Starting phenix.real_space_refine on Tue Apr 16 12:35:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv5_17954/04_2024/8pv5_17954_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv5_17954/04_2024/8pv5_17954.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv5_17954/04_2024/8pv5_17954_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv5_17954/04_2024/8pv5_17954_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv5_17954/04_2024/8pv5_17954_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv5_17954/04_2024/8pv5_17954.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv5_17954/04_2024/8pv5_17954.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv5_17954/04_2024/8pv5_17954_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv5_17954/04_2024/8pv5_17954_updated.pdb" } resolution = 2.86 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= 0.015 sd= 0.127 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 3337 5.49 5 Mg 3 5.21 5 S 229 5.16 5 C 77948 2.51 5 N 26797 2.21 5 O 36079 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "CF ASP 111": "OD1" <-> "OD2" Residue "CF ASP 154": "OD1" <-> "OD2" Residue "CF TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF GLU 218": "OE1" <-> "OE2" Residue "CF TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF GLU 233": "OE1" <-> "OE2" Residue "CH PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH GLU 304": "OE1" <-> "OE2" Residue "CH ASP 406": "OD1" <-> "OD2" Residue "CH TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH ASP 451": "OD1" <-> "OD2" Residue "CH PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH ASP 535": "OD1" <-> "OD2" Residue "CK GLU 37": "OE1" <-> "OE2" Residue "CK GLU 69": "OE1" <-> "OE2" Residue "CK GLU 70": "OE1" <-> "OE2" Residue "CK GLU 222": "OE1" <-> "OE2" Residue "CK ASP 252": "OD1" <-> "OD2" Residue "CL GLU 63": "OE1" <-> "OE2" Residue "CN TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CN PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CN GLU 39": "OE1" <-> "OE2" Residue "CN ASP 44": "OD1" <-> "OD2" Residue "CN ASP 90": "OD1" <-> "OD2" Residue "CN ASP 144": "OD1" <-> "OD2" Residue "CN TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CN GLU 243": "OE1" <-> "OE2" Residue "CO GLU 12": "OE1" <-> "OE2" Residue "CO PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CQ PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CQ GLU 141": "OE1" <-> "OE2" Residue "CQ GLU 160": "OE1" <-> "OE2" Residue "CQ GLU 163": "OE1" <-> "OE2" Residue "Cb ASP 20": "OD1" <-> "OD2" Residue "Cb GLU 37": "OE1" <-> "OE2" Residue "Cb ASP 43": "OD1" <-> "OD2" Residue "Cb GLU 62": "OE1" <-> "OE2" Residue "Cb TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cb TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cb ASP 100": "OD1" <-> "OD2" Residue "Cd PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cd GLU 137": "OE1" <-> "OE2" Residue "Cd GLU 169": "OE1" <-> "OE2" Residue "Cd PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cd ASP 312": "OD1" <-> "OD2" Residue "Cd ASP 323": "OD1" <-> "OD2" Residue "Cd ASP 388": "OD1" <-> "OD2" Residue "Cd ASP 392": "OD1" <-> "OD2" Residue "Cd GLU 405": "OE1" <-> "OE2" Residue "Cf TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cf TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cf ASP 121": "OD1" <-> "OD2" Residue "Cf PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cg ASP 150": "OD1" <-> "OD2" Residue "Cg GLU 154": "OE1" <-> "OE2" Residue "Ch PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ch PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ch PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ch PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ch ASP 415": "OD1" <-> "OD2" Residue "Cz GLU 65": "OE1" <-> "OE2" Residue "LA ASP 33": "OD1" <-> "OD2" Residue "LA GLU 47": "OE1" <-> "OE2" Residue "LA ASP 51": "OD1" <-> "OD2" Residue "LA TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA ASP 176": "OD1" <-> "OD2" Residue "LB PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB GLU 94": "OE1" <-> "OE2" Residue "LB TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB GLU 139": "OE1" <-> "OE2" Residue "LB GLU 148": "OE1" <-> "OE2" Residue "LB GLU 211": "OE1" <-> "OE2" Residue "LC ASP 161": "OD1" <-> "OD2" Residue "LC PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD GLU 133": "OE1" <-> "OE2" Residue "LD PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD ASP 232": "OD1" <-> "OD2" Residue "LD ASP 237": "OD1" <-> "OD2" Residue "LD GLU 245": "OE1" <-> "OE2" Residue "LE ASP 77": "OD1" <-> "OD2" Residue "LE ASP 110": "OD1" <-> "OD2" Residue "LE ASP 161": "OD1" <-> "OD2" Residue "LE TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF ASP 11": "OD1" <-> "OD2" Residue "LF PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF GLU 55": "OE1" <-> "OE2" Residue "LF GLU 188": "OE1" <-> "OE2" Residue "LF PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF GLU 238": "OE1" <-> "OE2" Residue "LG PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG GLU 107": "OE1" <-> "OE2" Residue "LG ASP 159": "OD1" <-> "OD2" Residue "LG ASP 