pdb=" N PHEBD 258 " --> pdb=" O PROBD 254 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ASNBD 259 " --> pdb=" O GLNBD 255 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALABD 260 " --> pdb=" O SERBD 256 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALABD 261 " --> pdb=" O TYRBD 257 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ALABD 262 " --> pdb=" O PHEBD 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'BD' and resid 254 through 262' Processing helix chain 'BD' and resid 274 through 291 Processing helix chain 'BD' and resid 293 through 298 Processing helix chain 'BD' and resid 302 through 312 removed outlier: 3.692A pdb=" N GLNBD 308 " --> pdb=" O TYRBD 304 " (cutoff:3.500A) Processing helix chain 'BD' and resid 315 through 326 Processing helix chain 'BD' and resid 327 through 333 removed outlier: 3.689A pdb=" N GLNBD 332 " --> pdb=" O LEUBD 328 " (cutoff:3.500A) Processing helix chain 'BD' and resid 338 through 350 removed outlier: 3.625A pdb=" N ARGBD 348 " --> pdb=" O GLUBD 344 " (cutoff:3.500A) Processing helix chain 'BD' and resid 357 through 371 Processing helix chain 'BD' and resid 372 through 383 removed outlier: 4.056A pdb=" N SERBD 383 " --> pdb=" O ALABD 379 " (cutoff:3.500A) Processing helix chain 'BD' and resid 384 through 390 Processing helix chain 'BD' and resid 410 through 420 removed outlier: 3.818A pdb=" N SERBD 419 " --> pdb=" O GLNBD 415 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N TYRBD 420 " --> pdb=" O ASPBD 416 " (cutoff:3.500A) Processing helix chain 'BD' and resid 421 through 426 removed outlier: 3.735A pdb=" N ARGBD 425 " --> pdb=" O SERBD 421 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LYSBD 426 " --> pdb=" O ALABD 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'BD' and resid 421 through 426' Processing helix chain 'BD' and resid 428 through 440 removed outlier: 3.814A pdb=" N THRBD 432 " --> pdb=" O PROBD 428 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THRBD 433 " --> pdb=" O GLNBD 429 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASPBD 438 " --> pdb=" O PHEBD 434 " (cutoff:3.500A) Proline residue: BD 440 - end of helix Processing helix chain 'BD' and resid 464 through 469 removed outlier: 5.008A pdb=" N ASNBD 468 " --> pdb=" O LYSBD 464 " (cutoff:3.500A) Proline residue: BD 469 - end of helix No H-bonds generated for 'chain 'BD' and resid 464 through 469' Processing helix chain 'BD' and resid 535 through 552 removed outlier: 5.625A pdb=" N THRBD 539 " --> pdb=" O GLYBD 535 " (cutoff:3.500A) Processing helix chain 'BD' and resid 561 through 571 Processing helix chain 'BD' and resid 574 through 585 Processing helix chain 'BD' and resid 586 through 592 Processing helix chain 'BD' and resid 597 through 610 Processing helix chain 'BD' and resid 616 through 630 Processing helix chain 'BD' and resid 631 through 642 Processing helix chain 'BD' and resid 643 through 649 Processing helix chain 'BD' and resid 661 through 670 Processing helix chain 'BD' and resid 689 through 696 Processing helix chain 'BD' and resid 702 through 712 removed outlier: 3.733A pdb=" N ASNBD 711 " --> pdb=" O ALABD 707 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLNBD 712 " --> pdb=" O TYRBD 708 " (cutoff:3.500A) Processing helix chain 'BD' and resid 716 through 721 removed outlier: 4.195A pdb=" N THRBD 721 " --> pdb=" O GLNBD 717 " (cutoff:3.500A) Processing helix chain 'BD' and resid 731 through 748 Processing helix chain 'BD' and resid 760 through 770 Processing helix chain 'BD' and resid 773 through 784 removed outlier: 3.752A pdb=" N SERBD 784 " --> pdb=" O GLYBD 780 " (cutoff:3.500A) Processing helix chain 'BD' and resid 785 through 791 Processing helix chain 'BD' and resid 796 through 809 Processing helix chain 'BD' and resid 815 through 829 Processing helix chain 'BD' and resid 830 through 841 removed outlier: 3.753A pdb=" N PHEBD 834 " --> pdb=" O GLYBD 830 " (cutoff:3.500A) Processing helix chain 'BD' and resid 842 through 848 Processing helix chain 'BD' and resid 864 through 875 removed outlier: 4.142A pdb=" N LYSBD 875 " --> pdb=" O ARGBD 871 " (cutoff:3.500A) Processing helix chain 'BD' and resid 493 through 498 Proline residue: BD 498 - end of helix No H-bonds generated for 'chain 'BD' and resid 493 through 498' Processing helix chain 'CM' and resid 19 through 32 Processing helix chain 'CM' and resid 36 through 61 removed outlier: 4.215A pdb=" N ALACM 51 " --> pdb=" O PHECM 47 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEUCM 52 " --> pdb=" O GLNCM 48 " (cutoff:3.500A) Processing helix chain 'CM' and resid 63 through 76 removed outlier: 3.533A pdb=" N ARGCM 74 " --> pdb=" O ARGCM 70 " (cutoff:3.500A) Processing helix chain 'CM' and resid 80 through 85 removed outlier: 5.152A pdb=" N TYRCM 84 " --> pdb=" O SERCM 80 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEUCM 85 " --> pdb=" O PROCM 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'CM' and resid 80 through 85' Processing helix chain 'CM' and resid 140 through 145 Processing helix chain 'CM' and resid 146 through 170 Processing helix chain 'CM' and resid 172 through 188 removed outlier: 5.349A pdb=" N GLYCM 181 " --> pdb=" O VALCM 177 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N LEUCM 182 " --> pdb=" O ASNCM 178 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYSCM 183 " --> pdb=" O THRCM 179 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLUCM 184 " --> pdb=" O ARGCM 180 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VALCM 185 " --> pdb=" O GLYCM 181 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASNCM 188 " --> pdb=" O GLUCM 184 " (cutoff:3.500A) Processing helix chain 'CM' and resid 191 through 211 Processing helix chain 'CM' and resid 213 through 234 removed outlier: 5.292A pdb=" N ILECM 219 " --> pdb=" O GLNCM 215 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VALCM 220 " --> pdb=" O ALACM 216 " (cutoff:3.500A) Proline residue: CM 234 - end of helix Processing helix chain 'CM' and resid 254 through 262 removed outlier: 3.640A pdb=" N PHECM 258 " --> pdb=" O PROCM 254 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ASNCM 259 " --> pdb=" O GLNCM 255 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALACM 260 " --> pdb=" O SERCM 256 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALACM 261 " --> pdb=" O TYRCM 257 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ALACM 262 " --> pdb=" O PHECM 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'CM' and resid 254 through 262' Processing helix chain 'CM' and resid 274 through 291 Processing helix chain 'CM' and resid 293 through 298 Processing helix chain 'CM' and resid 302 through 312 removed outlier: 3.746A pdb=" N GLNCM 308 " --> pdb=" O TYRCM 304 " (cutoff:3.500A) Processing helix chain 'CM' and resid 315 through 326 removed outlier: 3.516A pdb=" N LYSCM 325 " --> pdb=" O ARGCM 321 " (cutoff:3.500A) Processing helix chain 'CM' and resid 327 through 333 removed outlier: 3.712A pdb=" N GLNCM 332 " --> pdb=" O LEUCM 328 " (cutoff:3.500A) Processing helix chain 'CM' and resid 338 through 350 Processing helix chain 'CM' and resid 357 through 371 Processing helix chain 'CM' and resid 372 through 383 removed outlier: 3.917A pdb=" N SERCM 383 " --> pdb=" O ALACM 379 " (cutoff:3.500A) Processing helix chain 'CM' and resid 384 through 390 Processing helix chain 'CM' and resid 410 through 420 removed outlier: 3.687A pdb=" N SERCM 419 " --> pdb=" O GLNCM 415 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N TYRCM 420 " --> pdb=" O ASPCM 416 " (cutoff:3.500A) Processing helix chain 'CM' and resid 421 through 426 removed outlier: 3.839A pdb=" N ARGCM 425 " --> pdb=" O SERCM 421 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LYSCM 426 " --> pdb=" O ALACM 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'CM' and resid 421 through 426' Processing helix chain 'CM' and resid 428 through 440 removed outlier: 3.908A pdb=" N THRCM 432 " --> pdb=" O PROCM 428 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THRCM 433 " --> pdb=" O GLNCM 429 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASPCM 438 " --> pdb=" O PHECM 434 " (cutoff:3.500A) Proline residue: CM 440 - end of helix Processing helix chain 'CM' and resid 464 through 469 removed outlier: 5.003A pdb=" N ASNCM 468 " --> pdb=" O LYSCM 464 " (cutoff:3.500A) Proline residue: CM 469 - end of helix No