Starting phenix.real_space_refine on Sun Mar 3 13:09:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv1_17950/03_2024/8pv1_17950_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv1_17950/03_2024/8pv1_17950.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv1_17950/03_2024/8pv1_17950_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv1_17950/03_2024/8pv1_17950_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv1_17950/03_2024/8pv1_17950_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv1_17950/03_2024/8pv1_17950.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv1_17950/03_2024/8pv1_17950.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv1_17950/03_2024/8pv1_17950_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv1_17950/03_2024/8pv1_17950_updated.pdb" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.018 sd= 0.169 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 3441 5.49 5 Mg 3 5.21 5 S 254 5.16 5 C 85721 2.51 5 N 29145 2.21 5 O 38681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "CB GLU 115": "OE1" <-> "OE2" Residue "CB ASP 119": "OD1" <-> "OD2" Residue "CF PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF ASP 62": "OD1" <-> "OD2" Residue "CF ASP 108": "OD1" <-> "OD2" Residue "CF TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH ASP 79": "OD1" <-> "OD2" Residue "CH ASP 209": "OD1" <-> "OD2" Residue "CH GLU 229": "OE1" <-> "OE2" Residue "CH PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH GLU 296": "OE1" <-> "OE2" Residue "CH ASP 298": "OD1" <-> "OD2" Residue "CH PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH GLU 471": "OE1" <-> "OE2" Residue "CH TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH GLU 542": "OE1" <-> "OE2" Residue "CH PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CI PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CI ASP 237": "OD1" <-> "OD2" Residue "CI GLU 239": "OE1" <-> "OE2" Residue "CI ASP 242": "OD1" <-> "OD2" Residue "CI PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ ASP 221": "OD1" <-> "OD2" Residue "CJ TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CK GLU 22": "OE1" <-> "OE2" Residue "CK ASP 84": "OD1" <-> "OD2" Residue "CK ASP 252": "OD1" <-> "OD2" Residue "CL ASP 52": "OD1" <-> "OD2" Residue "CM ASP 171": "OD1" <-> "OD2" Residue "CM TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CM PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CM GLU 230": "OE1" <-> "OE2" Residue "CN TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CN PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CN GLU 98": "OE1" <-> "OE2" Residue "CO GLU 12": "OE1" <-> "OE2" Residue "CQ GLU 4": "OE1" <-> "OE2" Residue "CQ TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cb ASP 20": "OD1" <-> "OD2" Residue "Cb GLU 60": "OE1" <-> "OE2" Residue "Cd GLU 93": "OE1" <-> "OE2" Residue "Cd ASP 173": "OD1" <-> "OD2" Residue "Cd PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cd TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cd GLU 408": "OE1" <-> "OE2" Residue "Ce ASP 89": "OD1" <-> "OD2" Residue "Ce GLU 231": "OE1" <-> "OE2" Residue "Ce GLU 247": "OE1" <-> "OE2" Residue "Ce GLU 320": "OE1" <-> "OE2" Residue "Ce ASP 362": "OD1" <-> "OD2" Residue "Ce ASP 363": "OD1" <-> "OD2" Residue "Ce PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ce ASP 391": "OD1" <-> "OD2" Residue "Ce GLU 399": "OE1" <-> "OE2" Residue "Ce ASP 405": "OD1" <-> "OD2" Residue "Ce ASP 440": "OD1" <-> "OD2" Residue "Cf TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cf PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cf TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cf PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cf ASP 264": "OD1" <-> "OD2" Residue "Cf GLU 281": "OE1" <-> "OE2" Residue "Cg ASP 43": "OD1" <-> "OD2" Residue "Cg GLU 48": "OE1" <-> "OE2" Residue "Cg GLU 102": "OE1" <-> "OE2" Residue "Cg GLU 120": "OE1" <-> "OE2" Residue "Ch TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ch PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ch ASP 457": "OD1" <-> "OD2" Residue "Cz TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA GLU 47": "OE1" <-> "OE2" Residue "LA GLU 74": "OE1" <-> "OE2" Residue "LA ASP 122": "OD1" <-> "OD2" Residue "LA TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA ASP 176": "OD1" <-> "OD2" Residue "LB PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB GLU 74": "OE1" <-> "OE2" Residue "LB GLU 94": "OE1" <-> "OE2" Residue "LB PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB GLU 214": "OE1" <-> "OE2" Residue "LB ASP 290": "OD1" <-> "OD2" Residue "LC PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC ASP 286": "OD1" <-> "OD2" Residue "LD TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD ASP 216": "OD1" <-> "OD2" Residue "LD ASP 232": "OD1" <-> "OD2" Residue "LD GLU 245": "OE1" <-> "OE2" Residue "LD TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE ASP 77": "OD1" <-> "OD2" Residue "LE ASP 110": "OD1" <-> "OD2" Residue "LE ASP 115": "OD1" <-> "OD2" Residue "LE ASP 120": "OD1" <-> "OD2" Residue "LE GLU 121": "OE1" <-> "OE2" Residue "LE TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF ASP 11": "OD1" <-> "OD2" Residue "LF PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF GLU 65": "OE1" <-> "OE2" Residue "LF GLU 176": "OE1" <-> "OE2" Residue "LF PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF GLU 230": "OE1" <-> "OE2" Residue "LG ASP 42": "OD1" <-> "OD2" Residue "LG ASP 86": "OD1" <-> "OD2" Residue "LG TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG GLU 209": "OE1" <-> "OE2" Residue "LG PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG GLU 250": "OE1" <-> "OE2" Residue "LH TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH GLU 65": "OE1" <-> "OE2" Residue "LH ASP 74": "OD1" <-> "OD2" Residue "LH GLU 141": "OE1" <-> "OE2" Residue "LH GLU 150": "OE1" <-> "OE2" Residue "LH ASP 199": "OD1" <-> "OD2" Residue "LH TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LJ TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LK ASP 52": "OD1" <-> "OD2" Residue "LK GLU 95": "OE1" <-> "OE2" Residue "LK ASP 164": "OD1" <-> "OD2" Residue "LL ASP 52": "OD1" <-> "OD2" Residue "LL PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LL GLU 107": "OE1" <-> "OE2" Residue "LL GLU 146": "OE1" <-> "OE2" Residue "LL GLU 158": "OE1" <-> "OE2" Residue "LL GLU 172": "OE1" <-> "OE2" Residue "LM GLU 23": "OE1" <-> "OE2" Residue "LM ASP 35": "OD1" <-> "OD2" Residue "LM GLU 107": "OE1" <-> "OE2" Residue "LN ASP 17": "OD1" <-> "OD2" Residue "LN TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN GLU 103": "OE1" <-> "OE2" Residue "LN ASP 124": "OD1" <-> "OD2" Residue "LN PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO ASP 11": "OD1" <-> "OD2" Residue "LO GLU 102": "OE1" <-> "OE2" Residue "LO GLU 146": "OE1" <-> "OE2" Residue "LO ASP 153": "OD1" <-> "OD2" Residue "LO TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LP GLU 99": "OE1" <-> "OE2" Residue "LQ PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LQ GLU 127": "OE1" <-> "OE2" Residue "LQ GLU 175": "OE1" <-> "OE2" Residue "LR ASP 25": "OD1" <-> "OD2" Residue "LR GLU 31": "OE1" <-> "OE2" Residue "LR ASP 47": "OD1" <-> "OD2" Residue "LR GLU 65": "OE1" <-> "OE2" Residue "LR TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS GLU 34": "OE1" <-> "OE2" Residue "LS TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS ASP 82": "OD1" <-> "OD2" Residue "LS GLU 96": "OE1" <-> "OE2" Residue "LS PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS GLU 133": "OE1" <-> "OE2" Residue "LS PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT GLU 86": "OE1" <-> "OE2" Residue "LT GLU 94": "OE1" <-> "OE2" Residue "LT GLU 157": "OE1" <-> "OE2" Residue "LU PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU ASP 35": "OD1" <-> "OD2" Residue "LU TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU GLU 111": "OE1" <-> "OE2" Residue "LV PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LV ASP 91": "OD1" <-> "OD2" Residue "LV PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX GLU 72": "OE1" <-> "OE2" Residue "LX GLU 91": "OE1" <-> "OE2" Residue "LX PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX ASP 117": "OD1" <-> "OD2" Residue "LX ASP 144": "OD1" <-> "OD2" Residue "LY GLU 37": "OE1" <-> "OE2" Residue "LY GLU 66": "OE1" <-> "OE2" Residue "LY GLU 82": "OE1" <-> "OE2" Residue "LY ASP 111": "OD1" <-> "OD2" Residue "LY GLU 126": "OE1" <-> "OE2" Residue "LZ TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ GLU 107": "OE1" <-> "OE2" Residue "LZ GLU 118": "OE1" <-> "OE2" Residue "La ASP 85": "OD1" <-> "OD2" Residue "La ASP 103": "OD1" <-> "OD2" Residue "La TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "La GLU 133": "OE1" <-> "OE2" Residue "La GLU 135": "OE1" <-> "OE2" Residue "Lc GLU 60": "OE1" <-> "OE2" Residue "Lc GLU 79": "OE1" <-> "OE2" Residue "Lc ASP 97": "OD1" <-> "OD2" Residue "Ld GLU 69": "OE1" <-> "OE2" Residue "Le PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Le PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lf TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lf ASP 39": "OD1" <-> "OD2" Residue "Lf TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lg TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lg GLU 97": "OE1" <-> "OE2" Residue "Lh GLU 19": "OE1" <-> "OE2" Residue "Lh GLU 107": "OE1" <-> "OE2" Residue "Li GLU 55": "OE1" <-> "OE2" Residue "Li PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lk ASP 51": "OD1" <-> "OD2" Residue "Lp GLU 30": "OE1" <-> "OE2" Residue "Lq GLU 58": "OE1" <-> "OE2" Time to flip residues: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 157250 Number of models: 1 Model: "" Number of chains: 68 Chain: "C1" Number of atoms: 65888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3078, 65888 Classifications: {'RNA': 3078} Modifications used: {'rna2p': 1, 'rna2p_pur': 318, 'rna2p_pyr': 218, 'rna3p': 25, 'rna3p_pur': 1357, 'rna3p_pyr': 1151} Link IDs: {'rna2p': 537, 'rna3p': 2540} Chain breaks: 8 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 18 Chain: "C2" Number of atoms: 3319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3319 Classifications: {'RNA': 156} Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 12, 'rna3p_pur': 62, 'rna3p_pyr': 64} Link IDs: {'rna2p': 30, 'rna3p': 125} Chain: "C3" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1754 Classifications: {'RNA': 82} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 9, 'rna3p_pur': 31, 'rna3p_pyr': 31} Link IDs: {'rna2p': 19, 'rna3p': 62} Chain breaks: 1 Chain: "C4" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2536 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 54, 'rna3p_pyr': 53} Link IDs: {'rna2p': 12, 'rna3p': 106} Chain: "CB" Number of atoms: 2107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2107 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 245} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "CF" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1934 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 232} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "CH" Number of atoms: 5063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5063 Classifications: {'peptide': 627} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 600} Chain breaks: 2 Chain: "CI" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1234 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 142} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "CJ" Number of atoms: 3116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3116 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 356} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "CK" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1903 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 221} Chain breaks: 2 Chain: "CL" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 622 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 72} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "CM" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1773 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 205} Chain breaks: 2 Chain: "CN" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1853 Classifications: {'peptide': 246} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 237} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "CO" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 468 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain breaks: 2 Chain: "CQ" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1480 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "Cb" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 830 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "Cd" Number of atoms: 3691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3691 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Ce" Number of atoms: 2148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2148 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 246} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Cf" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2282 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "Cg" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1478 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 19, 'TRANS': 168} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Ch" Number of atoms: 3812 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 485, 3809 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 466} Conformer: "B" Number of residues, atoms: 485, 3809 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 466} bond proxies already assigned to first conformer: 3904 Chain: "Cz" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 869 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "LA" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1454 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 175} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "LB" Number of atoms: 3104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3104 Classifications: {'peptide': 389} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 373} Chain: "LC" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2751 Classifications: {'peptide': 363} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 338} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "LD" Number of atoms: 2266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2266 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 6, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "LE" Number of atoms: 1477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1477 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "LF" Number of atoms: 2023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 2023 Classifications: {'peptide': 248} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 234} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "LG" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1889 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 223} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "LH" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1495 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain: "LJ" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1357 Classifications: {'peptide': 169} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 163} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "LK" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1184 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 149} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "LL" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1587 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 189} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 21 Chain: "LM" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1126 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "LN" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1704 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain: "LO" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1611 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 192} Chain: "LP" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1343 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 164} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "LQ" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1200 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "LR" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1241 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 151} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "LS" Number of atoms: 1426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1426 Classifications: {'peptide': 174} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 163} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "LT" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1027 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 121} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "LU" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 846 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "LV" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 991 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 125} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "LX" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1133 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 136} Chain: "LY" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1056 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 6, 'TRANS': 126} Chain: "LZ" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1112 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "La" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 872 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain breaks: 1 Chain: "Lc" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 705 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Ld" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 105} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "Le" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1017 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "Lf" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 862 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "Lg" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 109} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Lh" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1003 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "Li" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 827 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 98} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS%COO:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Lj" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 698 Classifications: {'peptide': 88} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 83} Chain: "Lk" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 632 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 4, 'TRANS': 71} Chain: "Ll" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Lp" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 698 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "Lq" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1073 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 6, 'TRANS': 132} Chain: "CH" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "CQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Cb" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Cd" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 2, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Lg" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lj" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lp" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "CH" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Cd" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 93620 SG CYSCQ 6 146.566 179.618 100.861 1.00 14.90 S ATOM 93648 SG CYSCQ 9 150.205 180.620 101.437 1.00 14.74 S ATOM 93833 SG CYSCQ 32 149.435 177.392 99.690 1.00 12.86 S ATOM 93865 SG CYSCQ 36 148.683 177.820 103.454 1.00 13.53 S ATOM 95477 SG CYSCb 52 127.901 186.325 123.303 1.00 27.44 S ATOM 95500 SG CYSCb 55 131.065 184.434 123.472 1.00 27.65 S ATOM A13JL SG CYSLg 45 142.264 159.361 199.036 1.00 21.15 S ATOM A13K3 SG CYSLg 48 139.941 161.270 196.756 1.00 24.61 S ATOM A13RB SG CYSLg 82 141.919 163.177 199.445 1.00 21.45 S ATOM A13RT SG CYSLg 85 139.111 161.063 200.470 1.00 23.34 S ATOM A15HQ SG CYSLj 19 164.070 112.552 171.897 1.00 13.67 S ATOM A15II SG CYSLj 22 164.931 110.220 168.967 1.00 12.97 S ATOM A15L8 SG CYSLj 34 161.392 111.389 169.489 1.00 14.47 S ATOM A15LP SG CYSLj 37 162.870 108.976 171.985 1.00 15.50 S ATOM A16ZF SG CYSLp 39 123.599 162.066 192.406 1.00 26.97 S ATOM A1703 SG CYSLp 42 125.399 165.391 192.894 1.00 28.73 S ATOM A1738 SG CYSLp 57 126.624 163.004 190.325 1.00 27.04 S ATOM A173T SG CYSLp 60 127.168 162.079 193.907 1.00 31.61 S Time building chain proxies: 60.67, per 1000 atoms: 0.39 Number of scatterers: 157250 At special positions: 0 Unit cell: (235.125, 229.9, 318.725, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 254 16.00 P 3441 15.00 Mg 3 11.99 O 38681 8.00 N 29145 7.00 C 85721 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 59.13 Conformation dependent library (CDL) restraints added in 11.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNCQ1000 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 36 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 9 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 32 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 6 " pdb=" ZNCb1000 " pdb="ZN ZNCb1000 " - pdb=" ND1 HISCb 74 " pdb="ZN ZNCb1000 " - pdb=" NE2 HISCb 68 " pdb="ZN ZNCb1000 " - pdb=" SG CYSCb 52 " pdb="ZN ZNCb1000 " - pdb=" SG CYSCb 55 " pdb=" ZNLg1000 " pdb="ZN ZNLg1000 " - pdb=" SG CYSLg 82 " pdb="ZN ZNLg1000 " - pdb=" SG CYSLg 85 " pdb="ZN ZNLg1000 " - pdb=" SG CYSLg 48 " pdb="ZN ZNLg1000 " - pdb=" SG CYSLg 45 " pdb=" ZNLj1000 " pdb="ZN ZNLj1000 " - pdb=" SG CYSLj 34 " pdb="ZN ZNLj1000 " - pdb=" SG CYSLj 37 " pdb="ZN ZNLj1000 " - pdb=" SG CYSLj 22 " pdb="ZN ZNLj1000 " - pdb=" SG CYSLj 19 " pdb=" ZNLp 101 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 57 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 42 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 39 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 60 " Number of angles added : 26 20718 Ramachandran restraints generated. 