161": "OD1" <-> "OD2" Residue "LG GLU 209": "OE1" <-> "OE2" Residue "LG TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG ASP 231": "OD1" <-> "OD2" Residue "LG PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH GLU 7": "OE1" <-> "OE2" Residue "LH ASP 74": "OD1" <-> "OD2" Residue "LH ASP 101": "OD1" <-> "OD2" Residue "LH PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LJ TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LJ PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LJ TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LK ASP 52": "OD1" <-> "OD2" Residue "LK ASP 91": "OD1" <-> "OD2" Residue "LK GLU 131": "OE1" <-> "OE2" Residue "LK ASP 144": "OD1" <-> "OD2" Residue "LK ASP 153": "OD1" <-> "OD2" Residue "LL ASP 52": "OD1" <-> "OD2" Residue "LL PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LL GLU 106": "OE1" <-> "OE2" Residue "LL ASP 137": "OD1" <-> "OD2" Residue "LL GLU 158": "OE1" <-> "OE2" Residue "LL ASP 191": "OD1" <-> "OD2" Residue "LM ASP 35": "OD1" <-> "OD2" Residue "LM ASP 114": "OD1" <-> "OD2" Residue "LM PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LM GLU 131": "OE1" <-> "OE2" Residue "LN TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO ASP 192": "OD1" <-> "OD2" Residue "LP GLU 99": "OE1" <-> "OE2" Residue "LP TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LQ TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LQ PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LQ GLU 157": "OE1" <-> "OE2" Residue "LR GLU 19": "OE1" <-> "OE2" Residue "LR ASP 47": "OD1" <-> "OD2" Residue "LR TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LR PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS ASP 82": "OD1" <-> "OD2" Residue "LS PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU ASP 31": "OD1" <-> "OD2" Residue "LU PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LV TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LV GLU 70": "OE1" <-> "OE2" Residue "LX PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX ASP 100": "OD1" <-> "OD2" Residue "LX ASP 117": "OD1" <-> "OD2" Residue "LX PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX ASP 147": "OD1" <-> "OD2" Residue "LY ASP 64": "OD1" <-> "OD2" Residue "LZ PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "La TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "La ASP 97": "OD1" <-> "OD2" Residue "La GLU 140": "OE1" <-> "OE2" Residue "La GLU 146": "OE1" <-> "OE2" Residue "Lc TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lc TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Le PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Le PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Le ASP 30": "OD1" <-> "OD2" Residue "Le GLU 84": "OE1" <-> "OE2" Residue "Le TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lf TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lg GLU 62": "OE1" <-> "OE2" Residue "Lh ASP 101": "OD1" <-> "OD2" Residue "Li GLU 63": "OE1" <-> "OE2" Residue "Li PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lj TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lj TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lj PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lk ASP 19": "OD1" <-> "OD2" Residue "Lq GLU 11": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 144398 Number of models: 1 Model: "" Number of chains: 62 Chain: "C1" Number of atoms: 65497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3060, 65497 Classifications: {'RNA': 3060} Modifications used: {'rna2p': 1, 'rna2p_pur': 316, 'rna2p_pyr': 216, 'rna3p': 25, 'rna3p_pur': 1348, 'rna3p_pyr': 1146} Link IDs: {'rna2p': 533, 'rna3p': 2526} Chain breaks: 8 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 18 Chain: "C2" Number of atoms: 3239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 3239 Classifications: {'RNA': 152} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 9, 'rna3p_pur': 63, 'rna3p_pyr': 63} Link IDs: {'rna2p': 26, 'rna3p': 125} 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: "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: 5053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5053 Classifications: {'peptide': 627} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 600} Chain breaks: 2 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: "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: "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: "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: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1885 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 223} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 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: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1226 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 148} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 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: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 959 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 113} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 