H-bonds generated for 'chain 'CM' and resid 464 through 469' Processing helix chain 'CM' and resid 535 through 552 removed outlier: 5.667A pdb=" N THRCM 539 " --> pdb=" O GLYCM 535 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLYCM 552 " --> pdb=" O ARGCM 548 " (cutoff:3.500A) Processing helix chain 'CM' and resid 561 through 571 Processing helix chain 'CM' and resid 574 through 585 Processing helix chain 'CM' and resid 586 through 592 Processing helix chain 'CM' and resid 597 through 610 Processing helix chain 'CM' and resid 616 through 630 Processing helix chain 'CM' and resid 631 through 642 Processing helix chain 'CM' and resid 643 through 649 Processing helix chain 'CM' and resid 661 through 670 Processing helix chain 'CM' and resid 689 through 696 Processing helix chain 'CM' and resid 702 through 712 removed outlier: 4.088A pdb=" N ASNCM 711 " --> pdb=" O ALACM 707 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLNCM 712 " --> pdb=" O TYRCM 708 " (cutoff:3.500A) Processing helix chain 'CM' and resid 716 through 721 removed outlier: 3.870A pdb=" N THRCM 721 " --> pdb=" O GLNCM 717 " (cutoff:3.500A) Processing helix chain 'CM' and resid 731 through 748 Processing helix chain 'CM' and resid 760 through 770 Processing helix chain 'CM' and resid 773 through 784 Processing helix chain 'CM' and resid 785 through 791 Processing helix chain 'CM' and resid 796 through 809 Processing helix chain 'CM' and resid 815 through 829 Processing helix chain 'CM' and resid 830 through 841 removed outlier: 4.310A pdb=" N PHECM 834 " --> pdb=" O GLYCM 830 " (cutoff:3.500A) Processing helix chain 'CM' and resid 842 through 848 Processing helix chain 'CM' and resid 864 through 875 removed outlier: 4.027A pdb=" N LYSCM 875 " --> pdb=" O ARGCM 871 " (cutoff:3.500A) Processing helix chain 'CM' and resid 493 through 498 Proline residue: CM 498 - end of helix No H-bonds generated for 'chain 'CM' and resid 493 through 498' Processing helix chain 'BF' and resid 104 through 118 removed outlier: 4.089A pdb=" N ASNBF 108 " --> pdb=" O GLYBF 104 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ARGBF 109 " --> pdb=" O PROBF 105 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N PHEBF 110 " --> pdb=" O SERBF 106 " (cutoff:3.500A) Processing helix chain 'CO' and resid 104 through 118 removed outlier: 3.939A pdb=" N ASNCO 108 " --> pdb=" O GLYCO 104 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ARGCO 109 " --> pdb=" O PROCO 105 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N PHECO 110 " --> pdb=" O SERCO 106 " (cutoff:3.500A) Processing helix chain 'BG' and resid 195 through 203 removed outlier: 4.206A pdb=" N GLUBG 199 " --> pdb=" O VALBG 195 " (cutoff:3.500A) Processing helix chain 'BG' and resid 216 through 226 removed outlier: 4.106A pdb=" N GLYBG 220 " --> pdb=" O METBG 216 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N METBG 221 " --> pdb=" O ASNBG 217 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASNBG 226 " --> pdb=" O ALABG 222 " (cutoff:3.500A) Processing helix chain 'BG' and resid 236 through 241 removed outlier: 4.065A pdb=" N ILEBG 240 " --> pdb=" O SERBG 236 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ASNBG 241 " --> pdb=" O ALABG 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'BG' and resid 236 through 241' Processing helix chain 'CP' and resid 195 through 203 removed outlier: 4.178A pdb=" N GLUCP 199 " --> pdb=" O VALCP 195 " (cutoff:3.500A) Processing helix chain 'CP' and resid 216 through 226 removed outlier: 4.183A pdb=" N GLYCP 220 " --> pdb=" O METCP 216 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N METCP 221 " --> pdb=" O ASNCP 217 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASNCP 226 " --> pdb=" O ALACP 222 " (cutoff:3.500A) Processing helix chain 'CP' and resid 236 through 241 removed outlier: 3.989A pdb=" N ILECP 240 " --> pdb=" O SERCP 236 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ASNCP 241 " --> pdb=" O ALACP 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'CP' and resid 236 through 241' Processing helix chain 'BH' and resid 19 through 32 removed outlier: 4.989A pdb=" N ALABH 23 " --> pdb=" O ASPBH 19 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASNBH 32 " --> pdb=" O PHEBH 28 " (cutoff:3.500A) Processing helix chain 'BH' and resid 33 through 47 Processing helix chain 'BH' and resid 55 through 60 removed outlier: 4.534A pdb=" N ALABH 59 " --> pdb=" O ALABH 55 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SERBH 60 " --> pdb=" O PROBH 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'BH' and resid 55 through 60' Processing helix chain 'BH' and resid 61 through 75 removed outlier: 4.318A pdb=" N ASNBH 66 " --> pdb=" O GLNBH 62 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ALABH 67 " --> pdb=" O LEUBH 63 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLYBH 75 " --> pdb=" O ILEBH 71 " (cutoff:3.500A) Processing helix chain 'BH' and resid 76 through 89 Processing helix chain 'BH' and resid 92 through 102 removed outlier: 3.775A pdb=" N TRPBH 101 " --> pdb=" O THRBH 97 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N SERBH 102 " --> pdb=" O TYRBH 98 " (cutoff:3.500A) Processing helix chain 'BH' and resid 103 through 120 Processing helix chain 'BH' and resid 132 through 146 removed outlier: 4.986A pdb=" N GLUBH 146 " --> pdb=" O ILEBH 142 " (cutoff:3.500A) Processing helix chain 'BH' and resid 147 through 160 removed outlier: 4.253A pdb=" N ASPBH 160 " --> pdb=" O ASNBH 156 " (cutoff:3.500A) Processing helix chain 'BH' and resid 195 through 208 Processing helix chain 'BH' and resid 209 through 218 removed outlier: 4.598A pdb=" N GLUBH 215 " --> pdb=" O ASPBH 211 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEUBH 216 " --> pdb=" O THRBH 212 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N PHEBH 217 " --> pdb=" O LEUBH 213 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N THRBH 218 " --> pdb=" O ILEBH 214 " (cutoff:3.500A) Processing helix chain 'BH' and resid 233 through 244 Processing helix chain 'CQ' and resid 19 through 32 removed outlier: 4.917A pdb=" N ALACQ 23 " --> pdb=" O ASPCQ 19 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ASNCQ 32 " --> pdb=" O PHECQ 28 " (cutoff:3.500A) Processing helix chain 'CQ' and resid 33 through 47 Processing helix chain 'CQ' and resid 55 through 60 removed outlier: 4.351A pdb=" N ALACQ 59 " --> pdb=" O ALACQ 55 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N SERCQ 60 " --> pdb=" O PROCQ 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'CQ' and resid 55 through 60' Processing helix chain 'CQ' and resid 61 through 75 removed outlier: 4.266A pdb=" N ASNCQ 66 " --> pdb=" O GLNCQ 62 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ALACQ 67 " --> pdb=" O LEUCQ 63 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLYCQ 75 " --> pdb=" O ILECQ 71 " (cutoff:3.500A) Processing helix chain 'CQ' and resid 76 through 89 Processing helix chain 'CQ' and resid 92 through 102 removed outlier: 3.744A pdb=" N TRPCQ 101 " --> pdb=" O THRCQ 97 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N SERCQ 102 " --> pdb=" O TYRCQ 98 " (cutoff:3.500A) Processing helix chain 'CQ' and resid 103 through 120 Processing helix chain 'CQ' and resid 132 through 146 removed outlier: 4.986A pdb=" N GLUCQ 146 " --> pdb=" O ILECQ 142 " (cutoff:3.500A) Processing helix chain 'CQ' and resid 147 through 160 removed outlier: 4.368A pdb=" N ASPCQ 160 " --> pdb=" O ASNCQ 156 " (cutoff:3.500A) Processing helix chain 'CQ' and resid 195 through 208 Processing helix chain 'CQ' and resid 209 through 218 removed outlier: 4.669A pdb=" N GLUCQ 215 " --> pdb=" O ASPCQ 211 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEUCQ 216 " --> pdb=" O THRCQ 212 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHECQ 217 " --> pdb=" O LEUCQ 213 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N THRCQ 218 " --> pdb=" O ILECQ 214 " (cutoff:3.500A) Processing helix chain 'CQ' and resid 233 through 244 Processing helix chain 'DG' and resid 216 through 226 removed outlier: 4.321A pdb=" N GLYDG 220 " --> pdb=" O METDG 216 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N METDG 221 " --> pdb=" O ASNDG 217 " (cutoff:3.500A) Processing helix chain 'DG' and resid 241 through 246 removed outlier: 4.092A pdb=" N SERDG 245 " --> pdb=" O ASNDG 241 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VALDG 