10359 Oldfield, 0 Emsley, 10359 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 19704 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 385 helices and 102 sheets defined 45.6% alpha, 14.2% beta 1078 base pairs and 1922 stacking pairs defined. Time for finding SS restraints: 84.28 Creating SS restraints... Processing helix chain 'CB' and resid 19 through 40 removed outlier: 3.779A pdb=" N THRCB 23 " --> pdb=" O ASPCB 19 " (cutoff:3.500A) Processing helix chain 'CB' and resid 52 through 60 removed outlier: 4.598A pdb=" N GLUCB 59 " --> pdb=" O SERCB 55 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N THRCB 60 " --> pdb=" O THRCB 56 " (cutoff:3.500A) Processing helix chain 'CB' and resid 104 through 114 removed outlier: 4.365A pdb=" N TYRCB 108 " --> pdb=" O PROCB 104 " (cutoff:3.500A) Processing helix chain 'CB' and resid 117 through 125 removed outlier: 5.409A pdb=" N GLYCB 125 " --> pdb=" O ARGCB 121 " (cutoff:3.500A) Processing helix chain 'CB' and resid 129 through 137 Processing helix chain 'CB' and resid 139 through 151 removed outlier: 3.737A pdb=" N HISCB 150 " --> pdb=" O LEUCB 146 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASPCB 151 " --> pdb=" O PHECB 147 " (cutoff:3.500A) Processing helix chain 'CB' and resid 159 through 168 removed outlier: 3.624A pdb=" N LEUCB 163 " --> pdb=" O ILECB 159 " (cutoff:3.500A) Proline residue: CB 164 - end of helix Processing helix chain 'CB' and resid 169 through 175 removed outlier: 5.043A pdb=" N THRCB 174 " --> pdb=" O THRCB 170 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N THRCB 175 " --> pdb=" O PHECB 171 " (cutoff:3.500A) Processing helix chain 'CB' and resid 216 through 230 Processing helix chain 'CB' and resid 251 through 269 Processing helix chain 'CB' and resid 274 through 279 removed outlier: 3.829A pdb=" N VALCB 278 " --> pdb=" O LYSCB 274 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ARGCB 279 " --> pdb=" O TRPCB 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'CB' and resid 274 through 279' Processing helix chain 'CB' and resid 302 through 307 removed outlier: 4.303A pdb=" N VALCB 306 " --> pdb=" O ASPCB 302 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N VALCB 307 " --> pdb=" O GLUCB 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'CB' and resid 302 through 307' Processing helix chain 'CF' and resid 19 through 37 removed outlier: 3.836A pdb=" N LYSCF 23 " --> pdb=" O GLYCF 19 " (cutoff:3.500A) Proline residue: CF 35 - end of helix Processing helix chain 'CF' and resid 50 through 61 removed outlier: 5.207A pdb=" N LYSCF 54 " --> pdb=" O ASNCF 50 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASPCF 55 " --> pdb=" O ASNCF 51 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASNCF 61 " --> pdb=" O ARGCF 57 " (cutoff:3.500A) Processing helix chain 'CF' and resid 69 through 78 Processing helix chain 'CF' and resid 88 through 97 removed outlier: 4.080A pdb=" N LEUCF 92 " --> pdb=" O GLYCF 88 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THRCF 93 " --> pdb=" O LEUCF 89 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARGCF 94 " --> pdb=" O HISCF 90 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TYRCF 95 " --> pdb=" O ARGCF 91 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEUCF 96 " --> pdb=" O LEUCF 92 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N THRCF 97 " --> pdb=" O THRCF 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'CF' and resid 88 through 97' Processing helix chain 'CF' and resid 108 through 119 removed outlier: 3.703A pdb=" N ILECF 112 " --> pdb=" O ASPCF 108 " (cutoff:3.500A) Processing helix chain 'CF' and resid 158 through 169 removed outlier: 4.290A pdb=" N GLUCF 162 " --> pdb=" O SERCF 158 " (cutoff:3.500A) Proline residue: CF 163 - end of helix Processing helix chain 'CF' and resid 202 through 213 Processing helix chain 'CF' and resid 237 through 243 removed outlier: 3.606A pdb=" N THRCF 242 " --> pdb=" O GLUCF 238 " (cutoff:3.500A) Processing helix chain 'CH' and resid 12 through 27 Processing helix chain 'CH' and resid 37 through 66 Processing helix chain 'CH' and resid 69 through 74 removed outlier: 6.036A pdb=" N HISCH 74 " --> pdb=" O LEUCH 70 " (cutoff:3.500A) Processing helix chain 'CH' and resid 75 through 85 Processing helix chain 'CH' and resid 86 through 118 removed outlier: 3.923A pdb=" N TYRCH 117 " --> pdb=" O ARGCH 113 " (cutoff:3.500A) Processing helix chain 'CH' and resid 120 through 143 removed outlier: 3.988A pdb=" N LEUCH 142 " --> pdb=" O LEUCH 138 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LYSCH 143 " --> pdb=" O ILECH 139 " (cutoff:3.500A) Processing helix chain 'CH' and resid 144 through 159 Processing helix chain 'CH' and resid 178 through 187 Processing helix chain 'CH' and resid 227 through 232 removed outlier: 3.532A pdb=" N METCH 231 " --> pdb=" O PROCH 227 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ASNCH 232 " --> pdb=" O LEUCH 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'CH' and resid 227 through 232' Processing helix chain 'CH' and resid 233 through 244 removed outlier: 3.979A pdb=" N SERCH 238 " --> pdb=" O ILECH 234 " (cutoff:3.500A) Processing helix chain 'CH' and resid 262 through 278 Proline residue: CH 275 - end of helix removed outlier: 3.920A pdb=" N ALACH 278 " --> pdb=" O LYSCH 274 " (cutoff:3.500A) Processing helix chain 'CH' and resid 293 through 298 removed outlier: 3.867A pdb=" N LEUCH 297 " --> pdb=" O LYSCH 293 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASPCH 298 " --> pdb=" O PHECH 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'CH' and resid 293 through 298' Processing helix chain 'CH' and resid 299 through 311 removed outlier: 3.955A pdb=" N THRCH 309 " --> pdb=" O ILECH 305 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYSCH 310 " --> pdb=" O ASNCH 306 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N SERCH 311 " --> pdb=" O ASPCH 307 " (cutoff:3.500A) Processing helix chain 'CH' and resid 326 through 352 removed outlier: 5.003A pdb=" N GLYCH 350 " --> pdb=" O LYSCH 346 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THRCH 351 " --> pdb=" O LEUCH 347 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N HISCH 352 " --> pdb=" O LYSCH 348 " (cutoff:3.500A) Processing helix chain 'CH' and resid 358 through 369 Processing helix chain 'CH' and resid 384 through 390 removed outlier: 4.672A pdb=" N LYSCH 388 " --> pdb=" O PROCH 384 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASNCH 389 " --> pdb=" O GLUCH 385 " (cutoff:3.500A) Processing helix chain 'CH' and resid 403 through 412 Processing helix chain 'CH' and resid 445 through 450 removed outlier: 3.645A pdb=" N TYRCH 449 " --> pdb=" O ASNCH 445 " (cutoff:3.500A) Processing helix chain 'CH' and resid 453 through 472 removed outlier: 4.014A pdb=" N LYSCH 457 " --> pdb=" O ASPCH 453 " (cutoff:3.500A) Processing helix chain 'CH' and resid 482 through 510 Processing helix chain 'CH' and resid 519 through 524 removed outlier: 3.853A pdb=" N VALCH 523 " --> pdb=" O PROCH 519 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LYSCH 524 " --> pdb=" O ARGCH 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'CH' and resid 519 through 524' Processing helix chain 'CH' and resid 526 through 538 Processing helix chain 'CH' and resid 540 through 545 removed outlier: 3.828A pdb=" N ILECH 544 " --> pdb=" O ASPCH 540 " (cutoff:3.500A) Processing helix chain 'CH' and resid 546 through 551 removed outlier: 5.569A pdb=" N GLNCH 551 " --> pdb=" O ARGCH 547 " (cutoff:3.500A) Processing helix chain 'CH' and resid 582 through 597 Processing helix chain 'CH' and resid 609 through 631 removed outlier: 4.046A pdb=" N GLNCH 624 " --> pdb=" O ALACH 620 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ARGCH 625 " --> pdb=" O LYSCH 621 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LYSCH 626 " --> pdb=" O LEUCH 622 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N METCH 627 " --> pdb=" O ALACH 623 " (cutoff:3.500A) Processing helix chain 'CH' and resid 645 through 650 Processing helix chain 'CH' and resid 429 through 434 removed outlier: 3.577A pdb=" N LYSCH 433 " --> pdb=" O PROCH 430 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYRCH 434 " --> pdb=" O GLUCH 431 " (cutoff:3.500A) Processing helix chain 'CI' and resid 199 through 211 removed outlier: 3.965A pdb=" N GLNCI 209 " --> pdb=" O GLYCI 205 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHECI 210 " --> pdb=" O TYRCI 206 " (cutoff:3.500A) Processing helix chain 'CI' and resid 237 through 249 Processing helix chain 'CI' and resid 284 through 296 Proline residue: CI 296 - end of helix Processing helix chain 'CI' and resid 298 through 324 removed outlier: 4.469A pdb=" N GLUCI 322 " --> pdb=" O GLUCI 318 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N METCI 323 " --> pdb=" O LYSCI 319 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 11 through 16 Processing helix chain 'CJ' and resid 18 through 27 Processing helix chain 'CJ' and resid 29 through 41 Processing helix chain 'CJ' and resid 49 through 54 removed outlier: 3.928A pdb=" N VALCJ 53 " --> pdb=" O ASPCJ 49 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 65 through 75 removed outlier: 4.008A pdb=" N HISCJ 74 " --> pdb=" O GLNCJ 70 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLUCJ 75 " --> pdb=" O TYRCJ 71 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 76 through 98 removed outlier: 3.570A pdb=" N LYSCJ 80 " --> pdb=" O PROCJ 76 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 99 through 111 removed outlier: 3.751A pdb=" N ASNCJ 109 " --> pdb=" O ARGCJ 105 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALACJ 110 " --> pdb=" O LEUCJ 106 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASNCJ 111 " --> pdb=" O GLUCJ 107 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 112 through 117 Processing helix chain 'CJ' and resid 123 through 132 removed outlier: 3.671A pdb=" N ARGCJ 128 " --> pdb=" O ASNCJ 124 " (cutoff:3.500A) Proline residue: CJ 132 - end of helix Processing helix chain 'CJ' and resid 133 through 155 removed outlier: 4.507A pdb=" N ASPCJ 142 " --> pdb=" O LEUCJ 138 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ASPCJ 143 " --> pdb=" O ARGCJ 139 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASNCJ 153 " --> pdb=" O PHECJ 149 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEUCJ 154 " --> pdb=" O LEUCJ 150 " (cutoff:3.500A) Proline residue: CJ 155 - end of helix Processing helix chain 'CJ' and resid 161 through 183 Processing helix chain 'CJ' and resid 223 through 250 removed outlier: 3.764A pdb=" N PHECJ 240 " --> pdb=" O THRCJ 236 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 258 through 265 Processing helix chain 'CJ' and resid 362 through 367 removed outlier: 3.963A pdb=" N LEUCJ 366 " --> pdb=" O ASPCJ 362 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N PHECJ 367 " --> pdb=" O PROCJ 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'CJ' and resid 362 through 367' Processing helix chain 'CJ' and resid 379 through 391 Processing helix chain 'CJ' and resid 457 through 468 removed outlier: 4.403A pdb=" N VALCJ 461 " --> pdb=" O GLNCJ 457 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TRPCJ 462 " --> pdb=" O PROCJ 458 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 472 through 477 removed outlier: 4.125A pdb=" N TYRCJ 476 " --> pdb=" O PROCJ 472 " (cutoff:3.500A) Processing helix chain 'CK' and resid 5 through 14 Processing helix chain 'CK' and resid 19 through 41 removed outlier: 4.643A pdb=" N GLYCK 32 " --> pdb=" O ALACK 28 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N HISCK 33 " --> pdb=" O ALACK 29 " (cutoff:3.500A) Processing helix chain 'CK' and resid 44 through 71 Processing helix chain 'CK' and resid 128 through 133 Processing helix chain 'CK' and resid 174 through 179 removed outlier: 3.673A pdb=" N ARGCK 178 " --> pdb=" O PROCK 174 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N TYRCK 179 " --> pdb=" O METCK 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'CK' and resid 174 through 179' Processing helix chain 'CK' and resid 206 through 213 Processing helix chain 'CK' and resid 248 through 253 Processing helix chain 'CL' and resid 17 through 42 Processing helix chain 'CL' and resid 61 through 80 Processing helix chain 'CL' and resid 3 through 8 Proline residue: CL 8 - end of helix No H-bonds generated for 'chain 'CL' and resid 3 through 8' Processing helix chain 'CM' and resid 14 through 35 Processing helix chain 'CM' and resid 53 through 78 Processing helix chain 'CM' and resid 102 through 113 Processing helix chain 'CM' and resid 126 through 137 Processing helix chain 'CM' and resid 146 through 156 Processing helix chain 'CM' and resid 171 through 179 removed outlier: 4.737A pdb=" N ILECM 175 " --> pdb=" O ASPCM 171 " (cutoff:3.500A) Processing helix chain 'CM' and resid 186 through 197 Processing helix chain 'CM' and resid 200 through 209 removed outlier: 5.065A pdb=" N TRPCM 209 " --> pdb=" O ALACM 205 " (cutoff:3.500A) Processing helix chain 'CM' and resid 215 through 221 removed outlier: 4.245A pdb=" N GLYCM 219 " --> pdb=" O ASNCM 215 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHECM 220 " --> pdb=" O PROCM 216 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ARGCM 221 " --> pdb=" O ASNCM 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'CM' and resid 215 through 221' Processing helix chain 'CM' and resid 239 through 249 removed outlier: 4.712A pdb=" N ALACM 243 " --> pdb=" O GLUCM 239 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEUCM 244 " --> pdb=" O HISCM 240 " (cutoff:3.500A) Processing helix chain 'CN' and resid 12 through 17 removed outlier: 3.851A pdb=" N PHECN 16 " --> pdb=" O GLUCN 12 " (cutoff:3.500A) Processing helix chain 'CN' and resid 32 through 43 removed outlier: 3.743A pdb=" N PHECN 38 " --> pdb=" O PHECN 34 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLNCN 43 " --> pdb=" O GLUCN 39 " (cutoff:3.500A) Processing helix chain 'CN' and resid 58 through 63 Processing helix chain 'CN' and resid 77 through 89 Proline residue: CN 89 - end of helix Processing helix chain 'CN' and resid 103 through 108 Processing helix chain 'CN' and resid 122 through 133 Processing helix chain 'CN' and resid 147 through 152 Processing helix chain 'CN' and resid 166 through 178 Processing helix chain 'CN' and resid 192 through 197 Processing helix chain 'CN' and resid 211 through 223 Processing helix chain 'CN' and resid 229 through 236 removed outlier: 4.434A pdb=" N ILECN 233 " --> pdb=" O GLYCN 229 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASNCN 234 " --> pdb=" O PROCN 230 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THRCN 235 " --> pdb=" O GLYCN 231 " (cutoff:3.500A) Processing helix chain 'CN' and resid 237 through 245 Processing helix chain 'CO' and resid 7 through 21 Processing helix chain 'CO' and resid 22 through 43 Processing helix chain 'CO' and resid 83 through 88 Processing helix chain 'CQ' and resid 33 through 43 Processing helix chain 'CQ' and resid 45 through 50 removed outlier: 5.434A pdb=" N LYSCQ 50 " --> pdb=" O PROCQ 46 " (cutoff:3.500A) Processing helix chain 'CQ' and resid 52 through 60 Processing helix chain 'CQ' and resid 66 through 71 removed outlier: 4.468A pdb=" N GLNCQ 70 " --> pdb=" O ASPCQ 66 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N PHECQ 71 " --> pdb=" O SERCQ 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'CQ' and resid 66 through 71' Processing helix chain 'CQ' and resid 82 through 131 removed outlier: 6.025A pdb=" N GLYCQ 114 " --> pdb=" O LYSCQ 110 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYSCQ 115 " --> pdb=" O ARGCQ 111 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ARGCQ 116 " --> pdb=" O METCQ 112 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ALACQ 117 " --> pdb=" O ALACQ 113 " (cutoff:3.500A) Processing helix chain 'CQ' and resid 138 through 153 Processing helix chain 'CQ' and resid 155 through 171 removed outlier: 4.559A pdb=" N LYSCQ 171 " --> pdb=" O LEUCQ 167 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 5 through 10 removed outlier: 3.650A pdb=" N METCb 9 " --> pdb=" O ALACb 5 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N THRCb 10 " --> pdb=" O LYSCb 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cb' and resid 5 through 10' Processing helix chain 'Cb' and resid 18 through 28 Processing helix chain 'Cb' and resid 29 through 40 removed outlier: 3.803A pdb=" N LYSCb 39 " --> pdb=" O TYRCb 35 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ALACb 40 " --> pdb=" O LYSCb 36 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 61 through 72 removed outlier: 3.724A pdb=" N LYSCb 70 " --> pdb=" O VALCb 66 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLYCb 71 " --> pdb=" O GLYCb 67 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LYSCb 72 " --> pdb=" O HISCb 68 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 73 through 84 Processing helix chain 'Cb' and resid 87 through 96 removed outlier: 3.544A pdb=" N ILECb 95 " --> pdb=" O ALACb 91 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 6 through 15 Processing helix chain 'Cd' and resid 31 through 43 removed outlier: 3.854A pdb=" N LEUCd 41 " --> pdb=" O THRCd 37 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYSCd 42 " --> pdb=" O LEUCd 38 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 73 through 79 removed outlier: 4.686A pdb=" N PHECd 77 " --> pdb=" O ASNCd 73 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THRCd 78 " --> pdb=" O ARGCd 74 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ASNCd 79 " --> pdb=" O LYSCd 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cd' and resid 73 through 79' Processing helix chain 'Cd' and resid 84 through 98 Processing helix chain 'Cd' and resid 113 through 118 removed outlier: 3.507A pdb=" N ILECd 117 " --> pdb=" O PROCd 113 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 122 through 139 removed outlier: 3.991A pdb=" N HISCd 130 " --> pdb=" O GLYCd 126 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ALACd 132 " --> pdb=" O LYSCd 128 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LYSCd 133 " --> pdb=" O LYSCd 129 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 140 through 145 Processing helix chain 'Cd' and resid 160 through 185 Processing helix chain 'Cd' and resid 211 through 216 removed outlier: 4.228A pdb=" N ASNCd 215 " --> pdb=" O GLUCd 211 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYSCd 216 " --> pdb=" O ALACd 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cd' and resid 211 through 216' Processing helix chain 'Cd' and resid 219 through 233 Processing helix chain 'Cd' and resid 244 through 249 Processing helix chain 'Cd' and resid 250 through 260 Processing helix chain 'Cd' and resid 272 through 277 removed outlier: 4.355A pdb=" N VALCd 276 " --> pdb=" O LYSCd 272 " (cutoff:3.500A) Proline residue: Cd 277 - end of helix No H-bonds generated for 'chain 'Cd' and resid 272 through 277' Processing helix chain 'Cd' and resid 278 through 292 removed outlier: 3.887A pdb=" N LYSCd 290 " --> pdb=" O ARGCd 286 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASPCd 291 " --> pdb=" O ILECd 287 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 306 through 322 Processing helix chain 'Cd' and resid 338 through 348 Processing helix chain 'Cd' and resid 389 through 397 Processing helix chain 'Cd' and resid 400 through 405 removed outlier: 3.933A pdb=" N VALCd 404 " --> pdb=" O ARGCd 400 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLUCd 405 " --> pdb=" O VALCd 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cd' and resid 400 through 405' Processing helix chain 'Cd' and resid 407 through 419 removed outlier: 4.013A pdb=" N ILECd 411 " --> pdb=" O PROCd 407 " (cutoff:3.500A) Proline residue: Cd 412 - end of helix removed outlier: 5.088A pdb=" N LYSCd 419 " --> pdb=" O LEUCd 415 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 420 through 428 Processing helix chain 'Cd' and resid 434 through 447 Processing helix chain 'Cd' and resid 456 through 471 removed outlier: 3.699A pdb=" N GLYCd 471 " --> pdb=" O ASPCd 467 " (cutoff:3.500A) Processing helix chain 'Ce' and resid 86 through 94 Processing helix chain 'Ce' and resid 186 through 192 removed outlier: 3.519A pdb=" N GLUCe 190 " --> pdb=" O PROCe 186 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N LYSCe 192 " --> pdb=" O THRCe 188 " (cutoff:3.500A) Processing helix chain 'Ce' and resid 218 through 269 Processing helix chain 'Ce' and resid 300 through 333 Processing helix chain 'Ce' and resid 334 through 353 Processing helix chain 'Ce' and resid 401 through 414 Processing helix chain 'Ce' and resid 435 through 441 Processing helix chain 'Cf' and resid 9 through 20 Processing helix chain 'Cf' and resid 39 through 54 Processing helix chain 'Cf' and resid 72 through 83 Processing helix chain 'Cf' and resid 125 through 130 removed outlier: 4.263A pdb=" N PHECf 129 " --> pdb=" O SERCf 125 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LYSCf 130 " --> pdb=" O ILECf 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cf' and resid 125 through 130' Processing helix chain 'Cf' and resid 155 through 169 Processing helix chain 'Cf' and resid 264 through 273 Processing helix chain 'Cf' and resid 314 through 319 removed outlier: 3.692A pdb=" N LYSCf 318 " --> pdb=" O METCf 314 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ARGCf 319 " --> pdb=" O LYSCf 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cf' and resid 314 through 319' Processing helix chain 'Cf' and resid 177 through 182 removed outlier: 3.907A pdb=" N LEUCf 181 " --> pdb=" O VALCf 178 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ARGCf 182 " --> pdb=" O GLUCf 179 " (cutoff:3.500A) Processing helix chain 'Cg' and resid 43 through 69 Processing helix chain 'Cg' and resid 103 through 113 Processing helix chain 'Cg' and resid 118 through 123 removed outlier: 3.619A pdb=" N ARGCg 123 " --> pdb=" O ARGCg 119 " (cutoff:3.500A) Processing helix chain 'Cg' and resid 156 through 163 Processing helix chain 'Cg' and resid 168 through 198 removed outlier: 4.276A pdb=" N ASPCg 172 " --> pdb=" O SERCg 168 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LYSCg 173 " --> pdb=" O VALCg 169 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ARGCg 174 " --> pdb=" O ARGCg 170 " (cutoff:3.500A) Processing helix chain 'Ch' and resid 61 through 74 Processing helix chain 'Ch' and resid 102 through 111 Processing helix chain 'Ch' and resid 331 through 338 removed outlier: 3.674A pdb=" N THRCh 337 " --> pdb=" O HISCh 333 " (cutoff:3.500A) Processing helix chain 'Ch' and resid 349 through 366 Processing helix chain 'Ch' and resid 388 through 393 removed outlier: 3.535A pdb=" N GLYCh 393 " --> pdb=" O ASPCh 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ch' and resid 388 through 393' Processing helix chain 'Cz' and resid 48 through 103 Processing helix chain 'Cz' and resid 104 through 121 Processing helix chain 'LA' and resid 33 through 39 Processing helix chain 'LA' and resid 103 through 108 removed outlier: 3.841A pdb=" N VALLA 107 " --> pdb=" O PROLA 103 " (cutoff:3.500A) Proline residue: LA 108 - end of helix No H-bonds generated for 'chain 'LA' and resid 103 through 108' Processing helix chain 'LA' and resid 181 through 193 removed outlier: 4.172A pdb=" N VALLA 191 " --> pdb=" O HISLA 187 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYSLA 192 " --> pdb=" O LYSLA 188 " (cutoff:3.500A) Processing helix chain 'LA' and resid 200 through 205 removed outlier: 3.791A pdb=" N METLA 204 " --> pdb=" O ARGLA 200 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ASNLA 205 " --> pdb=" O GLYLA 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'LA' and resid 200 through 205' Processing helix chain 'LB' and resid 13 through 18 removed outlier: 4.681A pdb=" N LEULB 17 " --> pdb=" O SERLB 13 " (cutoff:3.500A) Proline residue: LB 18 - end of helix No H-bonds generated for 'chain 'LB' and resid 13 through 18' Processing helix chain 'LB' and resid 111 through 120 removed outlier: 4.145A pdb=" N ARGLB 117 " --> pdb=" O GLULB 113 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHELB 118 " --> pdb=" O VALLB 114 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TYRLB 119 " --> pdb=" O LYSLB 115 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYSLB 120 " --> pdb=" O ARGLB 116 " (cutoff:3.500A) Processing helix chain 'LB' and resid 130 through 140 removed outlier: 3.927A pdb=" N LYSLB 135 " --> pdb=" O THRLB 131 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYSLB 136 " --> pdb=" O LYSLB 132 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYRLB 137 " --> pdb=" O TYRLB 133 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALALB 138 " --> pdb=" O ALALB 134 