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: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 981 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain breaks: 1 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: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1049 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 132} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 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 83155 SG CYSCQ 6 146.559 177.535 99.589 1.00 24.51 S ATOM 83183 SG CYSCQ 9 150.179 178.485 100.281 1.00 23.31 S ATOM 83368 SG CYSCQ 32 149.467 175.284 98.539 1.00 21.87 S ATOM 83400 SG CYSCQ 36 148.640 175.719 102.283 1.00 20.42 S ATOM 85012 SG CYSCb 52 128.065 183.984 122.051 1.00 38.03 S ATOM 85035 SG CYSCb 55 131.600 182.198 122.040 1.00 41.24 S ATOM A0TNV SG CYSLg 45 142.882 156.705 198.206 1.00 52.10 S ATOM A0TOD SG CYSLg 48 140.456 158.556 195.950 1.00 52.32 S ATOM A0TVL SG CYSLg 82 142.404 160.605 198.522 1.00 51.66 S ATOM A0TW3 SG CYSLg 85 139.829 158.314 199.708 1.00 57.59 S ATOM A0VLE SG CYSLj 19 164.449 110.482 171.018 1.00 19.71 S ATOM A0VM6 SG CYSLj 22 165.286 108.129 168.135 1.00 18.47 S ATOM A0VOW SG CYSLj 34 161.771 109.298 168.596 1.00 17.41 S ATOM A0VPD SG CYSLj 37 163.129 106.899 171.117 1.00 17.67 S ATOM A0X33 SG CYSLp 39 124.116 159.709 191.545 1.00 55.82 S ATOM A0X3R SG CYSLp 42 125.708 163.078 191.785 1.00 58.64 S ATOM A0X6W SG CYSLp 57 127.217 160.451 189.416 1.00 52.90 S ATOM A0X7H SG CYSLp 60 127.660 159.863 192.966 1.00 55.90 S Time building chain proxies: 55.12, per 1000 atoms: 0.38 Number of scatterers: 144398 At special positions: 0 Unit cell: (235.125, 226.765, 256.025, 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 229 16.00 P 3337 15.00 Mg 3 11.99 O 36079 8.00 N 26797 7.00 C 77948 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: 54.91 Conformation dependent library (CDL) restraints added in 10.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNCQ1000 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 9 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 32 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 36 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 6 " pdb=" ZNCb1000 " pdb="ZN ZNCb1000 " - pdb=" NE2 HISCb 68 " pdb="ZN ZNCb1000 " - pdb=" ND1 HISCb 74 " pdb="ZN ZNCb1000 " - pdb=" SG CYSCb 52 " pdb="ZN ZNCb1000 " - pdb=" SG CYSCb 55 " pdb=" ZNLg1000 " pdb="ZN ZNLg1000 " - pdb=" SG CYSLg 85 " pdb="ZN ZNLg1000 " - pdb=" SG CYSLg 48 " pdb="ZN ZNLg1000 " - pdb=" SG CYSLg 45 " pdb="ZN ZNLg1000 " - pdb=" SG CYSLg 82 " pdb=" ZNLj1000 " pdb="ZN ZNLj1000 " - pdb=" SG CYSLj 34 " pdb="ZN ZNLj1000 " - pdb=" SG CYSLj 22 " pdb="ZN ZNLj1000 " - pdb=" SG CYSLj 37 " 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 39 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 60 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 42 " Number of angles added : 25 18158 Ramachandran restraints generated. 9079 Oldfield, 0 Emsley, 9079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17214 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: 329 helices and 93 sheets defined 44.0% alpha, 14.5% beta 1047 base pairs and 1883 stacking pairs defined. Time for finding SS restraints: 79.03 Creating SS restraints... Processing helix chain 'CF' and resid 19 through 37 removed outlier: 3.806A pdb=" N LYSCF 23 " --> pdb=" O GLYCF 19 " (cutoff:3.500A) Proline residue: CF 35 - end of helix Processing helix chain 'CF' and resid 52 through 61 removed outlier: 3.863A 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: 3.881A pdb=" N LEUCF 92 " --> pdb=" O GLYCF 88 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THRCF 93 " --> pdb=" O LEUCF 89 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARGCF 94 " --> pdb=" O HISCF 90 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N TYRCF 95 " --> pdb=" O ARGCF 91 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEUCF 96 " --> pdb=" O LEUCF 92 " (cutoff:3.500A) removed outlier: 5.656A 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 120 removed outlier: 3.800A pdb=" N ILECF 112 " --> pdb=" O ASPCF 108 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SERCF 120 " --> pdb=" O PHECF 116 " (cutoff:3.500A) Processing helix chain 'CF' and resid 161 through 169 Processing helix chain 'CF' and resid 202 through 213 Processing helix chain 'CF' and resid 237 through 243 removed outlier: 3.670A 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: 3.527A pdb=" N GLNCH 73 " --> pdb=" O VALCH 69 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N HISCH 74 " --> pdb=" O LEUCH 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'CH' and resid 69 through 74' Processing helix chain 'CH' and resid 75 through 85 Processing helix chain 'CH' and resid 86 through 118 removed outlier: 3.841A pdb=" N TYRCH 117 " --> pdb=" O ARGCH 113 " (cutoff:3.500A) Processing helix chain 'CH' and resid 120 through 143 removed outlier: 4.104A pdb=" N LEUCH 142 " --> pdb=" O LEUCH 138 " (cutoff:3.500A) removed outlier: 4.455A 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: 5.678A