246 " --> pdb=" O ILEDG 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'DG' and resid 241 through 246' Processing helix chain 'DY' and resid 216 through 226 removed outlier: 4.481A pdb=" N GLYDY 220 " --> pdb=" O METDY 216 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N METDY 221 " --> pdb=" O ASNDY 217 " (cutoff:3.500A) Processing helix chain 'DY' and resid 241 through 246 removed outlier: 3.917A pdb=" N SERDY 245 " --> pdb=" O ASNDY 241 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VALDY 246 " --> pdb=" O ILEDY 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'DY' and resid 241 through 246' Processing helix chain 'DH' and resid 214 through 226 removed outlier: 4.741A pdb=" N PHEDH 218 " --> pdb=" O ASNDH 214 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLYDH 220 " --> pdb=" O METDH 216 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N METDH 221 " --> pdb=" O ASNDH 217 " (cutoff:3.500A) Processing helix chain 'DZ' and resid 214 through 226 removed outlier: 4.855A pdb=" N PHEDZ 218 " --> pdb=" O ASNDZ 214 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLYDZ 220 " --> pdb=" O METDZ 216 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N METDZ 221 " --> pdb=" O ASNDZ 217 " (cutoff:3.500A) Processing helix chain 'DI' and resid 19 through 32 removed outlier: 3.719A pdb=" N LEUDI 31 " --> pdb=" O ARGDI 27 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ASNDI 32 " --> pdb=" O PHEDI 28 " (cutoff:3.500A) Processing helix chain 'DI' and resid 33 through 47 Processing helix chain 'DI' and resid 60 through 75 removed outlier: 4.421A pdb=" N ALADI 64 " --> pdb=" O SERDI 60 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ASNDI 66 " --> pdb=" O GLNDI 62 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ALADI 67 " --> pdb=" O LEUDI 63 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLYDI 75 " --> pdb=" O ILEDI 71 " (cutoff:3.500A) Processing helix chain 'DI' and resid 76 through 89 Processing helix chain 'DI' and resid 92 through 102 removed outlier: 3.563A pdb=" N TRPDI 101 " --> pdb=" O THRDI 97 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N SERDI 102 " --> pdb=" O TYRDI 98 " (cutoff:3.500A) Processing helix chain 'DI' and resid 103 through 120 Processing helix chain 'DI' and resid 132 through 146 removed outlier: 5.019A pdb=" N GLUDI 146 " --> pdb=" O ILEDI 142 " (cutoff:3.500A) Processing helix chain 'DI' and resid 147 through 162 removed outlier: 3.931A pdb=" N ASPDI 160 " --> pdb=" O ASNDI 156 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N METDI 161 " --> pdb=" O ALADI 157 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLYDI 162 " --> pdb=" O VALDI 158 " (cutoff:3.500A) Processing helix chain 'DI' and resid 195 through 208 Processing helix chain 'DI' and resid 209 through 217 removed outlier: 4.128A pdb=" N GLUDI 215 " --> pdb=" O ASPDI 211 " (cutoff:3.500A) Processing helix chain 'DI' and resid 233 through 244 Processing helix chain 'EA' and resid 19 through 32 removed outlier: 3.648A pdb=" N LEUEA 31 " --> pdb=" O ARGEA 27 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ASNEA 32 " --> pdb=" O PHEEA 28 " (cutoff:3.500A) Processing helix chain 'EA' and resid 33 through 47 Processing helix chain 'EA' and resid 60 through 75 removed outlier: 5.100A pdb=" N ALAEA 64 " --> pdb=" O SEREA 60 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLUEA 65 " --> pdb=" O METEA 61 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ASNEA 66 " --> pdb=" O GLNEA 62 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ALAEA 67 " --> pdb=" O LEUEA 63 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N GLYEA 75 " --> pdb=" O ILEEA 71 " (cutoff:3.500A) Processing helix chain 'EA' and resid 76 through 89 Processing helix chain 'EA' and resid 92 through 102 removed outlier: 3.512A pdb=" N TRPEA 101 " --> pdb=" O THREA 97 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N SEREA 102 " --> pdb=" O TYREA 98 " (cutoff:3.500A) Processing helix chain 'EA' and resid 103 through 120 Processing helix chain 'EA' and resid 132 through 146 removed outlier: 4.963A pdb=" N GLUEA 146 " --> pdb=" O ILEEA 142 " (cutoff:3.500A) Processing helix chain 'EA' and resid 147 through 162 removed outlier: 3.990A pdb=" N ASPEA 160 " --> pdb=" O ASNEA 156 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N METEA 161 " --> pdb=" O ALAEA 157 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLYEA 162 " --> pdb=" O VALEA 158 " (cutoff:3.500A) Processing helix chain 'EA' and resid 195 through 208 Processing helix chain 'EA' and resid 209 through 217 removed outlier: 3.930A pdb=" N GLUEA 215 " --> pdb=" O ASPEA 211 " (cutoff:3.500A) Processing helix chain 'EA' and resid 233 through 244 Processing sheet with id= 1, first strand: chain 'BA' and resid 25 through 30 removed outlier: 5.214A pdb=" N THRBA 25 " --> pdb=" O VALBA 10 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THRBA 7 " --> pdb=" O VALBA 51 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'BA' and resid 4 through 7 Processing sheet with id= 3, first strand: chain 'CJ' and resid 25 through 30 removed outlier: 5.548A pdb=" N THRCJ 25 " --> pdb=" O VALCJ 10 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VALCJ 10 " --> pdb=" O THRCJ 25 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THRCJ 7 " --> pdb=" O VALCJ 51 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'CJ' and resid 4 through 7 Processing sheet with id= 5, first strand: chain 'BB' and resid 27 through 30 removed outlier: 6.610A pdb=" N THRBB 7 " --> pdb=" O VALBB 51 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'BB' and resid 3 through 7 removed outlier: 6.546A pdb=" N METBB 3 " --> pdb=" O ALABB 56 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'CK' and resid 27 through 30 removed outlier: 6.580A pdb=" N THRCK 7 " --> pdb=" O VALCK 51 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'CK' and resid 3 through 7 removed outlier: 6.604A pdb=" N METCK 3 " --> pdb=" O ALACK 56 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'DF' and resid 27 through 30 removed outlier: 6.586A pdb=" N THRDF 7 " --> pdb=" O VALDF 51 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'DF' and resid 3 through 7 removed outlier: 6.616A pdb=" N METDF 3 " --> pdb=" O ALADF 56 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'DX' and resid 27 through 30 removed outlier: 6.755A pdb=" N THRDX 7 " --> pdb=" O VALDX 51 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'DX' and resid 3 through 7 removed outlier: 6.434A pdb=" N METDX 3 " --> pdb=" O ALADX 56 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'BD' and resid 239 through 242 Processing sheet with id= 14, first strand: chain 'CM' and resid 239 through 242 Processing sheet with id= 15, first strand: chain 'BH' and resid 221 through 224 Processing sheet with id= 16, first strand: chain 'CQ' and resid 221 through 224 Processing sheet with id= 17, first strand: chain 'DI' and resid 254 through 259 removed outlier: 5.211A pdb=" N ASNDI 285 " --> pdb=" O LEUDI 306 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'EA' and resid 254 through 259 removed outlier: 5.086A pdb=" N ASNEA 285 " --> pdb=" O LEUEA 306 " (cutoff:3.500A) 8380 hydrogen bonds defined for protein. 25098 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: 45.62 Time building geometry restraints manager: 42.