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ASNLB 140 " --> pdb=" O LYSLB 136 " (cutoff:3.500A) Processing helix chain 'LB' and resid 142 through 155 Processing helix chain 'LB' and resid 166 through 171 removed outlier: 4.303A pdb=" N THRLB 170 " --> pdb=" O GLNLB 166 " (cutoff:3.500A) Proline residue: LB 171 - end of helix No H-bonds generated for 'chain 'LB' and resid 166 through 171' Processing helix chain 'LB' and resid 188 through 200 Processing helix chain 'LB' and resid 205 through 210 removed outlier: 4.031A pdb=" N ILELB 209 " --> pdb=" O THRLB 205 " (cutoff:3.500A) Processing helix chain 'LB' and resid 229 through 234 Processing helix chain 'LB' and resid 348 through 353 removed outlier: 3.981A pdb=" N LEULB 352 " --> pdb=" O SERLB 348 " (cutoff:3.500A) Processing helix chain 'LB' and resid 373 through 382 Processing helix chain 'LB' and resid 384 through 390 removed outlier: 3.716A pdb=" N LEULB 388 " --> pdb=" O LEULB 384 " (cutoff:3.500A) Processing helix chain 'LC' and resid 24 through 29 removed outlier: 4.651A pdb=" N SERLC 28 " --> pdb=" O PROLC 24 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALALC 29 " --> pdb=" O LYSLC 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 24 through 29' Processing helix chain 'LC' and resid 32 through 47 removed outlier: 4.148A pdb=" N LYSLC 45 " --> pdb=" O THRLC 41 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASNLC 46 " --> pdb=" O GLYLC 42 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LYSLC 47 " --> pdb=" O METLC 43 " (cutoff:3.500A) Processing helix chain 'LC' and resid 115 through 133 removed outlier: 3.685A pdb=" N ALALC 131 " --> pdb=" O LEULC 127 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VALLC 132 " --> pdb=" O ALALC 128 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ALALC 133 " --> pdb=" O ALALC 129 " (cutoff:3.500A) Processing helix chain 'LC' and resid 134 through 140 removed outlier: 3.524A pdb=" N GLYLC 140 " --> pdb=" O LEULC 136 " (cutoff:3.500A) Processing helix chain 'LC' and resid 154 through 159 removed outlier: 4.025A pdb=" N VALLC 158 " --> pdb=" O ASPLC 154 " (cutoff:3.500A) Processing helix chain 'LC' and resid 165 through 177 Processing helix chain 'LC' and resid 178 through 189 removed outlier: 4.033A pdb=" N LYSLC 189 " --> pdb=" O VALLC 185 " (cutoff:3.500A) Processing helix chain 'LC' and resid 194 through 200 removed outlier: 4.760A pdb=" N METLC 198 " --> pdb=" O GLYLC 194 " (cutoff:3.500A) Processing helix chain 'LC' and resid 220 through 228 removed outlier: 4.103A pdb=" N LYSLC 224 " --> pdb=" O LYSLC 220 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ASNLC 228 " --> pdb=" O LYSLC 224 " (cutoff:3.500A) Processing helix chain 'LC' and resid 241 through 247 Proline residue: LC 247 - end of helix Processing helix chain 'LC' and resid 258 through 272 removed outlier: 4.570A pdb=" N ASPLC 266 " --> pdb=" O ILELC 262 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ALALC 267 " --> pdb=" O LYSLC 263 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYSLC 272 " --> pdb=" O VALLC 268 " (cutoff:3.500A) Processing helix chain 'LC' and resid 286 through 293 Processing helix chain 'LC' and resid 294 through 300 removed outlier: 4.312A pdb=" N VALLC 299 " --> pdb=" O GLULC 295 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEULC 300 " --> pdb=" O ILELC 296 " (cutoff:3.500A) Processing helix chain 'LC' and resid 318 through 323 removed outlier: 4.593A pdb=" N LYSLC 323 " --> pdb=" O PROLC 319 " (cutoff:3.500A) Processing helix chain 'LC' and resid 324 through 330 Processing helix chain 'LC' and resid 331 through 340 removed outlier: 4.583A pdb=" N THRLC 335 " --> pdb=" O PROLC 331 " (cutoff:3.500A) Processing helix chain 'LC' and resid 355 through 364 Processing helix chain 'LC' and resid 214 through 219 removed outlier: 3.873A pdb=" N GLYLC 219 " --> pdb=" O SERLC 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 214 through 219' Processing helix chain 'LD' and resid 9 through 16 Processing helix chain 'LD' and resid 20 through 26 Processing helix chain 'LD' and resid 29 through 38 removed outlier: 3.763A pdb=" N ARGLD 35 " --> pdb=" O TYRLD 31 " (cutoff:3.500A) Processing helix chain 'LD' and resid 79 through 87 removed outlier: 4.178A pdb=" N LEULD 83 " --> pdb=" O TYRLD 79 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ARGLD 84 " --> pdb=" O SERLD 80 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ALALD 85 " --> pdb=" O HISLD 81 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TYRLD 86 " --> pdb=" O GLULD 82 " (cutoff:3.500A) Processing helix chain 'LD' and resid 94 through 114 Processing helix chain 'LD' and resid 130 through 136 Processing helix chain 'LD' and resid 160 through 173 removed outlier: 3.542A pdb=" N GLYLD 164 " --> pdb=" O ALALD 160 " (cutoff:3.500A) Processing helix chain 'LD' and resid 194 through 204 Processing helix chain 'LD' and resid 205 through 218 Processing helix chain 'LD' and resid 219 through 227 Processing helix chain 'LD' and resid 228 through 233 Processing helix chain 'LD' and resid 235 through 253 removed outlier: 3.991A pdb=" N LEULD 239 " --> pdb=" O GLULD 235 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLULD 240 " --> pdb=" O ALALD 236 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLULD 241 " --> pdb=" O ASPLD 237 " (cutoff:3.500A) Processing helix chain 'LD' and resid 266 through 278 removed outlier: 3.728A pdb=" N TYRLD 277 " --> pdb=" O GLULD 273 " (cutoff:3.500A) Processing helix chain 'LD' and resid 283 through 300 Processing helix chain 'LE' and resid 98 through 103 removed outlier: 3.955A pdb=" N VALLE 102 " --> pdb=" O ASNLE 98 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILELE 103 " --> pdb=" O ALALE 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'LE' and resid 98 through 103' Processing helix chain 'LE' and resid 115 through 124 Processing helix chain 'LE' and resid 131 through 140 Processing helix chain 'LE' and resid 155 through 174 removed outlier: 4.926A pdb=" N ALALE 168 " --> pdb=" O ALALE 164 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEULE 169 " --> pdb=" O ILELE 165 " (cutoff:3.500A) Processing helix chain 'LE' and resid 178 through 186 removed outlier: 5.360A pdb=" N SERLE 186 " --> pdb=" O TYRLE 182 " (cutoff:3.500A) Processing helix chain 'LF' and resid 8 through 14 Processing helix chain 'LF' and resid 15 through 34 removed outlier: 5.192A pdb=" N GLULF 31 " --> pdb=" O LYSLF 27 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ARGLF 32 " --> pdb=" O ALALF 28 " (cutoff:3.500A) Processing helix chain 'LF' and resid 35 through 79 removed outlier: 3.791A pdb=" N GLULF 45 " --> pdb=" O GLNLF 41 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLNLF 48 " --> pdb=" O LYSLF 44 " (cutoff:3.500A) Processing helix chain 'LF' and resid 102 through 113 Processing helix chain 'LF' and resid 126 through 137 removed outlier: 4.103A pdb=" N METLF 132 " --> pdb=" O ALALF 128 " (cutoff:3.500A) Processing helix chain 'LF' and resid 146 through 157 Processing helix chain 'LF' and resid 171 through 179 removed outlier: 4.198A pdb=" N ILELF 175 " --> pdb=" O ASPLF 171 " (cutoff:3.500A) Processing helix chain 'LF' and resid 186 through 197 Processing helix chain 'LF' and resid 200 through 209 removed outlier: 5.073A pdb=" N TRPLF 209 " --> pdb=" O ALALF 205 " (cutoff:3.500A) Processing helix chain 'LF' and resid 240 through 249 removed outlier: 3.833A pdb=" N LEULF 244 " --> pdb=" O HISLF 240 " (cutoff:3.500A) Processing helix chain 'LG' and resid 56 through 72 Processing helix chain 'LG' and resid 75 through 83 removed outlier: 5.184A pdb=" N PHELG 81 " --> pdb=" O ALALG 77 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLNLG 82 " --> pdb=" O ILELG 78 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYRLG 83 " --> pdb=" O ALALG 79 " (cutoff:3.500A) Processing helix chain 'LG' and resid 86 through 101 removed outlier: 4.279A pdb=" N LYSLG 99 " --> pdb=" O LYSLG 95 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYRLG 100 " --> pdb=" O LEULG 96 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARGLG 101 " --> pdb=" O LEULG 97 " (cutoff:3.500A) Processing helix chain 'LG' and resid 104 through 122 Processing helix chain 'LG' and resid 124 through 129 removed outlier: 3.812A pdb=" N VALLG 128 " --> pdb=" O LYSLG 124 " (cutoff:3.500A) Processing helix chain 'LG' and resid 138 through 149 Processing helix chain 'LG' and resid 168 through 177 Processing helix chain 'LG' and resid 185 through 194 removed outlier: 3.539A pdb=" N LEULG 192 " --> pdb=" O ARGLG 188 " (cutoff:3.500A) Processing helix chain 'LG' and resid 207 through 230 removed outlier: 4.803A pdb=" N ASNLG 212 " --> pdb=" O SERLG 208 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLULG 213 " --> pdb=" O GLULG 209 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEULG 226 " --> pdb=" O LYSLG 222 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLULG 227 " --> pdb=" O GLULG 223 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LYSLG 228 " --> pdb=" O GLYLG 224 " (cutoff:3.500A) Processing helix chain 'LG' and resid 231 through 236 removed outlier: 4.334A pdb=" N ARGLG 235 " --> pdb=" O ASPLG 231 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N TRPLG 236 " --> pdb=" O THRLG 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'LG' and resid 231 through 236' Processing helix chain 'LG' and resid 242 through 259 Processing helix chain 'LH' and resid 98 through 121 removed outlier: 3.954A pdb=" N LEULH 105 " --> pdb=" O ASPLH 101 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ARGLH 106 " --> pdb=" O VALLH 102 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THRLH 107 " --> pdb=" O ALALH 103 " (cutoff:3.500A) Processing helix chain 'LH' and resid 189 through 205 removed outlier: 3.836A pdb=" N CYSLH 204 " --> pdb=" O ILELH 200 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYSLH 205 " --> pdb=" O GLNLH 201 " (cutoff:3.500A) Processing helix chain 'LH' and resid 210 through 215 removed outlier: 4.786A pdb=" N LEULH 215 " --> pdb=" O ILELH 211 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 28 through 43 Processing helix chain 'LJ' and resid 74 through 89 Processing helix chain 'LJ' and resid 93 through 98 removed outlier: 4.069A pdb=" N PHELJ 97 " --> pdb=" O ARGLJ 93 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N SERLJ 98 " --> pdb=" O ARGLJ 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'LJ' and resid 93 through 98' Processing helix chain 'LJ' and resid 109 through 114 removed outlier: 4.482A pdb=" N LEULJ 113 " --> pdb=" O GLULJ 109 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLYLJ 114 " --> pdb=" O HISLJ 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'LJ' and resid 109 through 114' Processing helix chain 'LJ' and resid 136 through 142 removed outlier: 4.902A pdb=" N ALALJ 140 " --> pdb=" O GLYLJ 136 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYSLJ 141 " --> pdb=" O GLULJ 137 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 150 through 155 removed outlier: 5.806A pdb=" N ILELJ 155 " --> pdb=" O ALALJ 151 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 156 through 168 Processing helix chain 'LK' and resid 23 through 29 removed outlier: 4.763A pdb=" N ALALK 27 " --> pdb=" O GLYLK 23 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEULK 28 " --> pdb=" O ALALK 24 " (cutoff:3.500A) Processing helix chain 'LK' and resid 30 through 36 Proline residue: LK 34 - end of helix No H-bonds generated for 'chain 'LK' and resid 30 through 36' Processing helix chain 'LK' and resid 38 through 51 Processing helix chain 'LK' and resid 76 through 86 removed outlier: 3.880A pdb=" N LYSLK 86 " --> pdb=" O ILELK 82 " (cutoff:3.500A) Processing helix chain 'LK' and resid 105 through 117 Processing helix chain 'LK' and resid 124 through 140 Processing helix chain 'LK' and resid 147 through 158 Processing helix chain 'LL' and resid 17 through 22 removed outlier: 4.432A pdb=" N ARGLL 21 " --> pdb=" O HISLL 17 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VALLL 22 " --> pdb=" O TRPLL 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'LL' and resid 17 through 22' Processing helix chain 'LL' and resid 27 through 47 Processing helix chain 'LL' and resid 76 through 84 Processing helix chain 'LL' and resid 86 through 94 Proline residue: LL 91 - end of helix removed outlier: 3.788A pdb=" N GLYLL 94 " --> pdb=" O ALALL 90 " (cutoff:3.500A) Processing helix chain 'LL' and resid 105 through 123 removed outlier: 3.812A pdb=" N LEULL 109 " --> pdb=" O SERLL 105 " (cutoff:3.500A) Processing helix chain 'LL' and resid 139 through 144 removed outlier: 4.215A pdb=" N THRLL 144 " --> pdb=" O LYSLL 140 " (cutoff:3.500A) Processing helix chain 'LL' and resid 150 through 155 Processing helix chain 'LL' and resid 180 through 195 Processing helix chain 'LL' and resid 196 through 213 Processing helix chain 'LM' and resid 58 through 63 removed outlier: 3.642A pdb=" N ALALM 62 " --> pdb=" O PROLM 58 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEULM 63 " --> pdb=" O LEULM 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'LM' and resid 58 through 63' Processing helix chain 'LM' and resid 77 through 89 Processing helix chain 'LM' and resid 90 through 98 removed outlier: 5.412A pdb=" N ASNLM 98 " --> pdb=" O TRPLM 94 " (cutoff:3.500A) Processing helix chain 'LM' and resid 99 through 112 removed outlier: 3.763A pdb=" N LEULM 112 " --> pdb=" O ARGLM 108 " (cutoff:3.500A) Processing helix chain 'LM' and resid 113 through 140 Processing helix chain 'LN' and resid 2 through 14 removed outlier: 4.449A pdb=" N TYRLN 6 " --> pdb=" O GLYLN 2 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYSLN 13 " --> pdb=" O GLULN 9 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LYSLN 14 " --> pdb=" O LEULN 10 " (cutoff:3.500A) Processing helix chain 'LN' and resid 16 through 34 removed outlier: 4.886A pdb=" N ASNLN 34 " --> pdb=" O TYRLN 30 " (cutoff:3.500A) Processing helix chain 'LN' and resid 44 through 52 Processing helix chain 'LN' and resid 97 through 111 Processing helix chain 'LN' and resid 139 through 146 removed outlier: 3.854A pdb=" N ASPLN 145 " --> pdb=" O ALALN 141 " (cutoff:3.500A) Proline residue: LN 146 - end of helix Processing helix chain 'LN' and resid 148 through 153 removed outlier: 4.529A pdb=" N CYSLN 152 " --> pdb=" O ILELN 148 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASNLN 153 " --> pdb=" O ASNLN 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'LN' and resid 148 through 153' Processing helix chain 'LN' and resid 158 through 163 removed outlier: 3.516A pdb=" N ARGLN 162 " --> pdb=" O HISLN 158 " (cutoff:3.500A) Processing helix chain 'LN' and resid 165 through 173 Processing helix chain 'LN' and resid 186 through 196 Processing helix chain 'LO' and resid 16 through 31 Processing helix chain 'LO' and resid 47 through 61 removed outlier: 3.562A pdb=" N ALALO 51 " --> pdb=" O GLULO 47 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYSLO 61 " --> pdb=" O ALALO 57 " (cutoff:3.500A) Processing helix chain 'LO' and resid 77 through 91 removed outlier: 3.972A pdb=" N METLO 89 " --> pdb=" O ALALO 85 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILELO 90 " --> pdb=" O VALLO 86 " (cutoff:3.500A) Proline residue: LO 91 - end of helix Processing helix chain 'LO' and resid 94 through 105 removed outlier: 3.659A pdb=" N ARGLO 103 " --> pdb=" O ALALO 99 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEULO 104 " --> pdb=" O ALALO 100 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYSLO 105 " --> pdb=" O LEULO 101 " (cutoff:3.500A) Processing helix chain 'LO' and resid 112 through 118 removed outlier: 7.884A pdb=" N LYSLO 116 " --> pdb=" O PROLO 112 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYSLO 117 " --> pdb=" O PROLO 113 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LYSLO 118 " --> pdb=" O TYRLO 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'LO' and resid 112 through 118' Processing helix chain 'LO' and resid 126 through 131 Processing helix chain 'LO' and resid 139 through 148 Processing helix chain 'LO' and resid 153 through 189 removed outlier: 4.308A pdb=" N ALALO 189 " --> pdb=" O LYSLO 185 " (cutoff:3.500A) Processing helix chain 'LO' and resid 192 through 203 Processing helix chain 'LP' and resid 25 through 37 Processing helix chain 'LP' and resid 40 through 54 Processing helix chain 'LP' and resid 72 through 77 removed outlier: 4.877A pdb=" N TRPLP 76 " --> pdb=" O GLNLP 72 " (cutoff:3.500A) Processing helix chain 'LP' and resid 84 through 106 Processing helix chain 'LP' and resid 108 through 113 removed outlier: 3.873A pdb=" N LEULP 112 " --> pdb=" O ASPLP 108 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILELP 113 " --> pdb=" O THRLP 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'LP' and resid 108 through 113' Processing helix chain 'LP' and resid 172 through 185 Processing helix chain 'LQ' and resid 51 through 68 Processing helix chain 'LQ' and resid 70 through 83 removed outlier: 3.915A pdb=" N LYSLQ 74 " --> pdb=" O ALALQ 70 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N METLQ 82 " --> pdb=" O ARGLQ 78 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N SERLQ 83 " --> pdb=" O ARGLQ 79 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 91 through 100 removed outlier: 3.870A pdb=" N LYSLQ 100 " --> pdb=" O ALALQ 96 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 134 through 145 Processing helix chain 'LQ' and resid 150 through 158 Processing helix chain 'LQ' and resid 174 through 180 Processing helix chain 'LR' and resid 4 through 16 Processing helix chain 'LR' and resid 18 through 23 removed outlier: 3.704A pdb=" N VALLR 22 " --> pdb=" O GLYLR 18 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N TRPLR 23 " --> pdb=" O GLULR 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'LR' and resid 18 through 23' Processing helix chain 'LR' and resid 28 through 36 removed outlier: 3.758A pdb=" N ALALR 35 " --> pdb=" O GLULR 31 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ASNLR 36 " --> pdb=" O ILELR 32 " (cutoff:3.500A) Processing helix chain 'LR' and resid 37 through 48 Processing helix chain 'LR' and resid 60 through 73 Processing helix chain 'LR' and resid 77 through 82 removed outlier: 5.792A pdb=" N LYSLR 82 " --> pdb=" O PHELR 78 " (cutoff:3.500A) Processing helix chain 'LR' and resid 84 through 113 Proline residue: LR 90 - end of helix removed outlier: 6.724A pdb=" N VALLR 93 " --> pdb=" O METLR 89 " (cutoff:3.500A) Processing helix chain 'LR' and resid 116 through 130 Processing helix chain 'LR' and resid 134 through 156 Processing helix chain 'LS' and resid 33 through 49 Processing helix chain 'LS' and resid 98 through 114 Processing helix chain 'LS' and resid 117 through 122 removed outlier: 3.728A pdb=" N ILELS 121 " --> pdb=" O ARGLS 117 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N HISLS 122 " --> pdb=" O PHELS 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'LS' and resid 117 through 122' Processing helix chain 'LS' and resid 137 through 145 removed outlier: 4.370A pdb=" N LEULS 143 " --> pdb=" O TYRLS 139 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALALS 145 " --> pdb=" O LYSLS 141 " (cutoff:3.500A) Processing helix chain 'LT' and resid 92 through 97 removed outlier: 3.699A pdb=" N VALLT 96 " --> pdb=" O ARGLT 92 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYSLT 97 " --> pdb=" O ILELT 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'LT' and resid 92 through 97' Processing helix chain 'LT' and resid 102 through 123 Processing helix chain 'LT' and resid 155 through 160 Processing helix chain 'LT' and resid 46 through 51 removed outlier: 4.118A pdb=" N GLNLT 49 " --> pdb=" O GLYLT 46 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLYLT 51 " --> pdb=" O VALLT 48 " (cutoff:3.500A) Processing helix chain 'LU' and resid 25 through 32 Processing helix chain 'LU' and resid 35 through 47 Processing helix chain 'LU' and resid 79 through 95 Processing helix chain 'LV' and resid 68 through 74 removed outlier: 3.787A pdb=" N ARGLV 72 " --> pdb=" O LYSLV 68 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LYSLV 73 " --> pdb=" O PROLV 69 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LYSLV 74 " --> pdb=" O GLULV 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'LV' and resid 68 through 74' Processing helix chain 'LV' and resid 121 through 129 Proline residue: LV 129 - end of helix Processing helix chain 'LV' and resid 130 through 135 Processing helix chain 'LX' and resid 12 through 29 Processing helix chain 'LX' and resid 71 through 77 removed outlier: 4.997A pdb=" N ILELX 77 " --> pdb=" O HISLX 73 " (cutoff:3.500A) Processing helix chain 'LX' and resid 82 through 92 removed outlier: 3.641A pdb=" N GLULX 90 " --> pdb=" O LEULX 86 " (cutoff:3.500A) Processing helix chain 'LX' and resid 104 through 116 Processing helix chain 'LX' and resid 144 through 152 Processing helix chain 'LY' and resid 10 through 21 Processing helix chain 'LY' and resid 22 through 31 removed outlier: 3.585A pdb=" N VALLY 28 " --> pdb=" O SERLY 24 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SERLY 31 " --> pdb=" O ARGLY 27 " (cutoff:3.500A) Processing helix chain 'LY' and resid 35 through 43 Processing helix chain 'LY' and resid 99 through 104 removed outlier: 3.987A pdb=" N VALLY 103 " --> pdb=" O HISLY 99 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N VALLY 104 " --> pdb=" O PROLY 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'LY' and resid 99 through 104' Processing helix chain 'LY' and resid 111 through 133 Processing helix chain 'LZ' and resid 57 through 66 removed outlier: 4.039A pdb=" N LYSLZ 66 " --> pdb=" O GLULZ 62 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 75 through 80 removed outlier: 3.738A pdb=" N LEULZ 79 " --> pdb=" O ASNLZ 75 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N METLZ 80 " --> pdb=" O TYRLZ 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'LZ' and resid 75 through 80' Processing helix chain 'LZ' and resid 96 through 103 removed outlier: 4.264A pdb=" N PHELZ 100 " --> pdb=" O ASNLZ 96 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYSLZ 101 " --> pdb=" O ALALZ 97 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLULZ 102 " --> pdb=" O ASPLZ 98 " (cutoff:3.500A) Proline residue: LZ 103 - end of helix No H-bonds generated for 'chain 'LZ' and resid 96 through 103' Processing helix chain 'LZ' and resid 104 through 124 removed outlier: 3.572A pdb=" N GLYLZ 124 " --> pdb=" O ARGLZ 120 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 126 through 132 removed outlier: 3.657A pdb=" N PHELZ 130 " --> pdb=" O ASNLZ 126 " (cutoff:3.500A) Proline residue: LZ 132 - end of helix Processing helix chain 'La' and resid 6 through 12 removed outlier: 3.880A pdb=" N LYSLa 10 " --> pdb=" O SERLa 6 " (cutoff:3.500A) Processing helix chain 'La' and resid 64 through 69 removed outlier: 4.200A pdb=" N TYRLa 68 " --> pdb=" O LEULa 64 " (cutoff:3.500A) Processing helix chain 'La' and resid 74 through 83 removed outlier: 4.513A pdb=" N TRPLa 79 " --> pdb=" O ILELa 75 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N SERLa 80 " --> pdb=" O ASPLa 76 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEULa 81 " --> pdb=" O LYSLa 77 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VALLa 82 " --> pdb=" O LEULa 78 " (cutoff:3.500A) Proline residue: La 83 - end of helix Processing helix chain 'La' and resid 84 through 93 Processing helix chain 'La' and resid 103 through 108 removed outlier: 3.678A pdb=" N HISLa 107 " --> pdb=" O ASPLa 103 " (cutoff:3.500A) Processing helix chain 'La' and resid 131 through 142 Processing