pdb=" N ASNCH 232 " --> pdb=" O LEUCH 228 " (cutoff:3.500A) Processing helix chain 'CH' and resid 233 through 244 removed outlier: 3.958A 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: 4.182A pdb=" N ALACH 278 " --> pdb=" O LYSCH 274 " (cutoff:3.500A) Processing helix chain 'CH' and resid 293 through 298 removed outlier: 3.881A pdb=" N LEUCH 297 " --> pdb=" O LYSCH 293 " (cutoff:3.500A) removed outlier: 5.525A 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: 3.780A pdb=" N THRCH 309 " --> pdb=" O ILECH 305 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYSCH 310 " --> pdb=" O ASNCH 306 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N SERCH 311 " --> pdb=" O ASPCH 307 " (cutoff:3.500A) Processing helix chain 'CH' and resid 326 through 351 removed outlier: 4.773A pdb=" N GLYCH 350 " --> pdb=" O LYSCH 346 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N THRCH 351 " --> pdb=" O LEUCH 347 " (cutoff:3.500A) Processing helix chain 'CH' and resid 358 through 369 Processing helix chain 'CH' and resid 384 through 390 removed outlier: 4.572A pdb=" N LYSCH 388 " --> pdb=" O PROCH 384 " (cutoff:3.500A) removed outlier: 3.857A 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 431 through 436 removed outlier: 4.474A pdb=" N ASPCH 435 " --> pdb=" O GLUCH 431 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LYSCH 436 " --> pdb=" O TRPCH 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'CH' and resid 431 through 436' Processing helix chain 'CH' and resid 445 through 450 removed outlier: 3.552A pdb=" N TYRCH 449 " --> pdb=" O ASNCH 445 " (cutoff:3.500A) Processing helix chain 'CH' and resid 453 through 472 removed outlier: 4.118A 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: 3.815A pdb=" N VALCH 523 " --> pdb=" O PROCH 519 " (cutoff:3.500A) removed outlier: 5.084A 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: 3.614A pdb=" N ILECH 544 " --> pdb=" O ASPCH 540 " (cutoff:3.500A) Processing helix chain 'CH' and resid 546 through 551 removed outlier: 5.627A 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: 4.062A pdb=" N GLNCH 624 " --> pdb=" O ALACH 620 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARGCH 625 " --> pdb=" O LYSCH 621 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LYSCH 626 " --> pdb=" O LEUCH 622 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N METCH 627 " --> pdb=" O ALACH 623 " (cutoff:3.500A) Processing helix chain 'CH' and resid 645 through 650 Processing helix chain 'CK' and resid 5 through 14 Processing helix chain 'CK' and resid 19 through 41 removed outlier: 4.802A pdb=" N GLYCK 32 " --> pdb=" O ALACK 28 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N HISCK 33 " --> pdb=" O ALACK 29 " (cutoff:3.500A) Processing helix chain 'CK' and resid 44 through 72 removed outlier: 4.987A pdb=" N ASNCK 72 " --> pdb=" O HISCK 68 " (cutoff:3.500A) Processing helix chain 'CK' and resid 128 through 133 Processing helix chain 'CK' and resid 174 through 179 removed outlier: 3.624A pdb=" N ARGCK 178 " --> pdb=" O PROCK 174 " (cutoff:3.500A) removed outlier: 6.092A 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 'CN' and resid 12 through 17 removed outlier: 3.891A pdb=" N PHECN 16 " --> pdb=" O GLUCN 12 " (cutoff:3.500A) Processing helix chain 'CN' and resid 32 through 43 removed outlier: 3.717A pdb=" N PHECN 38 " --> pdb=" O PHECN 34 " (cutoff:3.500A) removed outlier: 3.610A 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: 4.387A pdb=" N ILECN 233 " --> pdb=" O GLYCN 229 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASNCN 234 " --> pdb=" O PROCN 230 " (cutoff:3.500A) Processing helix chain 'CN' and resid 237 through 246 removed outlier: 3.546A pdb=" N TYRCN 246 " --> pdb=" O VALCN 242 " (cutoff:3.500A) 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: 5.370A 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: 4.125A pdb=" N GLNCQ 70 " --> pdb=" O ASPCQ 66 " (cutoff:3.500A) removed outlier: 4.505A 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: 6.009A pdb=" N GLYCQ 114 " --> pdb=" O LYSCQ 110 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYSCQ 115 " --> pdb=" O ARGCQ 111 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ARGCQ 116 " --> pdb=" O METCQ 112 " (cutoff:3.500A) removed outlier: 5.264A 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: 4.723A pdb=" N LYSCQ 171 " --> pdb=" O LEUCQ 167 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 5 through 10 removed outlier: 3.671A pdb=" N METCb 9 " --> pdb=" O ALACb 5 " (cutoff:3.500A) removed outlier: 5.183A 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: 3.769A pdb=" N LYSCb 39 " --> pdb=" O TYRCb 35 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ALACb 40 " --> pdb=" O LYSCb 36 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 61 through 72 removed outlier: 3.651A pdb=" N LYSCb 70 " --> pdb=" O VALCb 66 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLYCb 71 " --> pdb=" O GLYCb 67 " (cutoff:3.500A) removed outlier: 5.345A 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: 3.684A 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: 