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 27547 1.33 - 1.45: 23976 1.45 - 1.57: 66501 1.57 - 1.69: 0 1.69 - 1.81: 1092 Bond restraints: 119116 Sorted by residual: bond pdb=" C34 45DEA 400 " pdb=" C36 45DEA 400 " ideal model delta sigma weight residual 1.444 1.534 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C34 45DDI 400 " pdb=" C36 45DDI 400 " ideal model delta sigma weight residual 1.444 1.530 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C34 45DBH 400 " pdb=" C36 45DBH 400 " ideal model delta sigma weight residual 1.444 1.530 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" C34 45DCQ 400 " pdb=" C36 45DCQ 400 " ideal model delta sigma weight residual 1.444 1.530 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" CGD CYCAK 200 " pdb=" O2D CYCAK 200 " ideal model delta sigma weight residual 1.249 1.310 -0.061 2.00e-02 2.50e+03 9.34e+00 ... (remaining 119111 not shown) Histogram of bond angle deviations from ideal: 97.32 - 106.09: 2342 106.09 - 114.86: 71420 114.86 - 123.63: 83789 123.63 - 132.40: 3768 132.40 - 141.17: 147 Bond angle restraints: 161466 Sorted by residual: angle pdb=" C1B CYCCW 200 " pdb=" CHB CYCCW 200 " pdb=" C4A CYCCW 200 " ideal model delta sigma weight residual 126.10 141.17 -15.07 3.00e+00 1.11e-01 2.53e+01 angle pdb=" C1B CYCCM 901 " pdb=" CHB CYCCM 901 " pdb=" C4A CYCCM 901 " ideal model delta sigma weight residual 126.10 140.88 -14.78 3.00e+00 1.11e-01 2.43e+01 angle pdb=" C1B CYCCD 200 " pdb=" CHB CYCCD 200 " pdb=" C4A CYCCD 200 " ideal model delta sigma weight residual 126.10 140.74 -14.64 3.00e+00 1.11e-01 2.38e+01 angle pdb=" C1B CYCAU 200 " pdb=" CHB CYCAU 200 " pdb=" C4A CYCAU 200 " ideal model delta sigma weight residual 126.10 140.47 -14.37 3.00e+00 1.11e-01 2.29e+01 angle pdb=" N GLYCA 34 " pdb=" CA GLYCA 34 " pdb=" C GLYCA 34 " ideal model delta sigma weight residual 112.73 118.44 -5.71 1.20e+00 6.94e-01 2.26e+01 ... (remaining 161461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.83: 67174 21.83 - 43.66: 3816 43.66 - 65.49: 380 65.49 - 87.32: 164 87.32 - 109.15: 24 Dihedral angle restraints: 71558 sinusoidal: 28382 harmonic: 43176 Sorted by residual: dihedral pdb=" CA GLYBK 108 " pdb=" C GLYBK 108 " pdb=" N LEUBK 109 " pdb=" CA LEUBK 109 " ideal model delta harmonic sigma weight residual 180.00 153.91 26.09 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA LYSCM 533 " pdb=" C LYSCM 533 " pdb=" N PHECM 534 " pdb=" CA PHECM 534 " ideal model delta harmonic sigma weight residual -180.00 -154.42 -25.58 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA SERDR 33 " pdb=" C SERDR 33 " pdb=" N GLYDR 34 " pdb=" CA GLYDR 34 " ideal model delta harmonic sigma weight residual 180.00 155.65 24.35 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 71555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 14906 0.049 - 0.099: 2883 0.099 - 0.148: 317 0.148 - 0.198: 14 0.198 - 0.247: 10 Chirality restraints: 18130 Sorted by residual: chirality pdb=" C3C CYCBI 200 " pdb=" C2C CYCBI 200 " pdb=" C4C CYCBI 200 " pdb=" CAC CYCBI 200 " both_signs ideal model delta sigma weight residual False 2.62 2.86 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C3C CYCDQ 200 " pdb=" C2C CYCDQ 200 " pdb=" C4C CYCDQ 200 " pdb=" CAC CYCDQ 200 " both_signs ideal model delta sigma weight residual False 2.62 2.86 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB ILEDG 242 " pdb=" CA ILEDG 242 " pdb=" CG1 ILEDG 242 " pdb=" CG2 ILEDG 242 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 18127 not shown) Planarity restraints: 20758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB CYCBQ 200 " -0.037 2.00e-02 2.50e+03 1.41e-01 4.46e+02 pdb=" OB CYCBQ 200 " 0.079 2.00e-02 2.50e+03 pdb=" C1B CYCBQ 200 " -0.015 2.00e-02 2.50e+03 pdb=" C2B CYCBQ 200 " 0.102 2.00e-02 2.50e+03 pdb=" C3B CYCBQ 200 " 0.140 2.00e-02 2.50e+03 pdb=" C4B CYCBQ 200 " 0.057 2.00e-02 2.50e+03 pdb=" CAB CYCBQ 200 " -0.299 2.00e-02 2.50e+03 pdb=" CHB CYCBQ 200 " -0.168 2.00e-02 2.50e+03 pdb=" CMB CYCBQ 200 " 0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CYCCM 901 " -0.028 2.00e-02 2.50e+03 1.39e-01 4.33e+02 pdb=" OB CYCCM 901 " 0.086 2.00e-02 2.50e+03 pdb=" C1B CYCCM 901 " -0.023 2.00e-02 2.50e+03 pdb=" C2B CYCCM 901 " 0.086 2.00e-02 2.50e+03 pdb=" C3B CYCCM 901 " 0.125 2.00e-02 2.50e+03 pdb=" C4B CYCCM 901 " 0.057 2.00e-02 2.50e+03 pdb=" CAB CYCCM 901 " -0.294 2.00e-02 2.50e+03 pdb=" CHB CYCCM 901 " -0.166 2.00e-02 2.50e+03 pdb=" CMB CYCCM 901 " 0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CYCBD 901 " 0.005 2.00e-02 2.50e+03 1.29e-01 3.77e+02 pdb=" OB CYCBD 901 " -0.048 2.00e-02 2.50e+03 pdb=" C1B CYCBD 901 " 0.014 2.00e-02 2.50e+03 pdb=" C2B CYCBD 901 " -0.084 2.00e-02 2.50e+03 pdb=" C3B CYCBD 901 " -0.128 2.00e-02 2.50e+03 pdb=" C4B CYCBD 901 " -0.068 2.00e-02 2.50e+03 pdb=" CAB CYCBD 901 " 0.271 2.00e-02 2.50e+03 pdb=" CHB CYCBD 901 " 0.170 2.00e-02 2.50e+03 pdb=" CMB CYCBD 901 " -0.133 2.00e-02 2.50e+03 ... (remaining 20755 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 2116 2.61 - 3.18: 118253 3.18 - 3.76: 207059 3.76 - 4.33: 274766 4.33 - 4.90: 450656 Nonbonded interactions: 1052850 Sorted by model distance: nonbonded pdb=" O ARGCY 16 " pdb=" OH TYRCZ 94 " model vdw 2.039 2.440 nonbonded pdb=" O ARGCV 16 " pdb=" OH TYRCW 94 " model vdw 2.043 2.440 nonbonded pdb=" OH TYRBT 88 " pdb=" OH TYRBT 116 " model vdw 2.049 2.440 nonbonded pdb=" OD1 ASNCV 71 " pdb=" OG1 THRCV 121 " model vdw 2.052 2.440 nonbonded pdb=" OG SERCR 19 " pdb=" OE1 GLUCR 22 " model vdw 2.054 2.440 ... (remaining 1052845 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 'AH' selection = chain 'AJ' selection = chain 'AN' selection = chain 'AP' selection = chain 'AR' selection = chain 'AV' selection = chain 'AX' selection = chain 'AZ' selection = chain 'BI' selection = chain 'BK' selection = chain 'BP' selection = chain 'BR' selection = chain 'BV' selection = chain 'BX' selection = chain 'BZ' selection = chain 'CC' selection = chain 'CE' selection = chain 'CG' selection = chain 'CR' selection = chain 'CT' selection = chain 'CV' selection = chain 'CY' selection = chain 'DA' selection = chain 'DC' selection = chain 'DJ' selection = chain 'DL' selection = chain 'DN' selection = chain 'DQ' selection = chain 'DS' selection = chain 'DU' } ncs_group { reference = (chain 'AB' and resid 1 through 161) selection = (chain 'AD' and resid 1 through 161) selection = (chain 'AF' and resid 1 through 161) selection = (chain 'AI' and resid 1 through 161) selection = (chain 'AL' and resid 1 through 161) selection = (chain 'AO' and resid 1 through 161) selection = (chain 'AQ' and resid 1 through 161) selection = chain 'AS' selection = (chain 'AU' and resid 1 through 161) selection = (chain 'AW' and resid 1 through 161) selection = (chain 'AY' and resid 1 through 161) selection = (chain 'BJ' and resid 1 through 161) selection = (chain 'BL' and resid 1 through 161) selection = (chain 'BN' and resid 1 through 161) selection = (chain 'BQ' and resid 1 through 161) selection = (chain 'BT' and resid 1 through 161) selection = (chain 'BW' and resid 1 through 161) selection = (chain 'BY' and resid 1 through 161) selection = chain 'CA' selection = (chain 'CD' and resid 1 through 161) selection = (chain 'CF' and resid 1 through 161) selection = (chain 'CH' and resid 1 through 161) selection = (chain 'CS' and resid 1 through 161) selection = (chain 'CU' and resid 1 through 161) selection = (chain 'CW' and resid 1 through 161) selection = (chain 'CZ' and resid 1 through 161) selection = (chain 'DB' and resid 1 through 161) selection = (chain 'DD' and resid 1 through 161) selection = (chain 'DK' and resid 1 through 161) selection = (chain 'DM' and resid 1 through 161) selection = (chain 'DO' and resid 1 through 161) selection = (chain 'DR' and resid 1 through 161) selection = (chain 'DT' and resid 1 through 161) selection = (chain 'DV' and resid 1 through 161) } ncs_group { reference = chain 'AE' selection = chain 'BM' } ncs_group { reference = chain 'AK' selection = chain 'BS' } ncs_group { reference = chain 'BA' selection = chain 'BB' selection = chain 'CJ' selection = chain 'CK' selection = chain 'DF' selection = chain 'DX' } ncs_group { reference = chain 'BD' selection = chain 'CM' } ncs_group { reference = chain 'BF' selection = chain 'CO' } ncs_group { reference = (chain 'BG' and (resid 196 through 248 or (resid 249 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name NE or name CZ or name N \ H1 or name NH2)))) selection = (chain 'CP' and (resid 196 through 248 or (resid 249 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name NE or name CZ or name N \ H1 or name NH2)))) selection = chain 'DG' selection = chain 'DH' selection = chain 'DY' selection = chain 'DZ' } ncs_group { reference = (chain 'BH' and (resid 17 through 178 or resid 185 through 313 or resid 400)) selection = (chain 'CQ' and (resid 17 through 178 or resid 185 through 313 or resid 400)) selection = (chain 'DI' and (resid 17 through 178 or resid 185 through 313 or resid 400)) selection = (chain 'EA' and (resid 17 through 178 or resid 185 through 313 or resid 400)) } 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 17.180 Check model and map are aligned: 1.290 Set scattering table: 0.770 Process input model: 238.330 Find NCS groups from input model: 8.500 Set up NCS constraints: 2.300 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: 0.020 Load rotamer database and sin/cos tables:10.