helix chain 'Lc' and resid 12 through 24 Processing helix chain 'Lc' and resid 29 through 40 Processing helix chain 'Lc' and resid 52 through 67 Processing helix chain 'Lc' and resid 76 through 85 Processing helix chain 'Ld' and resid 23 through 29 removed outlier: 3.933A pdb=" N ARGLd 27 " --> pdb=" O HISLd 23 " (cutoff:3.500A) Processing helix chain 'Ld' and resid 35 through 53 Processing helix chain 'Ld' and resid 60 through 69 Processing helix chain 'Le' and resid 22 through 27 removed outlier: 4.976A pdb=" N LYSLe 27 " --> pdb=" O SERLe 23 " (cutoff:3.500A) Processing helix chain 'Le' and resid 41 through 46 Processing helix chain 'Le' and resid 79 through 88 removed outlier: 3.651A pdb=" N LEULe 85 " --> pdb=" O LYSLe 81 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEULe 86 " --> pdb=" O ASPLe 82 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEULe 87 " --> pdb=" O VALLe 83 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N METLe 88 " --> pdb=" O GLULe 84 " (cutoff:3.500A) Processing helix chain 'Le' and resid 102 through 117 Processing helix chain 'Lf' and resid 39 through 47 removed outlier: 4.205A pdb=" N PHELf 45 " --> pdb=" O ALALf 41 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYRLf 46 " --> pdb=" O ALALf 42 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEULf 47 " --> pdb=" O ALALf 43 " (cutoff:3.500A) Processing helix chain 'Lg' and resid 59 through 67 removed outlier: 3.857A pdb=" N TYRLg 63 " --> pdb=" O ARGLg 59 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALALg 64 " --> pdb=" O PROLg 60 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THRLg 65 " --> pdb=" O ARGLg 61 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILELg 66 " --> pdb=" O GLULg 62 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N SERLg 67 " --> pdb=" O TYRLg 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'Lg' and resid 59 through 67' Processing helix chain 'Lg' and resid 82 through 119 Processing helix chain 'Lh' and resid 8 through 16 removed outlier: 3.523A pdb=" N LEULh 12 " --> pdb=" O LYSLh 8 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SERLh 14 " --> pdb=" O GLYLh 10 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYSLh 15 " --> pdb=" O GLNLh 11 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ASNLh 16 " --> pdb=" O LEULh 12 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 17 through 41 removed outlier: 3.749A pdb=" N ILELh 36 " --> pdb=" O SERLh 32 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 44 through 76 removed outlier: 3.868A pdb=" N LYSLh 48 " --> pdb=" O ALALh 44 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 82 through 87 Proline residue: Lh 87 - end of helix Processing helix chain 'Lh' and resid 90 through 96 Processing helix chain 'Lh' and resid 98 through 104 Processing helix chain 'Lh' and resid 106 through 116 Processing helix chain 'Li' and resid 34 through 39 removed outlier: 4.011A pdb=" N ARGLi 38 " --> pdb=" O ARGLi 34 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LYSLi 39 " --> pdb=" O PROLi 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'Li' and resid 34 through 39' Processing helix chain 'Li' and resid 43 through 58 Processing helix chain 'Li' and resid 60 through 73 Processing helix chain 'Li' and resid 74 through 87 Processing helix chain 'Li' and resid 88 through 110 Processing helix chain 'Lj' and resid 4 through 11 removed outlier: 3.643A pdb=" N GLYLj 9 " --> pdb=" O THRLj 5 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYSLj 10 " --> pdb=" O SERLj 6 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ARGLj 11 " --> pdb=" O SERLj 7 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 50 through 58 removed outlier: 3.718A pdb=" N LYSLj 57 " --> pdb=" O ALALj 53 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 65 through 77 removed outlier: 5.544A pdb=" N THRLj 69 " --> pdb=" O ARGLj 65 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VALLj 70 " --> pdb=" O TYRLj 66 " (cutoff:3.500A) Proline residue: Lj 71 - end of helix Processing helix chain 'Lk' and resid 7 through 17 Processing helix chain 'Lk' and resid 52 through 63 removed outlier: 4.660A pdb=" N LYSLk 59 " --> pdb=" O ALALk 55 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLNLk 60 " --> pdb=" O GLULk 56 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SERLk 61 " --> pdb=" O LYSLk 57 " (cutoff:3.500A) Proline residue: Lk 63 - end of helix Processing helix chain 'Ll' and resid 6 through 21 removed outlier: 5.459A pdb=" N ARGLl 21 " --> pdb=" O GLNLl 17 " (cutoff:3.500A) Processing helix chain 'Ll' and resid 24 through 30 removed outlier: 4.513A pdb=" N ARGLl 28 " --> pdb=" O PROLl 24 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEULl 29 " --> pdb=" O GLNLl 25 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARGLl 30 " --> pdb=" O TRPLl 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ll' and resid 24 through 30' Processing helix chain 'Lp' and resid 19 through 35 removed outlier: 3.886A pdb=" N LYSLp 28 " --> pdb=" O LYSLp 24 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLNLp 29 " --> pdb=" O LEULp 25 " (cutoff:3.500A) Processing helix chain 'Lp' and resid 73 through 92 Processing helix chain 'Lp' and resid 9 through 14 removed outlier: 3.911A pdb=" N LYSLp 13 " --> pdb=" O ILELp 10 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 5 through 14 Processing helix chain 'Lq' and resid 44 through 49 removed outlier: 5.434A pdb=" N ASPLq 49 " --> pdb=" O GLYLq 45 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 86 through 99 Processing helix chain 'Lq' and resid 104 through 124 removed outlier: 4.032A pdb=" N ARGLq 108 " --> pdb=" O ARGLq 104 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N GLNLq 109 " --> pdb=" O ALALq 105 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ALALq 110 " --> pdb=" O ASPLq 106 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARGLq 123 " --> pdb=" O LEULq 119 " (cutoff:3.500A) Proline residue: Lq 124 - end of helix Processing helix chain 'Lq' and resid 135 through 140 removed outlier: 5.071A pdb=" N ARGLq 139 " --> pdb=" O GLYLq 135 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'CB' and resid 80 through 83 Processing sheet with id= 2, first strand: chain 'CB' and resid 97 through 101 Processing sheet with id= 3, first strand: chain 'CB' and resid 239 through 245 removed outlier: 5.548A pdb=" N THRCB 239 " --> pdb=" O THRCB 68 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILECB 62 " --> pdb=" O VALCB 245 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHECB 281 " --> pdb=" O ILECB 293 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'CF' and resid 63 through 67 removed outlier: 6.861A pdb=" N VALCF 42 " --> pdb=" O LEUCF 224 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'CF' and resid 135 through 139 removed outlier: 6.738A pdb=" N VALCF 135 " --> pdb=" O ILECF 194 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N GLUCF 190 " --> pdb=" O PROCF 139 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'CF' and resid 232 through 236 Processing sheet with id= 7, first strand: chain 'CF' and resid 38 through 42 removed outlier: 8.340A pdb=" N GLNCF 38 " --> pdb=" O SERCF 229 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLYCF 225 " --> pdb=" O VALCF 42 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'CH' and resid 203 through 209 removed outlier: 4.842A pdb=" N ARGCH 167 " --> pdb=" O ARGCH 214 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THRCH 220 " --> pdb=" O VALCH 171 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLYCH 173 " --> pdb=" O THRCH 220 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLYCH 222 " --> pdb=" O GLYCH 173 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHECH 174 " --> pdb=" O PHECH 252 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ASPCH 254 " --> pdb=" O PHECH 174 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N METCH 281 " --> pdb=" O ALACH 247 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'CI' and resid 214 through 219 removed outlier: 4.946A pdb=" N ARGCI 230 " --> pdb=" O VALCI 219 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VALCI 188 " --> pdb=" O VALCI 263 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'CJ' and resid 186 through 191 removed outlier: 3.887A pdb=" N GLYCJ 194 " --> pdb=" O SERCJ 191 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'CJ' and resid 394 through 398 Processing sheet with id= 12, first strand: chain 'CK' and resid 148 through 151 Processing sheet with id= 13, first strand: chain 'CK' and resid 190 through 195 removed outlier: 3.705A pdb=" N VALCK 191 " --> pdb=" O HISCK 186 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASNCK 256 " --> pdb=" O THRCK 246 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N TYRCK 242 " --> pdb=" O LEUCK 260 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N THRCK 219 " --> pdb=" O ILECK 245 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'CM' and resid 139 through 144 removed outlier: 5.393A pdb=" N TRPCM 139 " --> pdb=" O ILECM 95 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYSCM 88 " --> pdb=" O VALCM 125 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASNCM 119 " --> pdb=" O ARGCM 94 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ASNCM 118 " --> pdb=" O LEUCM 213 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'CN' and resid 1 through 4 Processing sheet with id= 16, first strand: chain 'CN' and resid 23 through 27 Processing sheet with id= 17, first strand: chain 'CN' and resid 69 through 73 Processing sheet with id= 18, first strand: chain 'CN' and resid 114 through 117 Processing sheet with id= 19, first strand: chain 'CN' and resid 158 through 161 Processing sheet with id= 20, first strand: chain 'CQ' and resid 3 through 6 removed outlier: 4.678A pdb=" N ARGCQ 11 " --> pdb=" O CYSCQ 6 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'CQ' and resid 18 through 23 removed outlier: 3.658A pdb=" N LYSCQ 27 " --> pdb=" O ARGCQ 23 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'Cb' and resid 50 through 53 removed outlier: 4.471A pdb=" N TYRCb 50 " --> pdb=" O PHECb 59 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'Cd' and resid 293 through 297 removed outlier: 3.890A pdb=" N CYSCd 378 " --> pdb=" O LEUCd 331 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLYCd 333 " --> pdb=" O CYSCd 378 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILECd 373 " --> pdb=" O LEUCd 369 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VALCd 363 " --> pdb=" O PROCd 379 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'Cf' and resid 56 through 60 removed outlier: 5.675A pdb=" N ARGCf 34 " --> pdb=" O PHECf 60 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SERCf 92 " --> pdb=" O GLYCf 35 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N HISCf 98 " --> pdb=" O LEUCf 118 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N LEUCf 111 " --> pdb=" O PROCf 263 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARGCf 259 " --> pdb=" O GLUCf 115 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'Cf' and resid 140 through 146 removed outlier: 6.785A pdb=" N VALCf 229 " --> pdb=" O HISCf 249 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'Cf' and resid 287 through 290 removed outlier: 4.849A pdb=" N ASPCf 294 " --> pdb=" O ASPCf 290 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'Cg' and resid 21 through 25 Processing sheet with id= 28, first strand: chain 'Cg' and resid 71 through 75 removed outlier: 4.396A pdb=" N THRCg 71 " --> pdb=" O THRCg 82 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'Cg' and resid 124 through 129 removed outlier: 8.723A pdb=" N ASNCg 124 " --> pdb=" O LYSCg 137 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYSCg 137 " --> pdb=" O ASNCg 124 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'Ch' and resid 52 through 56 removed outlier: 4.128A pdb=" N THRCh 121 " --> pdb=" O HISCh 88 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEUCh 94 " --> pdb=" O ILECh 89 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'Ch' and resid 139 through 143 removed outlier: 5.227A pdb=" N ALACh 511 " --> pdb=" O GLYCh 507 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLYCh 507 " --> pdb=" O ALACh 511 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEUCh 502 " --> pdb=" O ALACh 497 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Ch' and resid 151 through 155 removed outlier: 6.308A pdb=" N ARGCh 161 " --> pdb=" O SERCh 155 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SERCh 160 " --> pdb=" O THRCh 176 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THRCh 170 " --> pdb=" O SERCh 166 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILECh 173 " --> pdb=" O LYSCh 182 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Ch' and resid 193 through 198 removed outlier: 5.680A pdb=" N TYRCh 203 " --> pdb=" O SERCh 198 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THRCh 212 " --> pdb=" O SERCh 208 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VALCh 215 " --> pdb=" O VALCh 224 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYSCh 222 " --> pdb=" O ASPCh 217 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'Ch' and resid 236 through 241 removed outlier: 5.877A pdb=" N ARGCh 252 " --> pdb=" O GLNCh 241 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALACh 251 " --> pdb=" O VALCh 267 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THRCh 261 " --> pdb=" O SERCh 257 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILECh 264 " --> pdb=" O GLUCh 273 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARGCh 271 " --> pdb=" O LEUCh 266 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'Ch' and resid 284 through 288 removed outlier: 3.569A pdb=" N CYSCh 285 " --> pdb=" O GLYCh 297 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N ASPCh 292 " --> pdb=" O ALACh 308 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SERCh 302 " --> pdb=" O SERCh 298 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VALCh 305 " --> pdb=" O VALCh 314 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THRCh 312 " --> pdb=" O ASPCh 307 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'Ch' and resid 326 through 330 removed outlier: 6.647A pdb=" N ARGCh 374 " --> pdb=" O SERCh 330 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THRCh 383 " --> pdb=" O SERCh 379 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'Ch' and resid 408 through 413 removed outlier: 5.770A pdb=" N LEUCh 418 " --> pdb=" O SERCh 413 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SERCh 427 " --> pdb=" O GLYCh 423 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYSCh 440 " --> pdb=" O LEUCh 430 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'Ch' and resid 450 through 455 removed outlier: 5.806A pdb=" N LEUCh 460 " --> pdb=" O SERCh 455 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THRCh 469 " --> pdb=" O SERCh 465 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'Ch' and resid 170 through 173 removed outlier: 3.572A pdb=" N PHECh 183 " --> pdb=" O ILECh 173 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'Ch' and resid 261 through 264 removed outlier: 3.808A pdb=" N HISCh 274 " --> pdb=" O ILECh 264 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'Ch' and resid 302 through 305 Processing sheet with id= 42, first strand: chain 'LA' and resid 47 through 50 removed outlier: 3.624A pdb=" N GLULA 47 " --> pdb=" O ARGLA 60 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARGLA 60 " --> pdb=" O LYSLA 46 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLNLA 86 " --> pdb=" O VALLA 45 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'LA' and resid 134 through 137 removed outlier: 6.589A pdb=" N ARGLA 147 " --> pdb=" O VALLA 137 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'LA' and resid 58 through 64 No H-bonds generated for sheet with id= 44 Processing sheet with id= 45, first strand: chain 'LA' and resid 145 through 150 removed outlier: 4.251A pdb=" N ALALA 154 " --> pdb=" O LEULA 150 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'LB' and resid 41 through 44 removed outlier: 6.449A pdb=" N GLNLB 183 " --> pdb=" O THRLB 44 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N HISLB 178 " --> pdb=" O THRLB 165 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N VALLB 159 " --> pdb=" O ILELB 184 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARGLB 160 " --> pdb=" O LEULB 89 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEULB 89 " --> pdb=" O ARGLB 160 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEULB 162 " --> pdb=" O VALLB 87 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLYLB 91 " --> pdb=" O LEULB 102 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'LB' and resid 53 through 58 removed outlier: 6.860A pdb=" N ILELB 78 " --> pdb=" O ALALB 51 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARGLB 335 " --> pdb=" O LYSLB 50 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILELB 336 " --> pdb=" O VALLB 221 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N VALLB 221 " --> pdb=" O ILELB 336 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N HISLB 274 " --> pdb=" O THRLB 222 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'LB' and resid 285 through 289 removed outlier: 3.641A pdb=" N ARGLB 285 " --> pdb=" O METLB 324 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLYLB 289 " --> pdb=" O ASNLB 320 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ASNLB 320 " --> pdb=" O GLYLB 289 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'LB' and resid 76 through 80 Processing sheet with id= 50, first strand: chain 'LB' and resid 87 through 91 removed outlier: 7.982A pdb=" N VALLB 87 " --> pdb=" O ALALB 107 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THRLB 103 " --> pdb=" O GLYLB 91 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'LB' and resid 84 through 87 removed outlier: 3.800A pdb=" N LYSLB 202 " --> pdb=" O VALLB 86 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'LB' and resid 214 through 217 removed outlier: 4.312A pdb=" N GLULB 214 " --> pdb=" O ILELB 283 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'LC' and resid 5 through 9 removed outlier: 4.814A pdb=" N ALALC 19 " --> pdb=" O VALLC 9 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'LC' and resid 231 through 235 removed outlier: 5.414A pdb=" N PHELC 254 " --> pdb=" O GLYLC 208 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'LD' and resid 60 through 66 Processing sheet with id= 56, first strand: chain 'LE' and resid 5 through 9 Processing sheet with id= 57, first strand: chain 'LE' and resid 56 through 61 removed outlier: 4.075A pdb=" N THRLE 56 " --> pdb=" O LEULE 72 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYSLE 68 " --> pdb=" O LEULE 60 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'LF' and resid 139 through 144 removed outlier: 7.580A pdb=" N TRPLF 139 " --> pdb=" O ILELF 95 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LYSLF 88 " --> pdb=" O VALLF 125 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASNLF 119 " --> pdb=" O ARGLF 94 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASNLF 118 " --> pdb=" O LEULF 213 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'LF' and resid 158 through 161 removed outlier: 6.477A pdb=" N GLYLF 158 " --> pdb=" O LEULF 169 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'LG' and resid 179 through 184 Processing sheet with id= 61, first strand: chain 'LH' and resid 5 through 12 removed outlier: 5.697A pdb=" N GLYLH 88 " --> pdb=" O VALLH 12 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'LH' and resid 54 through 57 Processing sheet with id= 63, first strand: chain 'LH' and resid 137 through 144 removed outlier: 4.070A pdb=" N CYSLH 148 " --> pdb=" O ASNLH 143 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N TYRLH 149 " --> pdb=" O METLH 167 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'LH' and resid 171 through 176 removed outlier: 5.484A pdb=" N GLULH 182 " --> pdb=" O SERLH 176 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASPLH 181 " --> pdb=" O TYRLH 129 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'LJ' and resid 46 through 50 removed outlier: 7.824A pdb=" N ILELJ 66 " --> pdb=" O VALLJ 24 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYSLJ 17 " --> pdb=" O CYSLJ 131 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N SERLJ 23 " --> pdb=" O GLYLJ 125 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N GLYLJ 125 " --> pdb=" O SERLJ 23 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'LK' and resid 11 through 16 removed outlier: 4.318A pdb=" N THRLK 59 " --> pdb=" O VALLK 74 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'LL' and resid 56 through 59 Processing sheet with id= 68, first strand: chain 'LM' and resid 18 through 21 removed outlier: 4.781A pdb=" N ARGLM 18 " --> pdb=" O ILELM 30 " (cutoff:3.500A) removed outlier: 9.624A pdb=" N LEULM 27 " --> pdb=" O PROLM 44 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEULM 40 " --> pdb=" O VALLM 31 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N SERLM 45 " --> pdb=" O LEULM 50 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEULM 50 " --> pdb=" O SERLM 45 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'LM' and resid 39 through 42 Processing sheet with id= 70, first strand: chain 'LN' and resid 35 through 39 removed outlier: 6.332A pdb=" N VALLN 35 " --> pdb=" O ARGLN 65 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILELN 61 " --> pdb=" O ALALN 39 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLYLN 58 " --> pdb=" O ASPLN 136 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THRLN 126 " --> pdb=" O ARGLN 68 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILELN 133 " --> pdb=" O LEULN 116 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'LN' and resid 117 through 121 removed outlier: 3.707A pdb=" N ASNLN 117 " --> pdb=" O ILELN 133 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TYRLN 129 " --> pdb=" O VALLN 121 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'LO' and resid 7 through 11 Processing sheet with id= 73, first strand: chain 'LP' and resid 14 through 20 Processing sheet with id= 74, first strand: chain 'LP' and resid 57 through 60 removed outlier: 5.406A pdb=" N ARGLP 80 " --> pdb=" O METLP 60 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'LP' and resid 124 through 131 removed outlier: 4.052A pdb=" N ARGLP 127 " --> pdb=" O TYRLP 139 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARGLP 135 " --> pdb=" O ARGLP 131 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'LQ' and resid 106 through 110 Processing sheet with id= 77, first strand: chain 'LQ' and resid 126 through 129 Processing sheet with id= 78, first strand: chain 'LS' and resid 24 through 30 removed outlier: 6.641A pdb=" N ILELS 10 " --> pdb=" O VALLS 59 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N THRLS 55 " --> pdb=" O LEULS 14 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'LS' and resid 86 through 96 removed outlier: 5.213A pdb=" N ASNLS 74 " --> pdb=" O LEULS 129 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'LS' and resid 6 through 10 removed outlier: 4.497A pdb=" N GLULS 6 " --> pdb=" O ILELS 64 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'LT' and resid 40 through 43 removed outlier: 3.852A pdb=" N LYSLT 60 " --> pdb=" O ILELT 42 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'LT' and resid 72 through 79 Processing sheet with id= 83, first strand: chain 'LU' and resid 60 through 64 removed outlier: 