3.797A pdb=" N LEUCd 41 " --> pdb=" O THRCd 37 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYSCd 42 " --> pdb=" O LEUCd 38 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 73 through 79 removed outlier: 4.748A pdb=" N PHECd 77 " --> pdb=" O ASNCd 73 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THRCd 78 " --> pdb=" O ARGCd 74 " (cutoff:3.500A) removed outlier: 5.861A 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 Processing helix chain 'Cd' and resid 122 through 139 removed outlier: 3.999A pdb=" N HISCd 130 " --> pdb=" O GLYCd 126 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ALACd 132 " --> pdb=" O LYSCd 128 " (cutoff:3.500A) removed outlier: 5.356A 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: 4.172A pdb=" N ASNCd 215 " --> pdb=" O GLUCd 211 " (cutoff:3.500A) removed outlier: 4.129A 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: 4.413A 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: 3.873A pdb=" N LYSCd 290 " --> pdb=" O ARGCd 286 " (cutoff:3.500A) removed outlier: 4.376A 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: 4.195A pdb=" N VALCd 404 " --> pdb=" O ARGCd 400 " (cutoff:3.500A) removed outlier: 6.205A 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: 3.956A pdb=" N ILECd 411 " --> pdb=" O PROCd 407 " (cutoff:3.500A) Proline residue: Cd 412 - end of helix removed outlier: 5.080A 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: 3.607A pdb=" N GLYCd 471 " --> pdb=" O ASPCd 467 " (cutoff:3.500A) 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: 4.130A pdb=" N PHECf 129 " --> pdb=" O SERCf 125 " (cutoff:3.500A) removed outlier: 5.430A 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 177 through 182 removed outlier: 3.829A pdb=" N LEUCf 181 " --> pdb=" O VALCf 178 " (cutoff:3.500A) removed outlier: 4.669A 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 Processing helix chain 'Cg' and resid 156 through 163 Processing helix chain 'Cg' and resid 168 through 198 removed outlier: 4.225A pdb=" N ASPCg 172 " --> pdb=" O SERCg 168 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LYSCg 173 " --> pdb=" O VALCg 169 " (cutoff:3.500A) removed outlier: 5.384A 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: 3.549A 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 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 38 Processing helix chain 'LA' and resid 103 through 108 removed outlier: 3.901A 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: 4.181A pdb=" N VALLA 191 " --> pdb=" O HISLA 187 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYSLA 192 " --> pdb=" O LYSLA 188 " (cutoff:3.500A) Processing helix chain 'LA' and resid 200 through 205 removed outlier: 3.700A pdb=" N METLA 204 " --> pdb=" O ARGLA 200 " (cutoff:3.500A) removed outlier: 5.345A 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 111 through 120 removed outlier: 3.955A pdb=" N ARGLB 117 " --> pdb=" O GLULB 113 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHELB 118 " --> pdb=" O VALLB 114 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYRLB 119 " --> pdb=" O LYSLB 115 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LYSLB 120 " --> pdb=" O ARGLB 116 " (cutoff:3.500A) Processing helix chain 'LB' and resid 130 through 139 removed outlier: 3.621A pdb=" N LYSLB 135 " --> pdb=" O THRLB 131 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYSLB 136 " --> pdb=" O LYSLB 132 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYRLB 137 " --> pdb=" O TYRLB 133 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALALB 138 " --> pdb=" O ALALB 134 " (cutoff:3.500A) Processing helix chain 'LB' and resid 142 through 155 Processing helix chain 'LB' and resid 166 through 171 removed outlier: 4.721A 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: 4.098A 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: 3.858A 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 Processing helix chain 'LC' and resid 24 through 29 removed outlier: 4.506A pdb=" N SERLC 28 " --> pdb=" O PROLC 24 " (cutoff:3.500A) removed outlier: 3.889A 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: 4.065A pdb=" N LYSLC 45 " --> pdb=" O THRLC 41 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASNLC 46 " --> pdb=" O GLYLC 42 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LYSLC 47 " --> pdb=" O METLC 43 " (cutoff:3.500A) Processing helix chain 'LC' and resid 115 through 133 removed outlier: 3.552A pdb=" N ALALC 131 " --> pdb=" O LEULC 127 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VALLC 132 " --> pdb=" O ALALC 128 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ALALC 133 " --> pdb=" O ALALC 129 " (cutoff:3.500A) Processing helix chain 'LC' and resid 134 through 140 Processing helix chain 'LC' and resid 154 through 159 removed outlier: 3.677A 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: 3.932A pdb=" N LYSLC 189 " --> pdb=" O VALLC 185 " (cutoff:3.500A) Processing helix chain 'LC' and resid 194 through 200 removed outlier: 4.715A pdb=" N METLC 198 " --> pdb=" O GLYLC 194 " (cutoff:3.500A) Processing helix chain 