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 280.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 0.005 0.090 119116 Z= 0.318 Angle : 0.625 15.075 161466 Z= 0.309 Chirality : 0.037 0.247 18130 Planarity : 0.008 0.141 20758 Dihedral : 13.518 109.151 44022 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 38.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.72 % Favored : 97.24 % Rotamer Outliers : 0.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % 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: 2.39 (0.07), residues: 14756 helix: 2.30 (0.05), residues: 11038 sheet: -0.28 (0.36), residues: 212 loop : -0.66 (0.11), residues: 3506 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29512 Ramachandran restraints generated. 14756 Oldfield, 0 Emsley, 14756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29512 Ramachandran restraints generated. 14756 Oldfield, 0 Emsley, 14756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2408 residues out of total 11980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2407 time to evaluate : 10.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 5 residues processed: 2408 average time/residue: 1.8628 time to fit residues: 6309.0849 Evaluate side-chains 1556 residues out of total 11980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1551 time to evaluate : 12.487 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 3 average time/residue: 1.2254 time to fit residues: 19.2835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1480 random chunks: chunk 1249 optimal weight: 4.9990 chunk 1121 optimal weight: 8.9990 chunk 622 optimal weight: 1.9990 chunk 383 optimal weight: 9.9990 chunk 756 optimal weight: 10.0000 chunk 599 optimal weight: 0.9990 chunk 1160 optimal weight: 0.0470 chunk 448 optimal weight: 9.9990 chunk 705 optimal weight: 5.9990 chunk 863 optimal weight: 0.9980 chunk 1344 optimal weight: 5.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 10 ASN AB 47 ASN ** AE 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 80 GLN ** AE 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 120 ASN AE 147 ASN AF 128 GLN ** AI 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 15 GLN ** AI 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 47 ASN ** AK 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 117 ASN AO 71 ASN AQ 71 ASN ** AS 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 71 ASN ** AY 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AZ 53 GLN AZ 71 ASN ** BD 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 193 GLN ** BL 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BM 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BM 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 117 ASN BN 2 GLN ** BN 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 117 ASN BN 128 GLN ** BQ 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 103 ASN BS 118 ASN ** BW 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BY 71 ASN ** CA 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 131 GLN CC 71 ASN ** CD 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CF 71 ASN CF 131 GLN ** CH 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CM 173 ASN CM 339 ASN CM 415 GLN ** CM 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CO 116 GLN CP 193 GLN ** CR 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CS 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CS 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CU 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 117 ASN CU 128 GLN CV 53 GLN CW 71 ASN ** CY 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CZ 131 GLN DB 2 GLN DB 10 ASN ** DB 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DD 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DF 35 ASN ** DI 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DI 293 ASN ** DJ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DK 2 GLN DM 10 ASN DM 71 ASN ** DO 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DO 71 ASN ** DQ 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DT 2 GLN ** DT 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DU 71 ASN ** DV 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 266 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 119116 Z= 0.230 Angle : 0.685 14.946 161466 Z= 0.332 Chirality : 0.040 0.291 18130 Planarity : 0.004 0.071 20758 Dihedral : 8.335 89.863 17762 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.48 % Favored : 97.47 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % 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: 2.04 (0.07), residues: 14756 helix: 2.01 (0.05), residues: 11050 sheet: -0.39 (0.39), residues: 196 loop : -0.66 (0.11), residues: 3510 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29512 Ramachandran restraints generated. 14756 Oldfield, 0 Emsley, 14756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29512 Ramachandran restraints generated. 14756 Oldfield, 0 Emsley, 14756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2152 residues out of total 11980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 1874 time to evaluate : 10.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 278 outliers final: 84 residues processed: 1977 average time/residue: 1.8497 time to fit residues: 5148.2874 Evaluate side-chains 1662 residues out of total 11980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 1578 time to evaluate : 10.407 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 48 residues processed: 46 average time/residue: 1.1024 time to fit residues: 98.7812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1480 random chunks: chunk 746 optimal weight: 4.9990 chunk 417 optimal weight: 5.9990 chunk 1118 optimal weight: 20.0000 chunk 915 optimal weight: 10.0000 chunk 370 optimal weight: 40.0000 chunk 1346 optimal weight: 7.9990 chunk 1454 optimal weight: 3.9990 chunk 1199 optimal weight: 5.9990 chunk 1335 optimal weight: 20.0000 chunk 459 optimal weight: 8.9990 chunk 1080 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 10 ASN AB 47 ASN AE 14 GLN AE 27 GLN ** AE 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 80 GLN AE 100 ASN AE 120 ASN AE 147 ASN ** AF 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 128 GLN AP 60 GLN ** AS 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 116 GLN BG 193 GLN BI 53 GLN BI 128 GLN ** BL 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BL 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BL 128 GLN ** BM 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BM 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 128 GLN ** BQ 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BS 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BY 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 128 GLN ** CD 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CD 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CF 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CM 15 GLN CM 415 GLN ** CM 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CP 193 GLN ** CR 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CS 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CS 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CS 128 GLN CU 15 GLN CU 128 GLN CV 53 GLN ** CW 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CY 71 ASN CZ 128 GLN ** DB 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DF 19 GLN ** DI 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DO 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DS 53 GLN ** DT 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DV 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 119116 Z= 0.337 Angle : 0.701 11.494 161466 Z= 0.344 Chirality : 0.041 0.348 18130 Planarity : 0.004 0.057 20758 Dihedral : 8.363 94.814 17762 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.64 % Favored : 97.30 % Rotamer Outliers : 3.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.07), residues: 14756 helix: 1.86 (0.05), residues: 11044 sheet: -0.36 (0.39), residues: 182 loop : -0.74 (0.11), residues: 3530 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29512 Ramachandran restraints generated. 14756 Oldfield, 0 Emsley, 14756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29512 Ramachandran restraints generated. 