5.578A pdb=" N GLYLU 108 " --> pdb=" O LYSLU 20 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'LV' and resid 23 through 26 removed outlier: 4.503A pdb=" N ALALV 23 " --> pdb=" O ILELV 38 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'LV' and resid 58 through 62 removed outlier: 4.334A pdb=" N ASPLV 58 " --> pdb=" O ILELV 80 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASPLV 99 " --> pdb=" O ALALV 84 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALALV 84 " --> pdb=" O ASPLV 99 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'LV' and resid 86 through 89 removed outlier: 3.906A pdb=" N VALLV 93 " --> pdb=" O ARGLV 89 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'LX' and resid 93 through 99 removed outlier: 6.579A pdb=" N ASNLX 93 " --> pdb=" O LEULX 139 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYSLX 133 " --> pdb=" O VALLX 99 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THRLX 132 " --> pdb=" O ARGLX 128 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYSLX 122 " --> pdb=" O ARGLX 138 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'LY' and resid 55 through 58 removed outlier: 4.122A pdb=" N LYSLY 65 " --> pdb=" O ILELY 57 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'LY' and resid 85 through 88 removed outlier: 4.422A pdb=" N GLNLY 92 " --> pdb=" O LYSLY 88 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'LZ' and resid 8 through 13 removed outlier: 4.546A pdb=" N ARGLZ 8 " --> pdb=" O ILELZ 24 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYSLZ 20 " --> pdb=" O VALLZ 12 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'LZ' and resid 41 through 44 Processing sheet with id= 92, first strand: chain 'La' and resid 99 through 102 Processing sheet with id= 93, first strand: chain 'Lc' and resid 25 through 28 removed outlier: 6.097A pdb=" N LYSLc 25 " --> pdb=" O LEULc 96 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'Ld' and resid 56 through 59 removed outlier: 4.954A pdb=" N ASPLd 56 " --> pdb=" O LEULd 97 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ALALd 17 " --> pdb=" O VALLd 117 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'Le' and resid 72 through 78 Processing sheet with id= 96, first strand: chain 'Lf' and resid 12 through 17 removed outlier: 6.058A pdb=" N LYSLf 12 " --> pdb=" O GLULf 35 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEULf 31 " --> pdb=" O LEULf 16 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARGLf 84 " --> pdb=" O THRLf 74 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LYSLf 65 " --> pdb=" O ALALf 57 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LYSLf 49 " --> pdb=" O ILELf 73 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ARGLf 50 " --> pdb=" O METLf 103 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'Lf' and resid 10 through 16 removed outlier: 4.091A pdb=" N ALALf 98 " --> pdb=" O HISLf 15 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'Lg' and resid 20 through 25 removed outlier: 4.399A pdb=" N ARGLg 20 " --> pdb=" O ILELg 36 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'Lk' and resid 2 through 5 removed outlier: 4.464A pdb=" N VALLk 48 " --> pdb=" O VALLk 5 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SERLk 22 " --> pdb=" O ARGLk 39 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LYSLk 27 " --> pdb=" O VALLk 71 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'Lp' and resid 46 through 50 removed outlier: 8.040A pdb=" N SERLp 46 " --> pdb=" O LYSLp 58 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILELp 54 " --> pdb=" O THRLp 50 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLYLp 53 " --> pdb=" O GLYLp 66 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYSLp 62 " --> pdb=" O CYSLp 57 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'Lq' and resid 19 through 22 removed outlier: 6.884A pdb=" N PHELq 19 " --> pdb=" O ARGLq 30 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'Lq' and resid 51 through 57 removed outlier: 5.218A pdb=" N ALALq 51 " --> pdb=" O LYSLq 66 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLYLq 60 " --> pdb=" O ALALq 57 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N SERLq 77 " --> pdb=" O LYSLq 67 " (cutoff:3.500A) 3737 hydrogen bonds defined for protein. 11106 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2731 hydrogen bonds 4562 hydrogen bond angles 0 basepair planarities 1078 basepair parallelities 1922 stacking parallelities Total time for adding SS restraints: 209.21 Time building geometry restraints manager: 64.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 21648 1.33 - 1.45: 62009 1.45 - 1.57: 76556 1.57 - 1.69: 6886 1.69 - 1.82: 421 Bond restraints: 167520 Sorted by residual: bond pdb=" C3' A2MC1 858 " pdb=" C2' A2MC1 858 " ideal model delta sigma weight residual 1.544 1.240 0.304 2.00e-02 2.50e+03 2.31e+02 bond pdb=" C3' A2MC1 637 " pdb=" C2' A2MC1 637 " ideal model delta sigma weight residual 1.544 1.241 0.303 2.00e-02 2.50e+03 2.30e+02 bond pdb=" C2' A2MC1 389 " pdb=" C1' A2MC1 389 " ideal model delta sigma weight residual 1.305 1.608 -0.303 2.00e-02 2.50e+03 2.30e+02 bond pdb=" C3' A2MC12289 " pdb=" C2' A2MC12289 " ideal model delta sigma weight residual 1.544 1.241 0.303 2.00e-02 2.50e+03 2.29e+02 bond pdb=" C3' A2MC11432 " pdb=" C2' A2MC11432 " ideal model delta sigma weight residual 1.544 1.242 0.302 2.00e-02 2.50e+03 2.29e+02 ... (remaining 167515 not shown) Histogram of bond angle deviations from ideal: 93.60 - 103.94: 11565 103.94 - 114.29: 113839 114.29 - 124.63: 102339 124.63 - 134.98: 15081 134.98 - 145.33: 11 Bond angle restraints: 242835 Sorted by residual: angle pdb=" C1' OMGC1 385 " pdb=" N9 OMGC1 385 " pdb=" C4 OMGC1 385 " ideal model delta sigma weight residual 108.29 128.95 -20.66 3.00e+00 1.11e-01 4.74e+01 angle pdb=" C1' OMGC11433 " pdb=" N9 OMGC11433 " pdb=" C4 OMGC11433 " ideal model delta sigma weight residual 108.29 128.35 -20.06 3.00e+00 1.11e-01 4.47e+01 angle pdb=" C1' OMGC12881 " pdb=" N9 OMGC12881 " pdb=" C4 OMGC12881 " ideal model delta sigma weight residual 108.29 127.60 -19.31 3.00e+00 1.11e-01 4.14e+01 angle pdb=" C1' OMGC12578 " pdb=" N9 OMGC12578 " pdb=" C4 OMGC12578 " ideal model delta sigma weight residual 108.29 127.42 -19.13 3.00e+00 1.11e-01 4.07e+01 angle pdb=" C1' A2MC12289 " pdb=" N9 A2MC12289 " pdb=" C8 A2MC12289 " ideal model delta sigma weight residual 88.50 107.62 -19.12 3.00e+00 1.11e-01 4.06e+01 ... (remaining 242830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 97160 35.99 - 71.98: 8176 71.98 - 107.97: 968 107.97 - 143.96: 19 143.96 - 179.95: 36 Dihedral angle restraints: 106359 sinusoidal: 75921 harmonic: 30438 Sorted by residual: dihedral pdb=" O4' CC1 961 " pdb=" C1' CC1 961 " pdb=" N1 CC1 961 " pdb=" C2 CC1 961 " ideal model delta sinusoidal sigma weight residual 200.00 27.02 172.98 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' CC13338 " pdb=" C1' CC13338 " pdb=" N1 CC13338 " pdb=" C2 CC13338 " ideal model delta sinusoidal sigma weight residual 200.00 38.35 161.65 1 1.50e+01 4.44e-03 8.32e+01 dihedral pdb=" O4' UC12100 " pdb=" C1' UC12100 " pdb=" N1 UC12100 " pdb=" C2 UC12100 " ideal model delta sinusoidal sigma weight residual 200.00 39.79 160.21 1 1.50e+01 4.44e-03 8.28e+01 ... (remaining 106356 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 26865 0.068 - 0.136: 2564 0.136 - 0.204: 187 0.204 - 0.271: 32 0.271 - 0.339: 8 Chirality restraints: 29656 Sorted by residual: chirality pdb=" CB ILELH 157 " pdb=" CA ILELH 157 " pdb=" CG1 ILELH 157 " pdb=" CG2 ILELH 157 " both_signs ideal model delta sigma weight residual False 2.64 2.98 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C3' UC11537 " pdb=" C4' UC11537 " pdb=" O3' UC11537 " pdb=" C2' UC11537 " both_signs ideal model delta sigma weight residual False -2.74 -2.41 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C3' CC12160 " pdb=" C4' CC12160 " pdb=" O3' CC12160 " pdb=" C2' CC12160 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 29653 not shown) Planarity restraints: 18143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMGC12578 " 0.071 2.00e-02 2.50e+03 5.95e-01 7.97e+03 pdb=" C4' OMGC12578 " 0.430 2.00e-02 2.50e+03 pdb=" O4' OMGC12578 " 0.602 2.00e-02 2.50e+03 pdb=" C3' OMGC12578 " -0.599 2.00e-02 2.50e+03 pdb=" O3' OMGC12578 " -0.644 2.00e-02 2.50e+03 pdb=" C2' OMGC12578 " -0.171 2.00e-02 2.50e+03 pdb=" O2' OMGC12578 " 0.986 2.00e-02 2.50e+03 pdb=" C1' OMGC12578 " 0.225 2.00e-02 2.50e+03 pdb=" N9 OMGC12578 " -0.901 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMCC11420 " -0.028 2.00e-02 2.50e+03 5.92e-01 7.88e+03 pdb=" C4' OMCC11420 " -0.451 2.00e-02 2.50e+03 pdb=" O4' OMCC11420 " -0.740 2.00e-02 2.50e+03 pdb=" C3' OMCC11420 " 0.595 2.00e-02 2.50e+03 pdb=" O3' OMCC11420 " 0.576 2.00e-02 2.50e+03 pdb=" C2' OMCC11420 " 0.236 2.00e-02 2.50e+03 pdb=" O2' OMCC11420 " -0.896 2.00e-02 2.50e+03 pdb=" C1' OMCC11420 " -0.195 2.00e-02 2.50e+03 pdb=" N1 OMCC11420 " 0.904 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMGC12774 " -0.048 2.00e-02 2.50e+03 5.78e-01 7.53e+03 pdb=" C4' OMGC12774 " -0.433 2.00e-02 2.50e+03 pdb=" O4' OMGC12774 " -0.618 2.00e-02 2.50e+03 pdb=" C3' OMGC12774 " 0.594 2.00e-02 2.50e+03 pdb=" O3' OMGC12774 " 0.595 2.00e-02 2.50e+03 pdb=" C2' OMGC12774 " 0.197 2.00e-02 2.50e+03 pdb=" O2' OMGC12774 " -0.937 2.00e-02 2.50e+03 pdb=" C1' OMGC12774 " -0.226 2.00e-02 2.50e+03 pdb=" N9 OMGC12774 " 0.875 2.00e-02 2.50e+03 ... (remaining 18140 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 3087 2.65 - 3.21: 124810 3.21 - 3.77: 301146 3.77 - 4.34: 410251 4.34 - 4.90: 571214 Nonbonded interactions: 1410508 Sorted by model distance: nonbonded pdb=" OG SERCd 340 " pdb="MG MGCd1002 " model vdw 2.081 2.170 nonbonded pdb=" O2G GTPCd1000 " pdb="MG MGCd1002 " model vdw 2.106 2.170 nonbonded pdb=" O1B GTPCd1000 " pdb="MG MGCd1002 " model vdw 2.124 2.170 nonbonded pdb="MG MGCd1002 " pdb=" O HOHCd1102 " model vdw 2.136 2.170 nonbonded pdb=" OG1 THRCI 214 " pdb=" OE1 GLUCI 234 " model vdw 2.179 2.440 ... (remaining 1410503 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 'CM' selection = (chain 'LF' and (resid 13 through 35 or resid 49 through 79 or resid 87 through \ 249)) } 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=0.21 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: 8.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 29.250 Check model and map are aligned: 1.800 Set scattering table: 1.070 Process input model: 551.040 Find NCS groups from input model: 4.070 Set up NCS constraints: 0.470 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: 0.030 Load rotamer database and sin/cos tables:9.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 605.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 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 : 0.006 0.304 167520 Z= 0.347 Angle : 0.727 20.662 242835 Z= 0.369 Chirality : 0.040 0.339 29656 Planarity : 0.019 0.595 18143 Dihedral : 21.033 179.955 86655 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.57 % Favored : 98.42 % Rotamer: Outliers : 0.02 % Allowed : 0.09 % Favored : 99.89 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.08), residues: 10359 helix: 0.71 (0.08), residues: 4033 sheet: 0.20 (0.13), residues: 1501 loop : -0.02 (0.08), residues: 4825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRPLD 95 HIS 0.011 0.001 HISCN 118 PHE 0.033 0.002 PHECI 198 TYR 0.037 0.002 TYRLN 81 ARG 0.015 0.001 ARGCN 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20718 Ramachandran restraints generated. 10359 Oldfield, 0 Emsley, 10359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20718 Ramachandran restraints generated. 10359 Oldfield, 0 Emsley, 10359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1382 residues out of total 8939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1381 time to evaluate : 9.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CI 234 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7003 (tm-30) REVERT: Cd 441 MET cc_start: 0.8862 (mtp) cc_final: 0.8638 (mtp) REVERT: Cz 66 ARG cc_start: 0.7761 (ttm110) cc_final: 0.7552 (ttp80) REVERT: LB 381 MET cc_start: 0.8252 (mmm) cc_final: 0.8037 (mmm) REVERT: LE 178 MET cc_start: 0.9009 (mtt) cc_final: 0.8673 (mtt) REVERT: LH 127 MET cc_start: 0.8920 (mtp) cc_final: 0.8598 (mtm) REVERT: LK 52 ASP cc_start: 0.6959 (t0) cc_final: 0.6427 (t0) REVERT: LN 103 GLU cc_start: 0.8227 (mt-10) cc_final: 0.8018 (mt-10) REVERT: LU 55 ASN cc_start: 0.7917 (t0) cc_final: 0.7619 (t0) REVERT: LX 147 ASP cc_start: 0.7697 (m-30) cc_final: 0.7496 (m-30) REVERT: La 87 ARG cc_start: 0.8953 (ttm170) cc_final: 0.8716 (ttm170) REVERT: Le 10 ILE cc_start: 0.9125 (mt) cc_final: 0.8911 (mt) REVERT: Li 47 GLN cc_start: 0.8030 (mt0) cc_final: 0.7673 (mt0) outliers start: 1 outliers final: 4 residues processed: 1381 average time/residue: 2.7149 time to fit residues: 5257.5630 Evaluate side-chains 1116 residues out of total 8939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1112 time to evaluate : 9.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CH residue 455 ASP Chi-restraints excluded: chain CJ residue 410 GLU Chi-restraints excluded: chain LD residue 261 ASP Chi-restraints excluded: chain Lk residue 70 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 1155 optimal weight: 5.9990 chunk 1036 optimal weight: 2.9990 chunk 575 optimal weight: 7.9990 chunk 354 optimal weight: 8.9990 chunk 699 optimal weight: 0.9980 chunk 553 optimal weight: 7.9990 chunk 1072 optimal weight: 8.9990 chunk 414 optimal weight: 7.9990 chunk 651 optimal weight: 7.9990 chunk 798 optimal weight: 0.0470 chunk 1242 optimal weight: 0.2980 overall best weight: 2.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CB 71 HIS CF 29 ASN ** CH 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CH 345 GLN CH 362 GLN CH 399 ASN CH 536 GLN CI 267 GLN CJ 79 GLN CK 143 HIS CK 190 ASN ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 101 ASN Ce 401 ASN Cf 128 GLN Cg 31 ASN Cg 128 ASN ** Ch 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 139 HIS LC 315 GLN LC 322 ASN LE 53 GLN LF 25 GLN LF 48 GLN LF 77 GLN LF 78 GLN LF 110 GLN LG 194 HIS LJ 16 GLN LL 17 HIS LM 98 ASN LM 110 GLN LN 86 ASN LP 170 HIS LQ 98 ASN LQ 101 ASN LR 34 ASN LS 13 HIS LV 134 ASN LX 19 GLN LX 110 GLN LX 124 ASN LY 116 ASN LY 127 GLN LZ 105 GLN Ld 49 GLN Lf 58 GLN Li 47 GLN Lk 65 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 167520 Z= 0.238 Angle : 0.663 17.904 242835 Z= 0.351 Chirality : 0.038 0.273 29656 Planarity : 0.006 0.135 18143 Dihedral : 22.728 179.973 65152 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.34 % Favored : 98.65 % Rotamer: Outliers : 1.37 % Allowed : 7.40 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 1.03 (0.08), residues: 10359 helix: 1.55 (0.08), residues: 4042 sheet: 0.16 (0.13), residues: 1546 loop : 0.23 (0.09), residues: 4771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPCg 105 HIS 0.007 0.001 HISCd 252 PHE 0.021 0.002 PHELC 121 TYR 0.018 0.002 TYRLq 16 ARG 0.011 0.001 ARGCd 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20718 Ramachandran restraints generated. 10359 Oldfield, 0 Emsley, 10359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20718 Ramachandran restraints generated. 10359 Oldfield, 0 Emsley, 10359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1266 residues out of total 8939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1146 time to evaluate : 9.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CI 239 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6713 (pm20) REVERT: CI 288 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.6341 (mpt) REVERT: CJ 227 MET cc_start: 0.8519 (mmp) cc_final: 0.8129 (mmp) REVERT: CK 31 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.7087 (tm-30) REVERT: Cf 87 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8054 (mtt) REVERT: Ch 370 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.8031 (mppt) REVERT: Cz 66 ARG cc_start: 0.7770 (ttm110) cc_final: 0.7489 (ttp80) REVERT: LB 381 MET cc_start: 0.8284 (mmm) cc_final: 0.8044 (mmm) REVERT: LF 223 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7230 (mtp-110) REVERT: LM 15 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8099 (pt0) REVERT: LO 185 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7862 (ttmt) REVERT: LP 180 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8729 (mp) REVERT: LS 5 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7864 (mt0) REVERT: LU 55 ASN cc_start: 0.8019 (t0) cc_final: 0.7631 (t0) REVERT: La 135 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8407 (tt0) REVERT: Lc 67 LYS cc_start: 0.8450 (mptp) cc_final: 0.8243 (mtmt) REVERT: Ld 70 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8111 (mt0) REVERT: Le 10 ILE cc_start: 0.9146 (mt) cc_final: 0.8935 (mt) REVERT: Lf 4 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7135 (mm-30) REVERT: Lh 33 GLN cc_start: 0.7269 (OUTLIER) cc_final: 0.6749 (mp10) outliers start: 120 outliers final: 49 residues processed: 1188 average time/residue: 2.5419 time to fit residues: 4220.4848 Evaluate side-chains 1147 residues out of total 8939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1084 time to evaluate : 9.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 255 LEU Chi-restraints excluded: chain CB residue 288 THR Chi-restraints excluded: chain CH residue 143 LYS Chi-restraints excluded: chain CH residue 309 THR Chi-restraints excluded: chain CH residue 323 THR Chi-restraints excluded: chain CH residue 372 THR Chi-restraints excluded: chain CH residue 455 ASP Chi-restraints excluded: chain CI residue 227 SER Chi-restraints excluded: chain CI residue 239 GLU Chi-restraints excluded: chain CI residue 288 MET Chi-restraints excluded: chain CI residue 310 GLU Chi-restraints excluded: chain CI residue 323 MET Chi-restraints excluded: chain CJ residue 475 LEU Chi-restraints excluded: chain CK residue 12 LYS Chi-restraints excluded: chain CK residue 31 GLU Chi-restraints excluded: chain CK residue 40 GLN Chi-restraints excluded: chain CK residue 66 LYS Chi-restraints excluded: chain CL residue 35 GLU Chi-restraints excluded: chain CN residue 91 ASP Chi-restraints excluded: chain CN residue 167 ILE Chi-restraints excluded: chain CO residue 40 ILE Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cd residue 169 GLU Chi-restraints excluded: chain Cf residue 87 MET Chi-restraints excluded: chain Cf residue 153 VAL Chi-restraints excluded: chain Ch residue 37 PHE Chi-restraints excluded: chain Ch residue 370 LYS Chi-restraints excluded: chain LB residue 103 THR Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 334 SER Chi-restraints excluded: chain LD residue 137 THR Chi-restraints excluded: chain LD residue 227 VAL Chi-restraints excluded: chain LE residue 106 SER Chi-restraints excluded: chain LE residue 165 ILE Chi-restraints excluded: chain LF residue 24 SER Chi-restraints excluded: chain LF residue 181 LYS Chi-restraints excluded: chain LF residue 223 ARG Chi-restraints excluded: chain LJ residue 49 SER Chi-restraints excluded: chain LK residue 87 GLU Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LM residue 15 GLU Chi-restraints excluded: chain LO residue 185 LYS Chi-restraints excluded: chain LP residue 180 ILE Chi-restraints excluded: chain LQ residue 32 ILE Chi-restraints excluded: chain LQ residue 113 THR Chi-restraints excluded: chain LR residue 86 ASP Chi-restraints excluded: chain LS residue 5 GLN Chi-restraints excluded: chain LT residue 111 GLU Chi-restraints excluded: chain LU residue 103 VAL Chi-restraints excluded: chain LX residue 37 THR Chi-restraints excluded: chain LX residue 83 GLU Chi-restraints excluded: chain LX residue 143 VAL Chi-restraints excluded: chain LZ residue 28 VAL Chi-restraints excluded: chain La residue 135 GLU Chi-restraints excluded: chain Lc residue 97 ASP Chi-restraints excluded: chain Ld residue 70 GLN Chi-restraints excluded: chain Lf residue 4 GLU Chi-restraints excluded: chain Lg residue 102 VAL Chi-restraints excluded: chain Lh residue 33 GLN Chi-restraints excluded: chain Lj residue 6 SER Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 52 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 690 optimal weight: 9.9990 chunk 385 optimal weight: 9.9990 chunk 1033 optimal weight: 4.9990 chunk 845 optimal weight: 3.9990 chunk 342 optimal weight: 6.9990 chunk 1244 optimal weight: 0.9990 chunk 1344 optimal weight: 7.9990 chunk 1108 optimal weight: 6.9990 chunk 1234 optimal weight: 4.9990 chunk 424 optimal weight: 7.9990 chunk 998 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CH 362 GLN CH 399 ASN CI 267 GLN ** CI 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 481 GLN CK 41 ASN ** CK 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CK 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CK 67 GLN CK 190 ASN ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ce 199 ASN Ce 216 ASN Ce 327 GLN Ce 401 ASN Cf 128 GLN Cg 31 ASN ** Ch 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ch 517 ASN LA 205 ASN LC 322 ASN LE 53 GLN LG 194 HIS LJ 16 GLN LL 17 HIS LM 98 ASN LN 86 ASN LQ 43 HIS LQ 98 ASN LQ 101 ASN LS 13 HIS LV 134 ASN LX 110 GLN LX 124 ASN LY 116 ASN LY 127 GLN La 62 HIS Ld 49 GLN Lf 58 GLN Li 47 GLN Lk 65 ASN Ll 17 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.127 167520 Z= 0.450 Angle : 0.780 18.410 242835 Z= 0.403 Chirality : 0.046 0.306 29656 Planarity : 0.008 0.148 18143 Dihedral : 22.788 179.235 65145 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.66 % Favored : 98.33 % Rotamer: Outliers : 1.94 % Allowed : 8.74 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.08), residues: 10359 helix: 1.50 (0.08), residues: 4059 sheet: 0.09 (0.13), residues: 1514 loop : 0.20 (0.09), residues: 4786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRPCd 364 HIS 0.013 0.002 HISLR 125 PHE 0.022 0.002 PHELC 121 TYR 0.027 0.003 TYRLO 55 ARG 0.013 0.001 ARGCh 271 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20718 Ramachandran restraints generated. 10359 Oldfield, 0 Emsley, 10359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20718 Ramachandran restraints generated. 10359 Oldfield, 0 Emsley, 10359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1278 residues out of total 8939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1108 time to evaluate : 9.153 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: CF 10 TYR cc_start: 0.8534 (t80) cc_final: 0.8277 (t80) REVERT: CH 360 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7166 (ttp80) REVERT: CH 405 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.7806 (ptp-110) REVERT: CK 31 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7149 (tm-30) REVERT: Ch 370 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8068 (mppt) REVERT: Cz 86 ARG cc_start: 0.7490 (ttm110) cc_final: 0.7137 (ttm-80) REVERT: LB 317 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7132 (mt-10) REVERT: LB 381 MET cc_start: 0.8394 (mmm) cc_final: 0.8109 (mmm) REVERT: LF 223 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7261 (mtp-110) REVERT: LL 108 SER cc_start: 0.8477 (p) cc_final: 0.8250 (p) REVERT: LM 5 ASN cc_start: 0.8466 (m110) cc_final: 0.8246 (m110) REVERT: LN 20 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7541 (ttp80) REVERT: LO 171 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: LO 185 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7936 (mtmt) REVERT: LP 180 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8845 (mp) REVERT: LS 5 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7996 (mt0) REVERT: LU 55 ASN cc_start: 0.8082 (t0) cc_final: 0.7726 (t0) REVERT: LU 61 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7984 (mtpt) REVERT: LZ 80 MET cc_start: 0.8834 (tpt) cc_final: 0.8627 (tpt) REVERT: La 146 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7261 (mt-10) REVERT: Ld 70 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8043 (mt0) REVERT: Le 10 ILE cc_start: 0.9162 (mt) cc_final: 0.8946 (mt) REVERT: Lf 4 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7259 (mm-30) REVERT: Lg 88 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7400 (t0) REVERT: Lh 33 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.6829 (mp10) outliers start: 170 outliers final: 74 residues processed: 1165 average time/residue: 2.5418 time to fit residues: 4142.4112 Evaluate side-chains 1160 residues out of total 8939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1069 time to evaluate : 9.