'LC' and resid 220 through 228 removed outlier: 4.003A pdb=" N LYSLC 224 " --> pdb=" O LYSLC 220 " (cutoff:3.500A) removed outlier: 4.409A 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: 5.175A pdb=" N ASPLC 266 " --> pdb=" O ILELC 262 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ALALC 267 " --> pdb=" O LYSLC 263 " (cutoff:3.500A) removed outlier: 3.652A 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: 4.084A pdb=" N VALLC 299 " --> pdb=" O GLULC 295 " (cutoff:3.500A) Processing helix chain 'LC' and resid 318 through 323 removed outlier: 4.465A 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: 4.608A 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: 4.008A 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: 3.711A pdb=" N ARGLD 35 " --> pdb=" O TYRLD 31 " (cutoff:3.500A) Processing helix chain 'LD' and resid 79 through 87 removed outlier: 4.294A pdb=" N LEULD 83 " --> pdb=" O TYRLD 79 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ARGLD 84 " --> pdb=" O SERLD 80 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ALALD 85 " --> pdb=" O HISLD 81 " (cutoff:3.500A) removed outlier: 4.250A 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 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: 4.035A pdb=" N LEULD 239 " --> pdb=" O GLULD 235 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLULD 240 " --> pdb=" O ALALD 236 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLULD 241 " --> pdb=" O ASPLD 237 " (cutoff:3.500A) Processing helix chain 'LD' and resid 266 through 278 removed outlier: 3.640A 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: 3.758A pdb=" N VALLE 102 " --> pdb=" O ASNLE 98 " (cutoff:3.500A) removed outlier: 5.765A 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 128 through 140 removed outlier: 5.011A pdb=" N LYSLE 132 " --> pdb=" O PHELE 128 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ALALE 133 " --> pdb=" O THRLE 129 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LYSLE 134 " --> pdb=" O ALALE 130 " (cutoff:3.500A) Processing helix chain 'LE' and resid 155 through 174 removed outlier: 4.760A pdb=" N ALALE 168 " --> pdb=" O ALALE 164 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEULE 169 " --> pdb=" O ILELE 165 " (cutoff:3.500A) Processing helix chain 'LE' and resid 178 through 186 removed outlier: 5.164A 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: 5.516A pdb=" N GLULF 31 " --> pdb=" O LYSLF 27 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARGLF 32 " --> pdb=" O ALALF 28 " (cutoff:3.500A) Processing helix chain 'LF' and resid 35 through 79 removed outlier: 3.872A pdb=" N GLULF 45 " --> pdb=" O GLNLF 41 " (cutoff:3.500A) removed outlier: 4.087A 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: 3.931A 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: 4.393A 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: 5.094A pdb=" N TRPLF 209 " --> pdb=" O ALALF 205 " (cutoff:3.500A) Processing helix chain 'LF' and resid 240 through 249 removed outlier: 3.836A 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: 5.095A pdb=" N PHELG 81 " --> pdb=" O ALALG 77 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLNLG 82 " --> pdb=" O ILELG 78 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TYRLG 83 " --> pdb=" O ALALG 79 " (cutoff:3.500A) Processing helix chain 'LG' and resid 86 through 101 removed outlier: 4.520A pdb=" N LYSLG 99 " --> pdb=" O LYSLG 95 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYRLG 100 " --> pdb=" O LEULG 96 " (cutoff:3.500A) removed outlier: 3.834A 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: 3.919A 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 Processing helix chain 'LG' and resid 207 through 230 removed outlier: 4.694A pdb=" N ASNLG 212 " --> pdb=" O SERLG 208 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLULG 213 " --> pdb=" O GLULG 209 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEULG 226 " --> pdb=" O LYSLG 222 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLULG 227 " --> pdb=" O GLULG 223 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LYSLG 228 " --> pdb=" O GLYLG 224 " (cutoff:3.500A) Processing helix chain 'LG' and resid 231 through 236 removed outlier: 4.134A pdb=" N ARGLG 235 " --> pdb=" O ASPLG 231 " (cutoff:3.500A) removed outlier: 5.806A 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: 3.958A pdb=" N LEULH 105 " --> pdb=" O ASPLH 101 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARGLH 106 " --> pdb=" O VALLH 102 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THRLH 107 " --> pdb=" O ALALH 103 " (cutoff:3.500A) Processing helix chain 'LH' and resid 189 through 205 removed outlier: 4.016A pdb=" N CYSLH 204 " --> pdb=" O ILELH 200 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LYSLH 205 " --> pdb=" O GLNLH 201 " (cutoff:3.500A) Processing helix chain 'LH' and resid 210 through 215 removed outlier: 4.707A 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: 4.045A pdb=" N PHELJ 97 " --> pdb=" O ARGLJ 93 " (cutoff:3.500A) removed outlier: 5.654A 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: 