14756 Oldfield, 0 Emsley, 14756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2076 residues out of total 11980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 383 poor density : 1693 time to evaluate : 10.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 383 outliers final: 131 residues processed: 1876 average time/residue: 1.8131 time to fit residues: 4837.0418 Evaluate side-chains 1666 residues out of total 11980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1535 time to evaluate : 9.426 Switching outliers to nearest non-outliers outliers start: 131 outliers final: 76 residues processed: 65 average time/residue: 0.9644 time to fit residues: 124.0960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1480 random chunks: chunk 1330 optimal weight: 9.9990 chunk 1012 optimal weight: 9.9990 chunk 698 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 642 optimal weight: 6.9990 chunk 904 optimal weight: 8.9990 chunk 1351 optimal weight: 30.0000 chunk 1430 optimal weight: 5.9990 chunk 705 optimal weight: 2.9990 chunk 1280 optimal weight: 7.9990 chunk 385 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 10 ASN AB 47 ASN AE 55 GLN ** AE 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 100 ASN AE 120 ASN AE 147 ASN ** AI 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 60 GLN AK 58 GLN ** AK 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 10 ASN ** AP 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 71 ASN ** AY 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 85 GLN BG 193 GLN ** BL 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BL 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BL 128 GLN ** BM 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BM 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 120 ASN ** BN 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BS 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 60 GLN ** BY 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CD 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CF 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CM 415 GLN ** CM 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CP 193 GLN CQ 14 ASN ** CR 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CS 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CS 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 128 GLN CU 128 GLN ** CW 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CZ 117 ASN ** DA 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DO 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DT 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DV 131 GLN ** DZ 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 119116 Z= 0.347 Angle : 0.713 14.221 161466 Z= 0.350 Chirality : 0.041 0.459 18130 Planarity : 0.005 0.058 20758 Dihedral : 8.382 100.623 17762 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.83 % Favored : 97.11 % Rotamer Outliers : 3.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.07), residues: 14756 helix: 1.71 (0.05), residues: 11032 sheet: -0.64 (0.36), residues: 220 loop : -0.72 (0.11), residues: 3504 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29512 Ramachandran restraints generated. 14756 Oldfield, 0 Emsley, 14756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29512 Ramachandran restraints generated. 14756 Oldfield, 0 Emsley, 14756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2050 residues out of total 11980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 394 poor density : 1656 time to evaluate : 10.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 394 outliers final: 164 residues processed: 1874 average time/residue: 1.8254 time to fit residues: 4900.7656 Evaluate side-chains 1708 residues out of total 11980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1544 time to evaluate : 10.469 Switching outliers to nearest non-outliers outliers start: 164 outliers final: 93 residues processed: 80 average time/residue: 1.1165 time to fit residues: 165.0682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1480 random chunks: chunk 1191 optimal weight: 7.9990 chunk 812 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 1065 optimal weight: 3.9990 chunk 590 optimal weight: 20.0000 chunk 1220 optimal weight: 5.9990 chunk 988 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 730 optimal weight: 5.9990 chunk 1284 optimal weight: 9.9990 chunk 360 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 10 ASN AB 47 ASN AB 110 ASN AE 10 GLN AE 27 GLN AE 55 GLN ** AE 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 80 GLN AE 147 ASN AH 128 GLN ** AI 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 47 ASN ** AY 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 193 GLN BJ 117 ASN ** BL 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BL 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BL 128 GLN ** BM 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BM 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 120 ASN ** BN 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BY 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CD 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CF 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CM 415 GLN ** CM 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CP 193 GLN ** CR 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CS 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CS 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CS 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 128 GLN ** CW 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DD 71 ASN DF 35 ASN ** DI 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DI 266 GLN ** DJ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DO 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DT 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DV 131 GLN ** DZ 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 119116 Z= 0.343 Angle : 0.723 15.355 161466 Z= 0.355 Chirality : 0.041 0.302 18130 Planarity : 0.005 0.058 20758 Dihedral : 8.421 100.482 17762 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.85 % Favored : 97.09 % Rotamer Outliers : 3.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.07), residues: 14756 helix: 1.66 (0.05), residues: 11002 sheet: -0.69 (0.36), residues: 220 loop : -0.79 (0.11), residues: 3534 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29512 Ramachandran restraints generated. 14756 Oldfield, 0 Emsley, 14756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29512 Ramachandran restraints generated. 14756 Oldfield, 0 Emsley, 14756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2012 residues out of total 11980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 397 poor density : 1615 time to evaluate : 10.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 397 outliers final: 175 residues processed: 1847 average time/residue: 1.8300 time to fit residues: 4837.5596 Evaluate side-chains 1689 residues out of total 11980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1514 time to evaluate : 10.367 Switching outliers to nearest non-outliers outliers start: 175 outliers final: 114 residues processed: 68 average time/residue: 1.0388 time to fit residues: 137.3644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1480 random chunks: chunk 481 optimal weight: 6.9990 chunk 1288 optimal weight: 20.0000 chunk 282 optimal weight: 6.9990 chunk 839 optimal weight: 9.9990 chunk 353 optimal weight: 8.9990 chunk 1431 optimal weight: 20.0000 chunk 1188 optimal weight: 9.9990 chunk 662 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 473 optimal weight: 20.0000 chunk 751 optimal weight: 0.