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 255 LEU Chi-restraints excluded: chain CH residue 78 ARG Chi-restraints excluded: chain CH residue 143 LYS Chi-restraints excluded: chain CH residue 297 LEU Chi-restraints excluded: chain CH residue 309 THR Chi-restraints excluded: chain CH residue 323 THR Chi-restraints excluded: chain CH residue 360 ARG Chi-restraints excluded: chain CH residue 372 THR Chi-restraints excluded: chain CH residue 405 ARG Chi-restraints excluded: chain CH residue 453 ASP Chi-restraints excluded: chain CH residue 455 ASP Chi-restraints excluded: chain CH residue 615 LYS Chi-restraints excluded: chain CI residue 227 SER Chi-restraints excluded: chain CI residue 263 VAL Chi-restraints excluded: chain CI residue 310 GLU Chi-restraints excluded: chain CI residue 311 GLN Chi-restraints excluded: chain CK residue 12 LYS Chi-restraints excluded: chain CK residue 31 GLU Chi-restraints excluded: chain CK residue 66 LYS Chi-restraints excluded: chain CN residue 91 ASP Chi-restraints excluded: chain CN residue 167 ILE Chi-restraints excluded: chain Cb residue 38 THR Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cd residue 86 ASP Chi-restraints excluded: chain Cd residue 95 MET Chi-restraints excluded: chain Cd residue 169 GLU Chi-restraints excluded: chain Cd residue 323 ASP Chi-restraints excluded: chain Ce residue 187 LYS Chi-restraints excluded: chain Ce residue 387 ASP Chi-restraints excluded: chain Cf residue 105 MET Chi-restraints excluded: chain Cf residue 153 VAL Chi-restraints excluded: chain Ch residue 370 LYS Chi-restraints excluded: chain LA residue 97 THR Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LB residue 103 THR Chi-restraints excluded: chain LB residue 317 GLU Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 266 ASP Chi-restraints excluded: chain LC residue 334 SER Chi-restraints excluded: chain LD residue 66 THR Chi-restraints excluded: chain LD residue 137 THR Chi-restraints excluded: chain LD residue 227 VAL Chi-restraints excluded: chain LD residue 237 ASP Chi-restraints excluded: chain LE residue 106 SER Chi-restraints excluded: chain LF residue 24 SER Chi-restraints excluded: chain LF residue 181 LYS Chi-restraints excluded: chain LF residue 223 ARG Chi-restraints excluded: chain LJ residue 71 THR Chi-restraints excluded: chain LJ residue 127 ASP Chi-restraints excluded: chain LJ residue 139 VAL Chi-restraints excluded: chain LK residue 87 GLU Chi-restraints excluded: chain LL residue 141 ASP Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LM residue 52 THR Chi-restraints excluded: chain LM residue 96 GLU Chi-restraints excluded: chain LN residue 20 ARG Chi-restraints excluded: chain LO residue 171 GLU Chi-restraints excluded: chain LO residue 185 LYS Chi-restraints excluded: chain LP residue 169 SER Chi-restraints excluded: chain LP residue 180 ILE Chi-restraints excluded: chain LQ residue 32 ILE Chi-restraints excluded: chain LQ residue 113 THR Chi-restraints excluded: chain LR residue 86 ASP Chi-restraints excluded: chain LS residue 1 MET Chi-restraints excluded: chain LS residue 5 GLN Chi-restraints excluded: chain LT residue 140 THR Chi-restraints excluded: chain LU residue 61 LYS Chi-restraints excluded: chain LU residue 103 VAL Chi-restraints excluded: chain LV residue 137 VAL Chi-restraints excluded: chain LX residue 37 THR Chi-restraints excluded: chain LX residue 83 GLU Chi-restraints excluded: chain LX residue 119 ASP Chi-restraints excluded: chain LX residue 143 VAL Chi-restraints excluded: chain LZ residue 28 VAL Chi-restraints excluded: chain LZ residue 85 THR Chi-restraints excluded: chain LZ residue 108 GLU Chi-restraints excluded: chain La residue 75 ILE Chi-restraints excluded: chain La residue 146 GLU Chi-restraints excluded: chain Lc residue 82 THR Chi-restraints excluded: chain Lc residue 97 ASP Chi-restraints excluded: chain Ld residue 70 GLN Chi-restraints excluded: chain Ld residue 115 SER Chi-restraints excluded: chain Lf residue 4 GLU Chi-restraints excluded: chain Lg residue 88 ASP Chi-restraints excluded: chain Lg residue 102 VAL Chi-restraints excluded: chain Lh residue 33 GLN Chi-restraints excluded: chain Lh residue 49 ILE Chi-restraints excluded: chain Lj residue 6 SER Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 52 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 1229 optimal weight: 2.9990 chunk 935 optimal weight: 1.9990 chunk 645 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 593 optimal weight: 3.9990 chunk 835 optimal weight: 6.9990 chunk 1248 optimal weight: 2.9990 chunk 1322 optimal weight: 9.9990 chunk 652 optimal weight: 0.9980 chunk 1183 optimal weight: 0.0670 chunk 356 optimal weight: 9.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CH 345 GLN CH 362 GLN CH 399 ASN CI 221 ASN ** CI 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 481 GLN ** CK 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CK 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CK 190 ASN CM 163 ASN CO 42 GLN ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 101 ASN Ce 199 ASN Ce 327 GLN Ce 401 ASN Cf 128 GLN Cg 31 ASN Ch 47 ASN Ch 56 ASN LB 379 GLN LC 322 ASN LE 53 GLN LG 62 GLN LH 72 GLN LJ 16 GLN LL 17 HIS LM 98 ASN LN 86 ASN LQ 98 ASN LQ 101 ASN LS 13 HIS LV 134 ASN LX 92 GLN LX 110 GLN LX 124 ASN LY 116 ASN Ld 49 GLN Ld 108 ASN Lf 58 GLN Li 47 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 167520 Z= 0.202 Angle : 0.637 17.434 242835 Z= 0.341 Chirality : 0.037 0.287 29656 Planarity : 0.006 0.131 18143 Dihedral : 22.700 179.564 65145 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.38 % Favored : 98.61 % Rotamer: Outliers : 1.70 % Allowed : 9.95 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 1.28 (0.08), residues: 10359 helix: 1.85 (0.08), residues: 4056 sheet: 0.11 (0.13), residues: 1516 loop : 0.34 (0.09), residues: 4787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPCg 105 HIS 0.007 0.001 HISCd 252 PHE 0.019 0.001 PHECh 37 TYR 0.017 0.001 TYRLO 55 ARG 0.011 0.000 ARGCh 271 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20718 Ramachandran restraints generated. 10359 Oldfield, 0 Emsley, 10359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20718 Ramachandran restraints generated. 10359 Oldfield, 0 Emsley, 10359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1258 residues out of total 8939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1109 time to evaluate : 9.314 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: CF 10 TYR cc_start: 0.8437 (t80) cc_final: 0.8237 (t80) REVERT: CH 405 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.7768 (ptp-110) REVERT: CQ 95 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8275 (tpt-90) REVERT: Ce 187 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7416 (mttt) REVERT: LB 180 MET cc_start: 0.8873 (ptm) cc_final: 0.8637 (ptp) REVERT: LB 381 MET cc_start: 0.8335 (mmm) cc_final: 0.8098 (mmm) REVERT: LD 212 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: LF 223 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7268 (mtp-110) REVERT: LG 100 TYR cc_start: 0.8946 (m-80) cc_final: 0.8616 (m-80) REVERT: LH 216 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7858 (m-30) REVERT: LL 108 SER cc_start: 0.8454 (p) cc_final: 0.8229 (p) REVERT: LN 20 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7434 (ttp80) REVERT: LO 171 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: LO 185 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7748 (ttmt) REVERT: LP 180 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8780 (mp) REVERT: LS 5 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7930 (mt0) REVERT: LU 61 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8009 (mtpt) REVERT: La 135 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8379 (tt0) REVERT: Le 10 ILE cc_start: 0.9139 (mt) cc_final: 0.8937 (mt) REVERT: Le 104 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7505 (ptm-80) REVERT: Lf 4 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7255 (mm-30) REVERT: Lh 33 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.6782 (mp10) outliers start: 149 outliers final: 62 residues processed: 1169 average time/residue: 2.5975 time to fit residues: 4254.0669 Evaluate side-chains 1147 residues out of total 8939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1069 time to evaluate : 9.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 255 LEU Chi-restraints excluded: chain CB residue 288 THR Chi-restraints excluded: chain CH residue 78 ARG Chi-restraints excluded: chain CH residue 143 LYS Chi-restraints excluded: chain CH residue 309 THR Chi-restraints excluded: chain CH residue 323 THR Chi-restraints excluded: chain CH residue 389 ASN Chi-restraints excluded: chain CH residue 405 ARG Chi-restraints excluded: chain CH residue 455 ASP Chi-restraints excluded: chain CH residue 615 LYS Chi-restraints excluded: chain CI residue 227 SER Chi-restraints excluded: chain CI residue 263 VAL Chi-restraints excluded: chain CI residue 311 GLN Chi-restraints excluded: chain CI residue 323 MET Chi-restraints excluded: chain CK residue 12 LYS Chi-restraints excluded: chain CK residue 40 GLN Chi-restraints excluded: chain CK residue 66 LYS Chi-restraints excluded: chain CN residue 75 THR Chi-restraints excluded: chain CN residue 91 ASP Chi-restraints excluded: chain CQ residue 95 ARG Chi-restraints excluded: chain Cb residue 38 THR Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cd residue 86 ASP Chi-restraints excluded: chain Cd residue 95 MET Chi-restraints excluded: chain Cd residue 119 ASP Chi-restraints excluded: chain Ce residue 187 LYS Chi-restraints excluded: chain Ce residue 387 ASP Chi-restraints excluded: chain Cf residue 105 MET Chi-restraints excluded: chain Cf residue 153 VAL Chi-restraints excluded: chain Cg residue 160 GLU Chi-restraints excluded: chain LB residue 47 MET Chi-restraints excluded: chain LB residue 103 THR Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 334 SER Chi-restraints excluded: chain LD residue 195 THR Chi-restraints excluded: chain LD residue 212 GLU Chi-restraints excluded: chain LD residue 227 VAL Chi-restraints excluded: chain LF residue 24 SER Chi-restraints excluded: chain LF residue 223 ARG Chi-restraints excluded: chain LG residue 208 SER Chi-restraints excluded: chain LG residue 246 GLN Chi-restraints excluded: chain LH residue 216 ASP Chi-restraints excluded: chain LJ residue 139 VAL Chi-restraints excluded: chain LL residue 135 LYS Chi-restraints excluded: chain LL residue 141 ASP Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LN residue 20 ARG Chi-restraints excluded: chain LO residue 171 GLU Chi-restraints excluded: chain LO residue 185 LYS Chi-restraints excluded: chain LO residue 197 GLU Chi-restraints excluded: chain LP residue 180 ILE Chi-restraints excluded: chain LQ residue 32 ILE Chi-restraints excluded: chain LQ residue 113 THR Chi-restraints excluded: chain LR residue 86 ASP Chi-restraints excluded: chain LS residue 1 MET Chi-restraints excluded: chain LS residue 5 GLN Chi-restraints excluded: chain LT residue 111 GLU Chi-restraints excluded: chain LT residue 140 THR Chi-restraints excluded: chain LU residue 61 LYS Chi-restraints excluded: chain LU residue 103 VAL Chi-restraints excluded: chain LX residue 83 GLU Chi-restraints excluded: chain LX residue 119 ASP Chi-restraints excluded: chain LX residue 143 VAL Chi-restraints excluded: chain LY residue 130 LYS Chi-restraints excluded: chain LZ residue 28 VAL Chi-restraints excluded: chain LZ residue 102 GLU Chi-restraints excluded: chain La residue 75 ILE Chi-restraints excluded: chain La residue 86 VAL Chi-restraints excluded: chain La residue 135 GLU Chi-restraints excluded: chain Le residue 104 ARG Chi-restraints excluded: chain Lf residue 4 GLU Chi-restraints excluded: chain Lg residue 33 VAL Chi-restraints excluded: chain Lh residue 33 GLN Chi-restraints excluded: chain Lh residue 49 ILE Chi-restraints excluded: chain Lj residue 6 SER Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 70 ASP Chi-restraints excluded: chain Lp residue 52 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 1101 optimal weight: 0.9980 chunk 750 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 984 optimal weight: 6.9990 chunk 545 optimal weight: 7.9990 chunk 1128 optimal weight: 7.9990 chunk 914 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 675 optimal weight: 9.9990 chunk 1186 optimal weight: 0.0570 chunk 333 optimal weight: 8.9990 overall best weight: 3.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CB 90 ASN CH 362 GLN CH 399 ASN CI 221 ASN ** CI 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 481 GLN ** CK 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CK 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CK 67 GLN CK 190 ASN CM 163 ASN CO 42 GLN ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ce 401 ASN Cf 128 GLN Cg 31 ASN LC 322 ASN LE 53 GLN LG 62 GLN LH 72 GLN LJ 16 GLN LL 17 HIS LM 5 ASN LM 98 ASN LN 86 ASN LQ 98 ASN LQ 101 ASN LS 13 HIS LU 55 ASN LX 92 GLN LX 110 GLN LX 124 ASN LY 116 ASN Ld 49 GLN Ld 108 ASN Lf 58 GLN Lh 11 GLN Li 47 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 167520 Z= 0.360 Angle : 0.714 17.592 242835 Z= 0.374 Chirality : 0.042 0.295 29656 Planarity : 0.007 0.142 18143 Dihedral : 22.714 179.996 65145 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.65 % Favored : 98.34 % Rotamer: Outliers : 1.93 % Allowed : 10.51 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 1.19 (0.08), residues: 10359 helix: 1.77 (0.08), residues: 4057 sheet: 0.09 (0.13), residues: 1514 loop : 0.30 (0.09), residues: 4788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPLM 85 HIS 0.011 0.001 HISLB 244 PHE 0.018 0.002 PHELd 47 TYR 0.024 0.002 TYRLO 55 ARG 0.012 0.001 ARGCh 271 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20718 Ramachandran restraints generated. 10359 Oldfield, 0 Emsley, 10359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20718 Ramachandran restraints generated. 10359 Oldfield, 0 Emsley, 10359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1264 residues out of total 8939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1095 time to evaluate : 9.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CF 10 TYR cc_start: 0.8481 (t80) cc_final: 0.8275 (t80) REVERT: CH 405 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.7783 (ptp-110) REVERT: CI 234 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7205 (tm-30) REVERT: CJ 227 MET cc_start: 0.8544 (mmp) cc_final: 0.8300 (mmp) REVERT: CK 31 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7141 (tm-30) REVERT: CL 73 ARG cc_start: 0.7709 (ttm-80) cc_final: 0.7358 (ttm170) REVERT: CQ 95 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8273 (tpt-90) REVERT: Ce 187 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7648 (mttt) REVERT: Cz 76 ARG cc_start: 0.7644 (ttt-90) cc_final: 0.7338 (ttt180) REVERT: LB 34 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8281 (ttmt) REVERT: LB 180 MET cc_start: 0.8886 (ptm) cc_final: 0.8647 (ptp) REVERT: LB 317 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7102 (mt-10) REVERT: LD 212 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: LF 223 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7287 (mtp-110) REVERT: LH 216 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8085 (m-30) REVERT: LL 108 SER cc_start: 0.8516 (p) cc_final: 0.8288 (p) REVERT: LN 20 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7486 (ttp80) REVERT: LO 171 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: LO 185 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7814 (mtmt) REVERT: LP 180 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8826 (mp) REVERT: LS 5 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8013 (mt0) REVERT: LU 55 ASN cc_start: 0.8052 (t0) cc_final: 0.7821 (t0) REVERT: LU 61 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7997 (mtpt) REVERT: La 58 MET cc_start: 0.8788 (mtm) cc_final: 0.8371 (mtm) REVERT: La 135 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8354 (tt0) REVERT: Ld 70 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7233 (mp10) REVERT: Le 104 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7528 (ptm-80) REVERT: Lf 4 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7263 (mm-30) REVERT: Lh 33 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.6755 (mp10) outliers start: 169 outliers final: 96 residues processed: 1165 average time/residue: 2.5552 time to fit residues: 4183.5104 Evaluate side-chains 1190 residues out of total 8939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1073 time to evaluate : 9.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 255 LEU Chi-restraints excluded: chain CB residue 288 THR Chi-restraints excluded: chain CH residue 143 LYS Chi-restraints excluded: chain CH residue 228 LEU Chi-restraints excluded: chain CH residue 297 LEU Chi-restraints excluded: chain CH residue 309 THR Chi-restraints excluded: chain CH residue 323 THR Chi-restraints excluded: chain CH residue 372 THR Chi-restraints excluded: chain CH residue 389 ASN Chi-restraints excluded: chain CH residue 405 ARG Chi-restraints excluded: chain CH residue 453 ASP Chi-restraints excluded: chain CH residue 455 ASP Chi-restraints excluded: chain CH residue 615 LYS Chi-restraints excluded: chain CH residue 622 LEU Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CI residue 227 SER Chi-restraints excluded: chain CI residue 234 GLU Chi-restraints excluded: chain CI residue 263 VAL Chi-restraints excluded: chain CI residue 311 GLN Chi-restraints excluded: chain CJ residue 475 LEU Chi-restraints excluded: chain CK residue 12 LYS Chi-restraints excluded: chain CK residue 31 GLU Chi-restraints excluded: chain CK residue 40 GLN Chi-restraints excluded: chain CK residue 66 LYS Chi-restraints excluded: chain CL residue 35 GLU Chi-restraints excluded: chain CN residue 75 THR Chi-restraints excluded: chain CN residue 91 ASP Chi-restraints excluded: chain CQ residue 95 ARG Chi-restraints excluded: chain Cb residue 38 THR Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cd residue 86 ASP Chi-restraints excluded: chain Cd residue 95 MET Chi-restraints excluded: chain Cd residue 323 ASP Chi-restraints excluded: chain Ce residue 187 LYS Chi-restraints excluded: chain Ce residue 387 ASP Chi-restraints excluded: chain Cf residue 105 MET Chi-restraints excluded: chain Cf residue 153 VAL Chi-restraints excluded: chain Cf residue 239 THR Chi-restraints excluded: chain Cg residue 11 LEU Chi-restraints excluded: chain Cg residue 71 THR Chi-restraints excluded: chain Ch residue 426 ASN Chi-restraints excluded: chain LA residue 96 LEU Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LB residue 34 LYS Chi-restraints excluded: chain LB residue 103 THR Chi-restraints excluded: chain LB residue 217 ASP Chi-restraints excluded: chain LB residue 303 LYS Chi-restraints excluded: chain LB residue 317 GLU Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 266 ASP Chi-restraints excluded: chain LC residue 334 SER Chi-restraints excluded: chain LD residue 66 THR Chi-restraints excluded: chain LD residue 195 THR Chi-restraints excluded: chain LD residue 212 GLU Chi-restraints excluded: chain LD residue 227 VAL Chi-restraints excluded: chain LE residue 106 SER Chi-restraints excluded: chain LF residue 24 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LF residue 181 LYS Chi-restraints excluded: chain LF residue 223 ARG Chi-restraints excluded: chain LG residue 208 SER Chi-restraints excluded: chain LG residue 246 GLN Chi-restraints excluded: chain LH residue 216 ASP Chi-restraints excluded: chain LJ residue 127 ASP Chi-restraints excluded: chain LJ residue 139 VAL Chi-restraints excluded: chain LL residue 141 ASP Chi-restraints excluded: chain LL residue 190 SER Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LM residue 52 THR Chi-restraints excluded: chain LM residue 96 GLU Chi-restraints excluded: chain LN residue 20 ARG Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LO residue 139 THR Chi-restraints excluded: chain LO residue 171 GLU Chi-restraints excluded: chain LO residue 185 LYS Chi-restraints excluded: chain LO residue 197 GLU Chi-restraints excluded: chain LP residue 169 SER Chi-restraints excluded: chain LP residue 180 ILE Chi-restraints excluded: chain LQ residue 32 ILE Chi-restraints excluded: chain LQ residue 113 THR Chi-restraints excluded: chain LR residue 30 SER Chi-restraints excluded: chain LR residue 86 ASP Chi-restraints excluded: chain LS residue 1 MET Chi-restraints excluded: chain LS residue 5 GLN Chi-restraints excluded: chain LS residue 119 ARG Chi-restraints excluded: chain LT residue 111 GLU Chi-restraints excluded: chain LT residue 140 THR Chi-restraints excluded: chain LT residue 151 LEU Chi-restraints excluded: chain LU residue 61 LYS Chi-restraints excluded: chain LU residue 103 VAL Chi-restraints excluded: chain LV residue 137 VAL Chi-restraints excluded: chain LX residue 37 THR Chi-restraints excluded: chain LX residue 83 GLU Chi-restraints excluded: chain LX residue 119 ASP Chi-restraints excluded: chain LX residue 143 VAL Chi-restraints excluded: chain LY residue 130 LYS Chi-restraints excluded: chain LZ residue 28 VAL Chi-restraints excluded: chain LZ residue 102 GLU Chi-restraints excluded: chain LZ residue 108 GLU Chi-restraints excluded: chain La residue 75 ILE Chi-restraints excluded: chain La residue 86 VAL Chi-restraints excluded: chain La residue 135 GLU Chi-restraints excluded: chain Ld residue 70 GLN Chi-restraints excluded: chain Ld residue 115 SER Chi-restraints excluded: chain Le residue 104 ARG Chi-restraints excluded: chain Lf residue 4 GLU Chi-restraints excluded: chain Lg residue 33 VAL Chi-restraints excluded: chain Lg residue 102 VAL Chi-restraints excluded: chain Lh residue 30 GLU Chi-restraints excluded: chain Lh residue 33 GLN Chi-restraints excluded: chain Lh residue 49 ILE Chi-restraints excluded: chain Lj residue 6 SER Chi-restraints excluded: chain Lj residue 65 ARG Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 54 LYS Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 52 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 444 optimal weight: 1.9990 chunk 1190 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 776 optimal weight: 0.8980 chunk 326 optimal weight: 20.0000 chunk 1323 optimal weight: 3.9990 chunk 1098 optimal weight: 1.9990 chunk 612 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 437 optimal weight: 0.4980 chunk 694 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CH 362 GLN CH 399 ASN CI 221 ASN ** CI 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 481 GLN CK 190 ASN CM 163 ASN CO 42 GLN ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 101 ASN Ce 401 ASN Cf 128 GLN Cg 31 ASN LC 322 ASN LE 53 GLN LG 62 GLN LH 72 GLN LJ 16 GLN LL 17 HIS LM 98 ASN LN 86 ASN LQ 98 ASN LQ 101 ASN LS 13 HIS LX 92 GLN LX 110 GLN LX 124 ASN LY 116 ASN LY 127 GLN Ld 49 GLN Ld 108 ASN Lf 58 GLN Li 47 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 167520 Z= 0.169 Angle : 0.633 17.074 242835 Z= 0.340 Chirality : 0.037 0.282 29656 Planarity : 0.006 0.128 18143 Dihedral : 22.708 179.656 65145 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.43 % Favored : 98.56 % Rotamer: Outliers : 1.84 % Allowed : 11.14 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 1.39 (0.08), residues: 10359 helix: 1.97 (0.08), residues: 4054 sheet: 0.12 (0.13), residues: 1489 loop : 0.39 (0.09), residues: 4816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPCg 105 HIS 0.013 0.001 HISLB 244 PHE 0.015 0.001 PHECQ 107 TYR 0.017 0.001 TYRCH 474 ARG 0.012 0.000 ARGCz 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20718 Ramachandran restraints generated. 