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 10 ASN AE 55 GLN AE 71 ASN AE 80 GLN AE 120 ASN AE 147 ASN ** AF 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 131 GLN AN 128 GLN ** AY 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 193 GLN BL 128 GLN ** BM 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BM 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 120 ASN ** BN 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BY 71 ASN ** CA 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CD 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CE 128 GLN CF 71 ASN CM 415 GLN ** CM 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CP 193 GLN ** CR 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CS 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CS 71 ASN ** CS 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CT 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 128 GLN ** CW 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DO 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DT 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DV 131 GLN ** DZ 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 119116 Z= 0.266 Angle : 0.709 13.591 161466 Z= 0.348 Chirality : 0.040 0.276 18130 Planarity : 0.004 0.074 20758 Dihedral : 8.419 95.654 17762 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.76 % Favored : 97.18 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.07), residues: 14756 helix: 1.68 (0.05), residues: 10998 sheet: -0.55 (0.35), residues: 232 loop : -0.80 (0.11), residues: 3526 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29512 Ramachandran restraints generated. 14756 Oldfield, 0 Emsley, 14756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29512 Ramachandran restraints generated. 14756 Oldfield, 0 Emsley, 14756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2001 residues out of total 11980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 366 poor density : 1635 time to evaluate : 10.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 366 outliers final: 171 residues processed: 1867 average time/residue: 1.8309 time to fit residues: 4913.3944 Evaluate side-chains 1687 residues out of total 11980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1516 time to evaluate : 10.289 Switching outliers to nearest non-outliers outliers start: 171 outliers final: 129 residues processed: 54 average time/residue: 1.2166 time to fit residues: 121.4926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1480 random chunks: chunk 1380 optimal weight: 0.8980 chunk 161 optimal weight: 10.0000 chunk 815 optimal weight: 10.0000 chunk 1045 optimal weight: 8.9990 chunk 810 optimal weight: 5.9990 chunk 1205 optimal weight: 20.0000 chunk 799 optimal weight: 5.9990 chunk 1426 optimal weight: 1.9990 chunk 892 optimal weight: 4.9990 chunk 869 optimal weight: 6.9990 chunk 658 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 10 ASN AB 47 ASN AE 55 GLN AE 71 ASN ** AE 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 147 ASN ** AF 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AH 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 131 GLN AO 47 ASN ** AY 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 13 GLN BB 13 GLN ** BD 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 193 GLN BL 128 GLN ** BM 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BM 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 120 ASN ** BN 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BY 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CD 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 24 ASN CM 415 GLN ** CM 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CR 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CS 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CS 71 ASN ** CS 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CW 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DF 35 ASN ** DI 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DK 10 ASN ** DM 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DO 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DQ 53 GLN ** DR 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DT 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DV 131 GLN ** DZ 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.090 119116 Z= 0.278 Angle : 0.739 16.361 161466 Z= 0.361 Chirality : 0.041 0.322 18130 Planarity : 0.004 0.066 20758 Dihedral : 8.410 98.274 17762 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.76 % Favored : 97.19 % Rotamer Outliers : 2.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.07), residues: 14756 helix: 1.66 (0.05), residues: 10962 sheet: -0.62 (0.35), residues: 232 loop : -0.84 (0.11), residues: 3562 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29512 Ramachandran restraints generated. 14756 Oldfield, 0 Emsley, 14756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29512 Ramachandran restraints generated. 14756 Oldfield, 0 Emsley, 14756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1960 residues out of total 11980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 357 poor density : 1603 time to evaluate : 10.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 357 outliers final: 185 residues processed: 1830 average time/residue: 1.8406 time to fit residues: 4860.7749 Evaluate side-chains 1694 residues out of total 11980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1509 time to evaluate : 10.405 Switching outliers to nearest non-outliers outliers start: 185 outliers final: 136 residues processed: 64 average time/residue: 1.1740 time to fit residues: 140.3582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1480 random chunks: chunk 882 optimal weight: 9.9990 chunk 569 optimal weight: 7.9990 chunk 851 optimal weight: 1.9990 chunk 429 optimal weight: 7.9990 chunk 280 optimal weight: 9.9990 chunk 276 optimal weight: 7.9990 chunk 906 optimal weight: 7.9990 chunk 971 optimal weight: 0.1980 chunk 705 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 1121 optimal weight: 6.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 10 ASN AB 47 ASN ** AE 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 120 ASN AE 147 ASN AF 110 ASN ** AH 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 117 ASN AL 131 GLN ** AY 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 173 ASN ** BD 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 193 GLN BJ 47 ASN ** BJ 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BL 110 ASN BL 128 GLN BL 131 GLN BM 71 ASN ** BM 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 120 ASN ** BN 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BY 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CM 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CR 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CS 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CS 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CT 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CW 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DI 30 GLN ** DI 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DO 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DV 131 GLN ** DZ 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 119116 Z= 0.247 Angle : 0.738 15.640 161466 Z= 0.361 Chirality : 0.041 0.386 18130 Planarity : 0.004 0.072 20758 Dihedral : 8.414 97.866 17762 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.75 % Favored : 97.19 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.07), residues: 14756 helix: 1.63 (0.05), residues: 10998 sheet: -0.75 (0.35), residues: 220 loop : -0.81 (0.11), residues: 3538 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29512 Ramachandran restraints generated. 14756 Oldfield, 0 Emsley, 14756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29512 Ramachandran restraints generated. 14756 Oldfield, 0 Emsley, 14756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1907 residues out of total 11980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 1613 time to evaluate : 10.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 294 outliers final: 184 residues processed: 1809 average time/residue: 1.7824 time to fit residues: 4647.5230 Evaluate side-chains 1694 residues out of total 11980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1510 time to evaluate : 9.420 Switching outliers to nearest non-outliers outliers start: 184 outliers final: 145 residues processed: 54 average time/residue: 1.2174 time to fit residues: 120.2187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1480 random chunks: chunk 1297 optimal weight: 0.7980 chunk 1366 optimal weight: 7.9990 chunk 1246 optimal weight: 9.9990 chunk 1329 optimal weight: 9.9990 chunk 800 optimal weight: 6.9990 chunk 579 optimal weight: 3.9990 chunk 1043 optimal weight: 6.9990 chunk 407 optimal weight: 0.8980 chunk 1201 optimal weight: 7.9990 chunk 1257 optimal weight: 8.9990 chunk 1324 optimal weight: 10.0000 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 10 ASN AB 47 ASN AE 55 GLN AE 71 ASN ** AE 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 147 ASN ** AH 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 71 ASN ** AI 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 117 ASN AL 131 GLN ** AW 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 13 GLN ** BD 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 797 ASN BG 193 GLN ** BJ 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BL 128 GLN BL 131 GLN ** BM 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 120 ASN ** BN 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BY 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CD 10 ASN CJ 24 ASN ** CM 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CR 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CS 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CS 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CT 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CW 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DF 35 ASN ** DI 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DJ 60 GLN ** DJ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DO 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DV 47 ASN DV 131 GLN ** DZ 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.112 119116 Z= 0.282 Angle : 0.778 15.528 161466 Z= 0.380 Chirality : 0.042 0.383 18130 Planarity : 0.005 0.085 20758 Dihedral : 8.421 99.096 17762 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.83 % Favored : 97.11 % Rotamer Outliers : 2.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.07), residues: 14756 helix: 1.56 (0.05), residues: 11000 sheet: -0.77 (0.34), residues: 220 loop : -0.83 (0.11), residues: 3536 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29512 Ramachandran restraints generated. 14756 Oldfield, 0 Emsley, 14756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29512 Ramachandran restraints generated. 14756 Oldfield, 0 Emsley, 14756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1820 residues out of total 11980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 1564 time to evaluate : 10.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 256 outliers final: 184 residues processed: 1738 average time/residue: 1.7597 time to fit residues: 4398.1010 Evaluate side-chains 1679 residues out of total 11980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1495 time to evaluate : 10.306 Switching outliers to nearest non-outliers outliers start: 184 outliers final: 149 residues processed: 47 average time/residue: 1.1943 time to fit residues: 106.3318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1480 random chunks: chunk 872 optimal weight: 8.9990 chunk 1405 optimal weight: 6.9990 chunk 857 optimal weight: 10.0000 chunk 666 optimal weight: 8.9990 chunk 977 optimal weight: 5.9990 chunk 1474 optimal weight: 10.0000 chunk 1357 optimal weight: 20.0000 chunk 1174 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 906 optimal weight: 9.9990 chunk 719 optimal weight: 1.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 10 ASN AB 47 ASN ** AD 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 117 ASN ** AE 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 147 ASN AF 110 ASN ** AH 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 71 ASN ** AI 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 58 GLN ** AK 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 131 GLN AS 10 ASN ** AW 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 117 ASN BL 128 GLN BL 131 GLN ** BM 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 120 ASN ** BN 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BY 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CD 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 24 ASN CJ 40 GLN ** CM 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CR 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CS 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CS 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CT 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CU 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CW 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DI 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DO 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.100 119116 Z= 0.271 Angle : 0.789 15.987 161466 Z= 0.386 Chirality : 0.042 0.326 18130 Planarity : 0.005 0.094 20758 Dihedral : 8.435 98.874 17762 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.89 % Favored : 97.05 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.07), residues: 14756 helix: 1.52 (0.05), residues: 10980 sheet: -0.63 (0.34), residues: 224 loop : -0.91 (0.11), residues: 3552 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29512 Ramachandran restraints generated. 14756 Oldfield, 0 Emsley, 14756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29512 Ramachandran restraints generated. 14756 Oldfield, 0 Emsley, 14756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1776 residues out of total 11980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1550 time to evaluate : 10.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 226 outliers final: 167 residues processed: 1712 average time/residue: 1.8269 time to fit residues: 4498.3601 Evaluate side-chains 1660 residues out of total 11980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1493 time to evaluate : 10.640 Switching outliers to nearest non-outliers outliers start: 167 outliers final: 141 residues processed: 35 average time/residue: 1.2968 time to fit residues: 87.2040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1480 random chunks: chunk 932 optimal weight: 4.9990 chunk 1250 optimal weight: 5.9990 chunk 359 optimal weight: 0.9990 chunk 1082 optimal weight: 7.9990 chunk 173 optimal weight: 0.9980 chunk 326 optimal weight: 5.9990 chunk 1175 optimal weight: 9.9990 chunk 492 optimal weight: 40.0000 chunk 1207 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 10 ASN AB 47 ASN ** AD 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 55 GLN ** AE 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 147 ASN AF 47 ASN AF 110 ASN ** AH 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 71 ASN ** AI 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 117 ASN AL 131 GLN ** AW 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 13 GLN ** BD 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 53 GLN ** BJ 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BL 131 GLN ** BM 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 120 ASN ** BN 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BR 60 GLN ** BW 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BY 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CD 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CM 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CQ 208 ASN CR 71 ASN ** CS 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CS 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CT 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CU 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CU 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CW 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DF 35 ASN ** DI 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DM 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DO 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DR 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DZ 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.076186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.060457 restraints weight = 470007.975| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.77 r_work: 0.3155 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.091 119116 Z= 0.244 Angle : 0.791 16.181 161466 Z= 0.386 Chirality : 0.041 0.305 18130 Planarity : 0.004 0.081 20758 Dihedral : 8.461 98.601 17762 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.84 % Favored : 97.11 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.07), residues: 14756 helix: 1.52 (0.05), residues: 10984 sheet: -0.59 (0.34), residues: 224 loop : -0.90 (0.11), residues: 3548 =============================================================================== Job complete usr+sys time: 61408.16 seconds wall clock time: 1055 minutes 37.35 seconds (63337.35 seconds total)