10359 Oldfield, 0 Emsley, 10359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20718 Ramachandran restraints generated. 10359 Oldfield, 0 Emsley, 10359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1249 residues out of total 8939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1088 time to evaluate : 9.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CH 405 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.7840 (ptp-110) REVERT: CK 31 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7075 (tm-30) REVERT: CL 73 ARG cc_start: 0.7697 (ttm-80) cc_final: 0.7370 (ttm170) REVERT: CM 25 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7878 (mt0) REVERT: CM 115 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7128 (mtt90) REVERT: CQ 95 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8246 (tpt-90) REVERT: Ce 187 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7383 (mttt) REVERT: LB 34 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8271 (ttmt) REVERT: LB 180 MET cc_start: 0.8873 (ptm) cc_final: 0.8639 (ptp) REVERT: LB 317 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7103 (mt-10) REVERT: LD 212 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: LF 223 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7293 (mtp-110) REVERT: LL 108 SER cc_start: 0.8462 (p) cc_final: 0.8239 (p) REVERT: LM 3 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7231 (tm-30) REVERT: LN 20 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7420 (ttp80) REVERT: LO 171 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7574 (mp0) REVERT: LO 185 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7782 (mtmt) REVERT: LP 180 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8767 (mp) REVERT: LS 5 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7959 (mt0) REVERT: LU 61 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8032 (mtpt) REVERT: LZ 1 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7923 (pmm) REVERT: La 58 MET cc_start: 0.8735 (mtm) cc_final: 0.8364 (mtm) REVERT: La 135 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8350 (tt0) REVERT: Ld 70 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7155 (mp10) REVERT: Lf 4 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7238 (mm-30) REVERT: Lh 33 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6729 (mp10) outliers start: 161 outliers final: 81 residues processed: 1163 average time/residue: 2.5484 time to fit residues: 4164.8508 Evaluate side-chains 1165 residues out of total 8939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1063 time to evaluate : 9.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 255 LEU Chi-restraints excluded: chain CB residue 288 THR Chi-restraints excluded: chain CH residue 143 LYS Chi-restraints excluded: chain CH residue 297 LEU Chi-restraints excluded: chain CH residue 309 THR Chi-restraints excluded: chain CH residue 323 THR Chi-restraints excluded: chain CH residue 405 ARG Chi-restraints excluded: chain CH residue 453 ASP Chi-restraints excluded: chain CH residue 455 ASP Chi-restraints excluded: chain CH residue 615 LYS Chi-restraints excluded: chain CH residue 622 LEU Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CI residue 227 SER Chi-restraints excluded: chain CI residue 263 VAL Chi-restraints excluded: chain CI residue 311 GLN Chi-restraints excluded: chain CI residue 323 MET Chi-restraints excluded: chain CJ residue 235 MET Chi-restraints excluded: chain CJ residue 475 LEU Chi-restraints excluded: chain CK residue 12 LYS Chi-restraints excluded: chain CK residue 31 GLU Chi-restraints excluded: chain CK residue 40 GLN Chi-restraints excluded: chain CK residue 66 LYS Chi-restraints excluded: chain CM residue 25 GLN Chi-restraints excluded: chain CM residue 115 ARG Chi-restraints excluded: chain CN residue 75 THR Chi-restraints excluded: chain CN residue 91 ASP Chi-restraints excluded: chain CO residue 40 ILE Chi-restraints excluded: chain CQ residue 95 ARG Chi-restraints excluded: chain Cb residue 38 THR Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cd residue 86 ASP Chi-restraints excluded: chain Cd residue 95 MET Chi-restraints excluded: chain Cd residue 119 ASP Chi-restraints excluded: chain Ce residue 187 LYS Chi-restraints excluded: chain Ce residue 387 ASP Chi-restraints excluded: chain Cf residue 105 MET Chi-restraints excluded: chain Cf residue 153 VAL Chi-restraints excluded: chain Cf residue 239 THR Chi-restraints excluded: chain Ch residue 426 ASN Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LB residue 34 LYS Chi-restraints excluded: chain LB residue 103 THR Chi-restraints excluded: chain LB residue 197 ARG Chi-restraints excluded: chain LB residue 317 GLU Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 266 ASP Chi-restraints excluded: chain LD residue 66 THR Chi-restraints excluded: chain LD residue 195 THR Chi-restraints excluded: chain LD residue 212 GLU Chi-restraints excluded: chain LD residue 227 VAL Chi-restraints excluded: chain LE residue 106 SER Chi-restraints excluded: chain LF residue 24 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LF residue 223 ARG Chi-restraints excluded: chain LG residue 208 SER Chi-restraints excluded: chain LG residue 246 GLN Chi-restraints excluded: chain LJ residue 127 ASP Chi-restraints excluded: chain LJ residue 139 VAL Chi-restraints excluded: chain LL residue 141 ASP Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LM residue 52 THR Chi-restraints excluded: chain LN residue 20 ARG Chi-restraints excluded: chain LO residue 171 GLU Chi-restraints excluded: chain LO residue 185 LYS Chi-restraints excluded: chain LO residue 197 GLU Chi-restraints excluded: chain LP residue 180 ILE Chi-restraints excluded: chain LQ residue 32 ILE Chi-restraints excluded: chain LQ residue 113 THR Chi-restraints excluded: chain LR residue 30 SER Chi-restraints excluded: chain LR residue 86 ASP Chi-restraints excluded: chain LS residue 5 GLN Chi-restraints excluded: chain LT residue 111 GLU Chi-restraints excluded: chain LT residue 140 THR Chi-restraints excluded: chain LT residue 151 LEU Chi-restraints excluded: chain LU residue 61 LYS Chi-restraints excluded: chain LU residue 103 VAL Chi-restraints excluded: chain LV residue 137 VAL Chi-restraints excluded: chain LX residue 83 GLU Chi-restraints excluded: chain LX residue 119 ASP Chi-restraints excluded: chain LX residue 143 VAL Chi-restraints excluded: chain LY residue 94 VAL Chi-restraints excluded: chain LY residue 130 LYS Chi-restraints excluded: chain LZ residue 1 MET Chi-restraints excluded: chain LZ residue 28 VAL Chi-restraints excluded: chain LZ residue 102 GLU Chi-restraints excluded: chain LZ residue 108 GLU Chi-restraints excluded: chain La residue 75 ILE Chi-restraints excluded: chain La residue 86 VAL Chi-restraints excluded: chain La residue 135 GLU Chi-restraints excluded: chain Lc residue 97 ASP Chi-restraints excluded: chain Ld residue 70 GLN Chi-restraints excluded: chain Ld residue 115 SER Chi-restraints excluded: chain Lf residue 4 GLU Chi-restraints excluded: chain Lg residue 33 VAL Chi-restraints excluded: chain Lh residue 33 GLN Chi-restraints excluded: chain Lh residue 49 ILE Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 38 VAL Chi-restraints excluded: chain Lk residue 70 ASP Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 52 VAL Chi-restraints excluded: chain Lq residue 86 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 1276 optimal weight: 0.9980 chunk 149 optimal weight: 7.9990 chunk 754 optimal weight: 0.5980 chunk 966 optimal weight: 0.0870 chunk 748 optimal weight: 7.9990 chunk 1114 optimal weight: 1.9990 chunk 739 optimal weight: 20.0000 chunk 1318 optimal weight: 0.5980 chunk 825 optimal weight: 1.9990 chunk 803 optimal weight: 5.9990 chunk 608 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CH 362 GLN CH 399 ASN CI 221 ASN CI 286 ASN CK 190 ASN CO 42 GLN ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 101 ASN Ce 401 ASN Cf 128 GLN Cg 31 ASN Cg 128 ASN LC 322 ASN LE 53 GLN LG 62 GLN LG 194 HIS LH 72 GLN LJ 16 GLN LL 17 HIS LM 98 ASN LM 110 GLN LN 86 ASN ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 98 ASN LQ 101 ASN LS 13 HIS LU 55 ASN LX 110 GLN LY 116 ASN Ld 49 GLN Ld 108 ASN Lf 58 GLN Li 47 GLN Lj 13 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 167520 Z= 0.136 Angle : 0.607 16.859 242835 Z= 0.329 Chirality : 0.035 0.276 29656 Planarity : 0.006 0.126 18143 Dihedral : 22.637 179.478 65145 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.48 % Favored : 98.51 % Rotamer: Outliers : 1.60 % Allowed : 11.70 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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 (0.08), residues: 10359 helix: 2.12 (0.08), residues: 4054 sheet: 0.13 (0.13), residues: 1487 loop : 0.46 (0.09), residues: 4818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPCg 105 HIS 0.011 0.001 HISLB 244 PHE 0.015 0.001 PHECI 235 TYR 0.017 0.001 TYRCF 10 ARG 0.014 0.000 ARGLi 107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20718 Ramachandran restraints generated. 10359 Oldfield, 0 Emsley, 10359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20718 Ramachandran restraints generated. 10359 Oldfield, 0 Emsley, 10359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1223 residues out of total 8939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1083 time to evaluate : 9.299 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: CF 10 TYR cc_start: 0.8331 (t80) cc_final: 0.8128 (t80) REVERT: CH 405 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.7767 (ptp-110) REVERT: CK 31 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: CL 73 ARG cc_start: 0.7673 (ttm-80) cc_final: 0.7382 (ttm170) REVERT: CM 25 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7795 (mt0) REVERT: CQ 95 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8200 (tpt-90) REVERT: Ce 187 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7421 (mttt) REVERT: LB 180 MET cc_start: 0.8863 (ptm) cc_final: 0.8645 (ptp) REVERT: LD 212 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: LF 223 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7254 (mtp-110) REVERT: LK 52 ASP cc_start: 0.6922 (t0) cc_final: 0.6704 (t0) REVERT: LK 83 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8083 (ttm170) REVERT: LN 20 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7372 (ttp80) REVERT: LO 171 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: LO 185 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7722 (ttmt) REVERT: LP 180 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8776 (mp) REVERT: LZ 1 MET cc_start: 0.8170 (pmt) cc_final: 0.7932 (pmm) REVERT: La 135 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: Ld 70 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7177 (mp10) REVERT: Lf 4 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7240 (mm-30) REVERT: Lh 29 THR cc_start: 0.8842 (m) cc_final: 0.8356 (m) REVERT: Lh 33 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.6746 (mp10) outliers start: 140 outliers final: 76 residues processed: 1143 average time/residue: 2.5796 time to fit residues: 4152.3630 Evaluate side-chains 1151 residues out of total 8939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1059 time to evaluate : 9.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 255 LEU Chi-restraints excluded: chain CB residue 288 THR Chi-restraints excluded: chain CH residue 143 LYS Chi-restraints excluded: chain CH residue 309 THR Chi-restraints excluded: chain CH residue 389 ASN Chi-restraints excluded: chain CH residue 405 ARG Chi-restraints excluded: chain CH residue 455 ASP Chi-restraints excluded: chain CI residue 227 SER Chi-restraints excluded: chain CI residue 263 VAL Chi-restraints excluded: chain CI residue 311 GLN Chi-restraints excluded: chain CJ residue 147 MET Chi-restraints excluded: chain CJ residue 235 MET Chi-restraints excluded: chain CK residue 12 LYS Chi-restraints excluded: chain CK residue 31 GLU Chi-restraints excluded: chain CK residue 40 GLN Chi-restraints excluded: chain CK residue 66 LYS Chi-restraints excluded: chain CM residue 25 GLN Chi-restraints excluded: chain CN residue 75 THR Chi-restraints excluded: chain CN residue 91 ASP Chi-restraints excluded: chain CO residue 40 ILE Chi-restraints excluded: chain CQ residue 95 ARG Chi-restraints excluded: chain Cb residue 38 THR Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cd residue 86 ASP Chi-restraints excluded: chain Cd residue 119 ASP Chi-restraints excluded: chain Ce residue 187 LYS Chi-restraints excluded: chain Ce residue 387 ASP Chi-restraints excluded: chain Cf residue 105 MET Chi-restraints excluded: chain Cf residue 153 VAL Chi-restraints excluded: chain Cg residue 71 THR Chi-restraints excluded: chain Ch residue 142 ILE Chi-restraints excluded: chain Ch residue 292 ASP Chi-restraints excluded: chain Ch residue 426 ASN Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LB residue 47 MET Chi-restraints excluded: chain LB residue 103 THR Chi-restraints excluded: chain LB residue 197 ARG Chi-restraints excluded: chain LB residue 207 ASP Chi-restraints excluded: chain LC residue 266 ASP Chi-restraints excluded: chain LD residue 195 THR Chi-restraints excluded: chain LD residue 212 GLU Chi-restraints excluded: chain LD residue 227 VAL Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LF residue 181 LYS Chi-restraints excluded: chain LF residue 223 ARG Chi-restraints excluded: chain LG residue 208 SER Chi-restraints excluded: chain LG residue 246 GLN Chi-restraints excluded: chain LG residue 253 LYS Chi-restraints excluded: chain LJ residue 49 SER Chi-restraints excluded: chain LJ residue 127 ASP Chi-restraints excluded: chain LK residue 83 ARG Chi-restraints excluded: chain LL residue 135 LYS Chi-restraints excluded: chain LL residue 141 ASP Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LM residue 96 GLU Chi-restraints excluded: chain LN residue 20 ARG Chi-restraints excluded: chain LO residue 171 GLU Chi-restraints excluded: chain LO residue 185 LYS Chi-restraints excluded: chain LO residue 197 GLU Chi-restraints excluded: chain LP residue 180 ILE Chi-restraints excluded: chain LQ residue 32 ILE Chi-restraints excluded: chain LQ residue 113 THR Chi-restraints excluded: chain LR residue 30 SER Chi-restraints excluded: chain LR residue 51 ILE Chi-restraints excluded: chain LR residue 86 ASP Chi-restraints excluded: chain LT residue 111 GLU Chi-restraints excluded: chain LT residue 140 THR Chi-restraints excluded: chain LU residue 103 VAL Chi-restraints excluded: chain LV residue 137 VAL Chi-restraints excluded: chain LX residue 83 GLU Chi-restraints excluded: chain LX residue 119 ASP Chi-restraints excluded: chain LY residue 94 VAL Chi-restraints excluded: chain LY residue 130 LYS Chi-restraints excluded: chain LZ residue 28 VAL Chi-restraints excluded: chain LZ residue 102 GLU Chi-restraints excluded: chain LZ residue 108 GLU Chi-restraints excluded: chain La residue 75 ILE Chi-restraints excluded: chain La residue 86 VAL Chi-restraints excluded: chain La residue 135 GLU Chi-restraints excluded: chain Lc residue 19 LEU Chi-restraints excluded: chain Lc residue 97 ASP Chi-restraints excluded: chain Ld residue 70 GLN Chi-restraints excluded: chain Ld residue 115 SER Chi-restraints excluded: chain Lf residue 4 GLU Chi-restraints excluded: chain Lg residue 33 VAL Chi-restraints excluded: chain Lh residue 33 GLN Chi-restraints excluded: chain Lh residue 49 ILE Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 38 VAL Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 52 VAL Chi-restraints excluded: chain Lq residue 86 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 815 optimal weight: 8.9990 chunk 526 optimal weight: 4.9990 chunk 787 optimal weight: 5.9990 chunk 397 optimal weight: 0.5980 chunk 259 optimal weight: 6.9990 chunk 255 optimal weight: 10.0000 chunk 838 optimal weight: 0.8980 chunk 898 optimal weight: 10.0000 chunk 651 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 chunk 1036 optimal weight: 5.9990 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CH 362 GLN CH 399 ASN CI 221 ASN CI 267 GLN CJ 481 GLN CK 190 ASN CO 42 GLN ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ce 401 ASN Cf 128 GLN Cg 31 ASN LC 322 ASN LE 53 GLN LG 62 GLN LH 72 GLN LJ 16 GLN LL 17 HIS LM 5 ASN LM 98 ASN LN 86 ASN LQ 98 ASN LQ 101 ASN LS 13 HIS LU 55 ASN LX 110 GLN LY 116 ASN Ld 49 GLN Ld 108 ASN Lf 58 GLN Li 47 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 167520 Z= 0.292 Angle : 0.670 17.384 242835 Z= 0.354 Chirality : 0.039 0.279 29656 Planarity : 0.006 0.137 18143 Dihedral : 22.631 179.916 65145 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.65 % Allowed : 12.09 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 1.43 (0.08), residues: 10359 helix: 2.01 (0.08), residues: 4058 sheet: 0.16 (0.13), residues: 1492 loop : 0.41 (0.09), residues: 4809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPLM 85 HIS 0.012 0.001 HISLB 244 PHE 0.017 0.002 PHELd 47 TYR 0.023 0.002 TYRLC 269 ARG 0.016 0.001 ARGCz 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20718 Ramachandran restraints generated. 10359 Oldfield, 0 Emsley, 10359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20718 Ramachandran restraints generated. 10359 Oldfield, 0 Emsley, 10359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1210 residues out of total 8939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1065 time to evaluate : 9.451 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: CH 405 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.7800 (ptp-110) REVERT: CK 31 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7115 (tm-30) REVERT: CM 25 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7800 (mt0) REVERT: CQ 95 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8243 (tpt-90) REVERT: Ce 187 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7445 (mttt) REVERT: LB 34 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8282 (ttmt) REVERT: LB 180 MET cc_start: 0.8880 (ptm) cc_final: 0.8626 (ptp) REVERT: LB 317 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7069 (mt-10) REVERT: LD 212 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: LF 223 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7278 (mtp-110) REVERT: LH 216 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7849 (m-30) REVERT: LK 52 ASP cc_start: 0.7031 (t0) cc_final: 0.6668 (t0) REVERT: LK 83 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7454 (ttm170) REVERT: LN 20 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7467 (ttp80) REVERT: LO 171 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: LO 185 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7741 (mtmt) REVERT: LP 180 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8793 (mp) REVERT: LS 5 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7980 (mt0) REVERT: LU 61 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8023 (mtpt) REVERT: LZ 1 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7927 (pmm) REVERT: La 135 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8345 (tt0) REVERT: Ld 70 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.7223 (mp10) REVERT: Lf 4 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7253 (mm-30) REVERT: Lh 33 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.6852 (mp10) outliers start: 145 outliers final: 80 residues processed: 1131 average time/residue: 2.5764 time to fit residues: 4084.2021 Evaluate side-chains 1160 residues out of total 8939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1058 time to evaluate : 9.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 255 LEU Chi-restraints excluded: chain CB residue 288 THR Chi-restraints excluded: chain CH residue 143 LYS Chi-restraints excluded: chain CH residue 297 LEU Chi-restraints excluded: chain CH residue 309 THR Chi-restraints excluded: chain CH residue 389 ASN Chi-restraints excluded: chain CH residue 405 ARG Chi-restraints excluded: chain CH residue 453 ASP Chi-restraints excluded: chain CH residue 455 ASP Chi-restraints excluded: chain CI residue 227 SER Chi-restraints excluded: chain CI residue 263 VAL Chi-restraints excluded: chain CI residue 311 GLN Chi-restraints excluded: chain CJ residue 147 MET Chi-restraints excluded: chain CJ residue 235 MET Chi-restraints excluded: chain CK residue 12 LYS Chi-restraints excluded: chain CK residue 31 GLU Chi-restraints excluded: chain CK residue 40 GLN Chi-restraints excluded: chain CK residue 66 LYS Chi-restraints excluded: chain CM residue 25 GLN Chi-restraints excluded: chain CN residue 75 THR Chi-restraints excluded: chain CN residue 91 ASP Chi-restraints excluded: chain CQ residue 95 ARG Chi-restraints excluded: chain Cb residue 38 THR Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cd residue 86 ASP Chi-restraints excluded: chain Cd residue 119 ASP Chi-restraints excluded: chain Ce residue 187 LYS Chi-restraints excluded: chain Ce residue 387 ASP Chi-restraints excluded: chain Cf residue 105 MET Chi-restraints excluded: chain Cf residue 113 MET Chi-restraints excluded: chain Cf residue 153 VAL Chi-restraints excluded: chain Cg residue 71 THR Chi-restraints excluded: chain Ch residue 142 ILE Chi-restraints excluded: chain Ch residue 292 ASP Chi-restraints excluded: chain Ch residue 426 ASN Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LB residue 34 LYS Chi-restraints excluded: chain LB residue 103 THR Chi-restraints excluded: chain LB residue 197 ARG Chi-restraints excluded: chain LB residue 207 ASP Chi-restraints excluded: chain LB residue 217 ASP Chi-restraints excluded: chain LB residue 303 LYS Chi-restraints excluded: chain LB residue 317 GLU Chi-restraints excluded: chain LC residue 100 MET Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 266 ASP Chi-restraints excluded: chain LD residue 66 THR Chi-restraints excluded: chain LD residue 195 THR Chi-restraints excluded: chain LD residue 212 GLU Chi-restraints excluded: chain LD residue 227 VAL Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LF residue 223 ARG Chi-restraints excluded: chain LG residue 208 SER Chi-restraints excluded: chain LG residue 246 GLN Chi-restraints excluded: chain LG residue 253 LYS Chi-restraints excluded: chain LH residue 216 ASP Chi-restraints excluded: chain LJ residue 49 SER Chi-restraints excluded: chain LJ residue 127 ASP Chi-restraints excluded: chain LK residue 83 ARG Chi-restraints excluded: chain LL residue 141 ASP Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LN residue 20 ARG Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LO residue 171 GLU Chi-restraints excluded: chain LO residue 185 LYS Chi-restraints excluded: chain LO residue 197 GLU Chi-restraints excluded: chain LP residue 180 ILE Chi-restraints excluded: chain LQ residue 32 ILE Chi-restraints excluded: chain LR residue 30 SER Chi-restraints excluded: chain LR residue 86 ASP Chi-restraints excluded: chain LS residue 5 GLN Chi-restraints excluded: chain LT residue 111 GLU Chi-restraints excluded: chain LT residue 140 THR Chi-restraints excluded: chain LT residue 151 LEU Chi-restraints excluded: chain LU residue 61 LYS Chi-restraints excluded: chain LU residue 103 VAL Chi-restraints excluded: chain LV residue 137 VAL Chi-restraints excluded: chain LX residue 83 GLU Chi-restraints excluded: chain LX residue 119 ASP Chi-restraints excluded: chain LX residue 143 VAL Chi-restraints excluded: chain LY residue 94 VAL Chi-restraints excluded: chain LY residue 130 LYS Chi-restraints excluded: chain LZ residue 1 MET Chi-restraints excluded: chain LZ residue 28 VAL Chi-restraints excluded: chain LZ residue 58 LYS Chi-restraints excluded: chain LZ residue 102 GLU Chi-restraints excluded: chain La residue 75 ILE Chi-restraints excluded: chain La residue 86 VAL Chi-restraints excluded: chain La residue 135 GLU Chi-restraints excluded: chain Ld residue 70 GLN Chi-restraints excluded: chain Ld residue 115 SER Chi-restraints excluded: chain Le residue 42 ARG Chi-restraints excluded: chain Lf residue 4 GLU Chi-restraints excluded: chain Lg residue 33 VAL Chi-restraints excluded: chain Lh residue 33 GLN Chi-restraints excluded: chain Lh residue 49 ILE Chi-restraints excluded: chain Li residue 27 THR Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 38 VAL Chi-restraints excluded: chain Lk residue 70 ASP Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 52 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 1199 optimal weight: 2.9990 chunk 1263 optimal weight: 2.9990 chunk 1152 optimal weight: 0.9990 chunk 1228 optimal weight: 7.9990 chunk 1262 optimal weight: 0.6980 chunk 739 optimal weight: 9.9990 chunk 535 optimal weight: 6.9990 chunk 964 optimal weight: 3.9990 chunk 377 optimal weight: 10.0000 chunk 1110 optimal weight: 1.9990 chunk 1162 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CH 399 ASN CI 221 ASN CI 267 GLN CJ 481 GLN ** CK 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CK 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CK 190 ASN CM 163 ASN CO 42 GLN ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ce 401 ASN Cf 128 GLN Cg 31 ASN LC 322 ASN LE 53 GLN LG 62 GLN LH 72 GLN LJ 16 GLN LL 17 HIS LM 98 ASN LN 86 ASN LQ 98 ASN LQ 101 ASN LS 13 HIS LX 110 GLN LY 116 ASN Ld 49 GLN Ld 108 ASN Lf 58 GLN Li 47 GLN Lj 13 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 167520 Z= 0.227 Angle : 0.648 17.289 242835 Z= 0.346 Chirality : 0.038 0.276 29656 Planarity : 0.006 0.134 18143 Dihedral : 22.633 179.958 65145 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.70 % Allowed : 12.11 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 1.45 (0.08), residues: 10359 helix: 2.03 (0.08), residues: 4054 sheet: 0.15 (0.13), residues: 1497 loop : 0.42 (0.09), residues: 4808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRPCB 300 HIS 0.012 0.001 HISLB 244 PHE 0.032 0.001 PHECh 37 TYR 0.019 0.002 TYRLC 269 ARG 0.020 0.000 ARGCz 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20718 Ramachandran restraints generated. 10359 Oldfield, 0 Emsley, 10359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20718 Ramachandran restraints generated. 10359 Oldfield, 0 Emsley, 10359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1217 residues out of total 8939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1068 time to evaluate : 9.419 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: CH 405 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.7780 (ptp-110) REVERT: CK 31 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7146 (tm-30) REVERT: CL 73 ARG cc_start: 0.7724 (ttm-80) cc_final: 0.7329 (ttm170) REVERT: CM 25 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7794 (mt0) REVERT: CQ 95 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8235 (tpt-90) REVERT: Ce 187 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7411 (mttt) REVERT: LB 34 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8285 (ttmt) REVERT: LB 180 MET cc_start: 0.8876 (ptm) cc_final: 0.8624 (ptp) REVERT: LB 317 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7082 (mt-10) REVERT: LD 212 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: LF 223 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7271 (mtp-110) REVERT: LH 216 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7859 (m-30) REVERT: LK 52 ASP cc_start: 0.7069 (t0) cc_final: 0.6696 (t0) REVERT: LK 83 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7439 (ttm170) REVERT: LN 20 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7452 (ttp80) REVERT: LO 171 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: LO 185 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7735 (mtmt) REVERT: LP 180 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8781 (mp) REVERT: LS 5 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7975 (mt0) REVERT: LU 61 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8040 (mtpt) REVERT: LZ 1 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7926 (pmm) REVERT: La 135 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8347 (tt0) REVERT: Ld 70 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7201 (mp10) REVERT: Lf 4 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7245 (mm-30) REVERT: Lh 30 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6919 (mp0) REVERT: Lh 33 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.6833 (mp10) outliers start: 149 outliers final: 98 residues processed: 1134 average time/residue: 2.5198 time to fit residues: 4019.5799 Evaluate side-chains 1180 residues out of total 8939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1059 time to evaluate : 9.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 255 LEU Chi-restraints excluded: chain CB residue 288 THR Chi-restraints excluded: chain CH residue 143 LYS Chi-restraints excluded: chain CH residue 297 LEU Chi-restraints excluded: chain CH residue 309 THR Chi-restraints excluded: chain CH residue 323 THR Chi-restraints excluded: chain CH residue 372 THR Chi-restraints excluded: chain CH residue 389 ASN Chi-restraints excluded: chain CH residue 405 ARG Chi-restraints excluded: chain CH residue 453 ASP Chi-restraints excluded: chain CH residue 455 ASP Chi-restraints excluded: chain CH residue 615 LYS Chi-restraints excluded: chain CH residue 622 LEU Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CI residue 227 SER Chi-restraints excluded: chain CI residue 263 VAL Chi-restraints excluded: chain CI residue 311 GLN Chi-restraints excluded: chain CJ residue 147 MET Chi-restraints excluded: chain CJ residue 164 MET Chi-restraints excluded: chain CK residue 12 LYS Chi-restraints excluded: chain CK residue 31 GLU Chi-restraints excluded: chain CK residue 40 GLN Chi-restraints excluded: chain CK residue 66 LYS Chi-restraints excluded: chain CL residue 63 GLU Chi-restraints excluded: chain CM residue 25 GLN Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CN residue 75 THR Chi-restraints excluded: chain CN residue 91 ASP Chi-restraints excluded: chain CQ residue 95 ARG Chi-restraints excluded: chain Cb residue 9 MET Chi-restraints excluded: chain Cb residue 38 THR Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cd residue 86 ASP Chi-restraints excluded: chain Cd residue 119 ASP Chi-restraints excluded: chain Cd residue 381 ILE Chi-restraints excluded: chain Ce residue 187 LYS Chi-restraints excluded: chain Ce residue 387 ASP Chi-restraints excluded: chain Cf residue 105 MET Chi-restraints excluded: chain Cf residue 153 VAL Chi-restraints excluded: chain Cg residue 71 THR Chi-restraints excluded: chain Ch residue 142 ILE Chi-restraints excluded: chain Ch residue 292 ASP Chi-restraints excluded: chain Ch residue 426 ASN Chi-restraints excluded: chain LA residue 96 LEU Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LB residue 34 LYS Chi-restraints excluded: chain LB residue 103 THR Chi-restraints excluded: chain LB residue 197 ARG Chi-restraints excluded: chain LB residue 207 ASP Chi-restraints excluded: chain LB residue 303 LYS Chi-restraints excluded: chain LB residue 317 GLU Chi-restraints excluded: chain LC residue 100 MET Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 266 ASP Chi-restraints excluded: chain LD residue 66 THR Chi-restraints excluded: chain LD residue 137 THR Chi-restraints excluded: chain LD residue 195 THR Chi-restraints excluded: chain LD residue 212 GLU Chi-restraints excluded: chain LD residue 227 VAL Chi-restraints excluded: chain LE residue 106 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LF residue 223 ARG Chi-restraints excluded: chain LG residue 208 SER Chi-restraints excluded: chain LG residue 246 GLN Chi-restraints excluded: chain LG residue 253 LYS Chi-restraints excluded: chain LH residue 216 ASP Chi-restraints excluded: chain LJ residue 49 SER Chi-restraints excluded: chain LJ residue 127 ASP Chi-restraints excluded: chain LJ residue 139 VAL Chi-restraints excluded: chain LK residue 83 ARG Chi-restraints excluded: chain LL residue 135 LYS Chi-restraints excluded: chain LL residue 141 ASP Chi-restraints excluded: chain LM residue 3 GLU Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LN residue 20 ARG Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LO residue 89 MET Chi-restraints excluded: chain LO residue 139 THR Chi-restraints excluded: chain LO residue 171 GLU Chi-restraints excluded: chain LO residue 185 LYS Chi-restraints excluded: chain LO residue 197 GLU Chi-restraints excluded: chain LP residue 180 ILE Chi-restraints excluded: chain LQ residue 32 ILE Chi-restraints excluded: chain LR residue 30 SER Chi-restraints excluded: chain LR residue 86 ASP Chi-restraints excluded: chain LS residue 5 GLN Chi-restraints excluded: chain LS residue 119 ARG Chi-restraints excluded: chain LT residue 111 GLU Chi-restraints excluded: chain LT residue 140 THR Chi-restraints excluded: chain LU residue 61 LYS Chi-restraints excluded: chain LU residue 103 VAL Chi-restraints excluded: chain LV residue 137 VAL Chi-restraints excluded: chain LX residue 83 GLU Chi-restraints excluded: chain LX residue 119 ASP Chi-restraints excluded: chain LX residue 143 VAL Chi-restraints excluded: chain LY residue 94 VAL Chi-restraints excluded: chain LY residue 130 LYS Chi-restraints excluded: chain LZ residue 1 MET Chi-restraints excluded: chain LZ residue 28 VAL Chi-restraints excluded: chain LZ residue 58 LYS Chi-restraints excluded: chain LZ residue 102 GLU Chi-restraints excluded: chain La residue 75 ILE Chi-restraints excluded: chain La residue 86 VAL Chi-restraints excluded: chain La residue 135 GLU Chi-restraints excluded: chain Lc residue 19 LEU Chi-restraints excluded: chain Ld residue 70 GLN Chi-restraints excluded: chain Ld residue 115 SER Chi-restraints excluded: chain Le residue 56 ILE Chi-restraints excluded: chain Lf residue 4 GLU Chi-restraints excluded: chain Lg residue 33 VAL Chi-restraints excluded: chain Lh residue 30 GLU Chi-restraints excluded: chain Lh residue 33 GLN Chi-restraints excluded: chain Lh residue 49 ILE Chi-restraints excluded: chain Li residue 27 THR Chi-restraints excluded: chain Lj residue 13 ASN Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 38 VAL Chi-restraints excluded: chain Lk residue 70 ASP Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 52 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 1224 optimal weight: 5.9990 chunk 806 optimal weight: 4.9990 chunk 1299 optimal weight: 0.0770 chunk 793 optimal weight: 4.9990 chunk 616 optimal weight: 0.8980 chunk 903 optimal weight: 0.9980 chunk 1362 optimal weight: 1.9990 chunk 1254 optimal weight: 10.0000 chunk 1085 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 838 optimal weight: 7.9990 overall best weight: 1.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CH 399 ASN CH 459 GLN CH 641 HIS CI 221 ASN CI 267 GLN CJ 481 GLN ** CK 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CK 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CK 190 ASN CM 163 ASN CO 42 GLN ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 101 ASN Ce 401 ASN Cf 128 GLN Cg 31 ASN LC 322 ASN LE 53 GLN LG 62 GLN LH 72 GLN LJ 16 GLN LL 17 HIS LM 98 ASN LN 86 ASN LQ 98 ASN LQ 101 ASN LS 13 HIS LU 55 ASN LX 110 GLN LY 116 ASN LY 127 GLN Ld 49 GLN Ld 108 ASN Lf 58 GLN Li 47 GLN Lj 13 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 167520 Z= 0.217 Angle : 0.642 17.211 242835 Z= 0.343 Chirality : 0.037 0.276 29656 Planarity : 0.006 0.133 18143 Dihedral : 22.622 179.990 65145 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.65 % Allowed : 12.15 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 1.46 (0.08), residues: 10359 helix: 2.03 (0.08), residues: 4054 sheet: 0.15 (0.13), residues: 1494 loop : 0.43 (0.09), residues: 4811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPCg 105 HIS 0.013 0.001 HISLB 244 PHE 0.015 0.001 PHECH 90 TYR 0.021 0.002 TYRLC 269 ARG 0.021 0.000 ARGCz 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20718 Ramachandran restraints generated. 10359 Oldfield, 0 Emsley, 10359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20718 Ramachandran restraints generated. 10359 Oldfield, 0 Emsley, 10359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1211 residues out of total 8939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1066 time to evaluate : 9.545 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: CH 405 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7780 (ptp-110) REVERT: CK 31 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7144 (tm-30) REVERT: CL 73 ARG cc_start: 0.7701 (ttm-80) cc_final: 0.7326 (ttm170) REVERT: CM 25 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7809 (mt0) REVERT: CQ 95 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8238 (tpt-90) REVERT: CQ 161 ARG cc_start: 0.6825 (mtm-85) cc_final: 0.6165 (mtm110) REVERT: Ce 187 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7467 (mttt) REVERT: LB 34 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8281 (ttmt) REVERT: LB 180 MET cc_start: 0.8873 (ptm) cc_final: 0.8622 (ptp) REVERT: LB 317 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7080 (mt-10) REVERT: LD 212 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: LE 35 GLN cc_start: 0.7636 (pt0) cc_final: 0.7431 (pt0) REVERT: LF 223 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7268 (mtp-110) REVERT: LH 216 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7857 (m-30) REVERT: LK 52 ASP cc_start: 0.7081 (t0) cc_final: 0.6692 (t0) REVERT: LK 83 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7435 (ttm170) REVERT: LN 20 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7431 (ttp80) REVERT: LO 171 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: LO 185 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7732 (mtmt) REVERT: LP 180 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8772 (mp) REVERT: LS 5 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7971 (mt0) REVERT: LZ 1 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7920 (pmm) REVERT: La 135 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8346 (tt0) REVERT: Ld 70 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.7194 (mp10) REVERT: Lf 4 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7241 (mm-30) REVERT: Lh 30 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6858 (mp0) REVERT: Lh 33 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6812 (mp10) outliers start: 145 outliers final: 99 residues processed: 1129 average time/residue: 2.5835 time to fit residues: 4109.1235 Evaluate side-chains 1177 residues out of total 8939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1056 time to evaluate : 9.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 255 LEU Chi-restraints excluded: chain CB residue 288 THR Chi-restraints excluded: chain CH residue 143 LYS Chi-restraints excluded: chain CH residue 297 LEU Chi-restraints excluded: chain CH residue 309 THR Chi-restraints excluded: chain CH residue 323 THR Chi-restraints excluded: chain CH residue 372 THR Chi-restraints excluded: chain CH residue 389 ASN Chi-restraints excluded: chain CH residue 405 ARG Chi-restraints excluded: chain CH residue 453 ASP Chi-restraints excluded: chain CH residue 455 ASP Chi-restraints excluded: chain CH residue 615 LYS Chi-restraints excluded: chain CH residue 622 LEU Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CI residue 227 SER Chi-restraints excluded: chain CI residue 263 VAL Chi-restraints excluded: chain CI residue 311 GLN Chi-restraints excluded: chain CI residue 323 MET Chi-restraints excluded: chain CJ residue 147 MET Chi-restraints excluded: chain CJ residue 164 MET Chi-restraints excluded: chain CK residue 12 LYS Chi-restraints excluded: chain CK residue 31 GLU Chi-restraints excluded: chain CK residue 40 GLN Chi-restraints excluded: chain CK residue 66 LYS Chi-restraints excluded: chain CL residue 63 GLU Chi-restraints excluded: chain CM residue 25 GLN Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CN residue 75 THR Chi-restraints excluded: chain CN residue 91 ASP Chi-restraints excluded: chain CN residue 114 THR Chi-restraints excluded: chain CQ residue 95 ARG Chi-restraints excluded: chain Cb residue 9 MET Chi-restraints excluded: chain Cb residue 38 THR Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cd residue 86 ASP Chi-restraints excluded: chain Cd residue 119 ASP Chi-restraints excluded: chain Cd residue 381 ILE Chi-restraints excluded: chain Ce residue 187 LYS Chi-restraints excluded: chain Ce residue 387 ASP Chi-restraints excluded: chain Cf residue 105 MET Chi-restraints excluded: chain Cf residue 153 VAL Chi-restraints excluded: chain Cg residue 71 THR Chi-restraints excluded: chain Ch residue 142 ILE Chi-restraints excluded: chain Ch residue 292 ASP Chi-restraints excluded: chain Ch residue 426 ASN Chi-restraints excluded: chain LA residue 96 LEU Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LB residue 34 LYS Chi-restraints excluded: chain LB residue 103 THR Chi-restraints excluded: chain LB residue 197 ARG Chi-restraints excluded: chain LB residue 207 ASP Chi-restraints excluded: chain LB residue 303 LYS Chi-restraints excluded: chain LB residue 317 GLU Chi-restraints excluded: chain LC residue 100 MET Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 266 ASP Chi-restraints excluded: chain LD residue 66 THR Chi-restraints excluded: chain LD residue 137 THR Chi-restraints excluded: chain LD residue 195 THR Chi-restraints excluded: chain LD residue 212 GLU Chi-restraints excluded: chain LD residue 227 VAL Chi-restraints excluded: chain LE residue 106 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LF residue 223 ARG Chi-restraints excluded: chain LG residue 208 SER Chi-restraints excluded: chain LG residue 246 GLN Chi-restraints excluded: chain LG residue 253 LYS Chi-restraints excluded: chain LH residue 216 ASP Chi-restraints excluded: chain LJ residue 49 SER Chi-restraints excluded: chain LJ residue 127 ASP Chi-restraints excluded: chain LJ residue 139 VAL Chi-restraints excluded: chain LK residue 83 ARG Chi-restraints excluded: chain LL residue 135 LYS Chi-restraints excluded: chain LL residue 141 ASP Chi-restraints excluded: chain LM residue 3 GLU Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LN residue 20 ARG Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LO residue 89 MET Chi-restraints excluded: chain LO residue 171 GLU Chi-restraints excluded: chain LO residue 185 LYS Chi-restraints excluded: chain LO residue 197 GLU Chi-restraints excluded: chain LP residue 169 SER Chi-restraints excluded: chain LP residue 180 ILE Chi-restraints excluded: chain LQ residue 32 ILE Chi-restraints excluded: chain LR residue 30 SER Chi-restraints excluded: chain LR residue 86 ASP Chi-restraints excluded: chain LS residue 5 GLN Chi-restraints excluded: chain LS residue 119 ARG Chi-restraints excluded: chain LT residue 111 GLU Chi-restraints excluded: chain LT residue 140 THR Chi-restraints excluded: chain LU residue 103 VAL Chi-restraints excluded: chain LV residue 137 VAL Chi-restraints excluded: chain LX residue 83 GLU Chi-restraints excluded: chain LX residue 119 ASP Chi-restraints excluded: chain LX residue 143 VAL Chi-restraints excluded: chain LY residue 94 VAL Chi-restraints excluded: chain LY residue 130 LYS Chi-restraints excluded: chain LZ residue 1 MET Chi-restraints excluded: chain LZ residue 28 VAL Chi-restraints excluded: chain LZ residue 58 LYS Chi-restraints excluded: chain LZ residue 102 GLU Chi-restraints excluded: chain La residue 75 ILE Chi-restraints excluded: chain La residue 86 VAL Chi-restraints excluded: chain La residue 135 GLU Chi-restraints excluded: chain Lc residue 19 LEU Chi-restraints excluded: chain Ld residue 70 GLN Chi-restraints excluded: chain Ld residue 115 SER Chi-restraints excluded: chain Le residue 56 ILE Chi-restraints excluded: chain Lf residue 4 GLU Chi-restraints excluded: chain Lg residue 33 VAL Chi-restraints excluded: chain Lh residue 30 GLU Chi-restraints excluded: chain Lh residue 33 GLN Chi-restraints excluded: chain Lh residue 49 ILE Chi-restraints excluded: chain Li residue 27 THR Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 38 VAL Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 52 VAL Chi-restraints excluded: chain Lq residue 86 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 665 optimal weight: 0.9990 chunk 862 optimal weight: 4.9990 chunk 1156 optimal weight: 1.9990 chunk 332 optimal weight: 8.9990 chunk 1000 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 301 optimal weight: 5.9990 chunk 1086 optimal weight: 3.9990 chunk 454 optimal weight: 0.9990 chunk 1116 optimal weight: 0.4980 chunk 137 optimal weight: 4.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CH 362 GLN CH 399 ASN CH 641 HIS CI 221 ASN CI 267 GLN CJ 481 GLN ** CK 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CK 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CK 190 ASN CM 163 ASN CO 42 GLN ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 101 ASN Ce 401 ASN Cf 128 GLN Cg 31 ASN Cg 128 ASN LC 322 ASN LE 53 GLN LG 62 GLN LH 72 GLN LJ 16 GLN LL 17 HIS LM 98 ASN LN 86 ASN LQ 98 ASN LQ 101 ASN LS 13 HIS LX 110 GLN LY 116 ASN Ld 49 GLN Ld 108 ASN Lf 58 GLN Li 47 GLN Lj 13 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.094572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.068744 restraints weight = 250405.311| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 0.93 r_work: 0.2737 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 167520 Z= 0.209 Angle : 0.639 17.180 242835 Z= 0.342 Chirality : 0.037 0.275 29656 Planarity : 0.006 0.132 18143 Dihedral : 22.615 179.999 65145 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.64 % Allowed : 12.26 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % 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: 1.47 (0.08), residues: 10359 helix: 2.06 (0.08), residues: 4054 sheet: 0.13 (0.13), residues: 1490 loop : 0.44 (0.09), residues: 4815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPCg 105 HIS 0.012 0.001 HISLB 244 PHE 0.015 0.001 PHECH 90 TYR 0.021 0.001 TYRLC 269 ARG 0.020 0.000 ARGLp 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 57417.97 seconds wall clock time: 995 minutes 35.42 seconds (59735.42 seconds total)