4.706A pdb=" N LEULJ 113 " --> pdb=" O GLULJ 109 " (cutoff:3.500A) removed outlier: 4.265A 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 137 through 142 removed outlier: 3.781A pdb=" N LYSLJ 141 " --> pdb=" O GLULJ 137 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 150 through 155 removed outlier: 5.952A 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: 4.741A pdb=" N ALALK 27 " --> pdb=" O GLYLK 23 " (cutoff:3.500A) removed outlier: 4.116A 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: 3.737A pdb=" N LYSLK 86 " --> pdb=" O ILELK 82 " (cutoff:3.500A) Processing helix chain 'LK' and resid 105 through 121 removed outlier: 5.009A pdb=" N PHELK 118 " --> pdb=" O ARGLK 114 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N LYSLK 119 " --> pdb=" O THRLK 115 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N PHELK 121 " --> pdb=" O ARGLK 117 " (cutoff:3.500A) 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: 4.398A pdb=" N ARGLL 21 " --> pdb=" O HISLL 17 " (cutoff:3.500A) removed outlier: 3.580A 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: 3.871A pdb=" N GLYLL 94 " --> pdb=" O ALALL 90 " (cutoff:3.500A) Processing helix chain 'LL' and resid 105 through 123 removed outlier: 3.752A pdb=" N LEULL 109 " --> pdb=" O SERLL 105 " (cutoff:3.500A) Processing helix chain 'LL' and resid 139 through 144 removed outlier: 4.284A 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: 4.823A pdb=" N LEULM 63 " --> pdb=" O LEULM 59 " (cutoff:3.500A) Processing helix chain 'LM' and resid 77 through 89 Processing helix chain 'LM' and resid 90 through 98 removed outlier: 5.438A pdb=" N ASNLM 98 " --> pdb=" O TRPLM 94 " (cutoff:3.500A) Processing helix chain 'LM' and resid 99 through 112 removed outlier: 4.408A pdb=" N LEULM 112 " --> pdb=" O ARGLM 108 " (cutoff:3.500A) Processing helix chain 'LM' and resid 113 through 139 Processing helix chain 'LN' and resid 2 through 14 removed outlier: 4.264A pdb=" N TYRLN 6 " --> pdb=" O GLYLN 2 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYSLN 13 " --> pdb=" O GLULN 9 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LYSLN 14 " --> pdb=" O LEULN 10 " (cutoff:3.500A) Processing helix chain 'LN' and resid 16 through 34 removed outlier: 4.662A 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: 3.647A 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: 4.469A pdb=" N CYSLN 152 " --> pdb=" O ILELN 148 " (cutoff:3.500A) removed outlier: 4.271A 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: 3.586A 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 38 through 43 removed outlier: 4.203A pdb=" N LEULO 42 " --> pdb=" O ARGLO 38 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASNLO 43 " --> pdb=" O CYSLO 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'LO' and resid 38 through 43' Processing helix chain 'LO' and resid 47 through 61 removed outlier: 3.607A pdb=" N ALALO 51 " --> pdb=" O GLULO 47 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYSLO 61 " --> pdb=" O ALALO 57 " (cutoff:3.500A) Processing helix chain 'LO' and resid 77 through 91 removed outlier: 3.798A pdb=" N METLO 89 " --> pdb=" O ALALO 85 " (cutoff:3.500A) removed outlier: 3.601A 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: 4.258A pdb=" N ARGLO 103 " --> pdb=" O ALALO 99 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEULO 104 " --> pdb=" O ALALO 100 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LYSLO 105 " --> pdb=" O LEULO 101 " (cutoff:3.500A) Processing helix chain 'LO' and resid 112 through 118 removed outlier: 7.736A pdb=" N LYSLO 116 " --> pdb=" O PROLO 112 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYSLO 117 " --> pdb=" O PROLO 113 " (cutoff:3.500A) removed outlier: 5.531A 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: 4.091A 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: 4.848A 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 172 through 185 Processing helix chain 'LQ' and resid 51 through 68 Processing helix chain 'LQ' and resid 70 through 83 removed outlier: 4.022A pdb=" N LYSLQ 74 " --> pdb=" O ALALQ 70 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N SERLQ 83 " --> pdb=" O ARGLQ 79 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 91 through 100 removed outlier: 3.937A 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: 3.744A pdb=" N VALLR 22 " --> pdb=" O GLYLR 18 " (cutoff:3.500A) removed outlier: 6.039A 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: 3.614A pdb=" N ALALR 35 " --> pdb=" O GLULR 31 " (cutoff:3.500A) removed outlier: 5.433A 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: 5.534A 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: 6.611A 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 153 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: 5.403A pdb=" N HISLS 122 " --> pdb=" O PHELS 118 " (cutoff:3.500A) Processing helix chain 'LS' and resid 137 through 145 removed outlier: 4.351A pdb=" N LEULS 143 " --> pdb=" O TYRLS 139 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALALS 145 " --> pdb=" O LYSLS 141 " (cutoff:3.500A) Processing helix chain 'LT' and resid 92 through 97 removed outlier: 3.684A pdb=" N VALLT 96 " --> pdb=" O ARGLT 92 " (cutoff:3.500A) removed outlier: 4.936A 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 '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 75 removed outlier: 3.701A pdb=" N ARGLV 72 " --> pdb=" O LYSLV 68 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYSLV 73 " --> pdb=" O PROLV 69 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LYSLV 74 " --> pdb=" O GLULV 70 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VALLV 75 " --> pdb=" O LEULV 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'LV' and resid 68 through 75' Processing helix chain 'LV' and resid 121 through 128 Processing helix chain 'LV' and resid 129 through 135 Processing helix chain 'LX' and resid 71 through 77 removed outlier: 4.998A pdb=" N ILELX 77 " --> pdb=" O HISLX 73 " (cutoff:3.500A) Processing helix chain 'LX' and resid 82 through 92 removed outlier: 4.220A 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: 3.572A pdb=" N VALLY 28 " --> pdb=" O SERLY 24 " (cutoff:3.500A) removed outlier: 4.230A 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: 3.842A pdb=" N VALLY 103 " --> pdb=" O HISLY 99 " (cutoff:3.500A) removed outlier: 5.223A 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: 4.242A pdb=" N LYSLZ 66 " --> pdb=" O GLULZ 62 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 75 through 80 removed outlier: 3.549A pdb=" N LEULZ 79 " --> pdb=" O ASNLZ 75 " (cutoff:3.500A) removed outlier: 5.548A 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: 4.080A pdb=" N PHELZ 100 " --> pdb=" O ASNLZ 96 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYSLZ 101 " --> pdb=" O ALALZ 97 " (cutoff:3.500A) removed outlier: 4.085A 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 Processing helix chain 'LZ' and resid 126 through 131 removed outlier: 3.661A pdb=" N PHELZ 130 " --> pdb=" O ASNLZ 126 " (cutoff:3.500A) Processing helix chain 'La' and resid 2 through 7 removed outlier: 3.937A pdb=" N SERLa 6 " --> pdb=" O PROLa 2 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LYSLa 7 " --> pdb=" O THRLa 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'La' and resid 2 through 7' Processing helix chain 'La' and resid 64 through 69 removed outlier: 4.223A pdb=" N TYRLa 68 " --> pdb=" O LEULa 64 " (cutoff:3.500A) Processing helix chain 'La' and resid 74 through 83 removed outlier: 4.483A pdb=" N TRPLa 79 " --> pdb=" O ILELa 75 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N SERLa 80 " --> pdb=" O ASPLa 76 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEULa 81 " --> pdb=" O LYSLa 77 " (cutoff:3.500A) removed outlier: 4.453A 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: 3.610A 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 23 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: 4.121A 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: 4.999A 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 87 removed outlier: 3.665A pdb=" N LEULe 85 " --> pdb=" O LYSLe 81 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEULe 86 " --> pdb=" O ASPLe 82 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEULe 87 " --> pdb=" O VALLe 83 " (cutoff:3.500A) Processing helix chain 'Le' and resid 102 through 117 Processing helix chain 'Lf' and resid 39 through 47 removed outlier: 3.996A pdb=" N PHELf 45 " --> pdb=" O ALALf 41 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N TYRLf 46 " --> pdb=" O ALALf 42 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEULf 47 " --> pdb=" O ALALf 43 " (cutoff:3.500A) Processing helix chain 'Lg' and resid 59 through 67 removed outlier: 3.818A pdb=" N TYRLg 63 " --> pdb=" O ARGLg 59 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALALg 64 " --> pdb=" O PROLg 60 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THRLg 65 " --> pdb=" O ARGLg 61 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILELg 66 " --> pdb=" O GLULg 62 " (cutoff:3.500A) removed outlier: 5.698A 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: 4.314A pdb=" N SERLh 14 " --> pdb=" O GLYLh 10 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYSLh 15 " --> pdb=" O GLNLh 11 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ASNLh 16 " --> pdb=" O LEULh 12 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 17 through 39 removed outlier: 3.542A pdb=" N ILELh 36 " --> pdb=" O SERLh 32 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 44 through 76 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: 3.752A pdb=" N ARGLi 38 " --> pdb=" O ARGLi 34 " (cutoff:3.500A) removed outlier: 4.546A 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: 3.667A pdb=" N GLYLj 9 " --> pdb=" O THRLj 5 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYSLj 10 " --> pdb=" O SERLj 6 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ARGLj 11 " --> pdb=" O SERLj 7 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 50 through 58 removed outlier: 3.668A pdb=" N LYSLj 57 " --> pdb=" O ALALj 53 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 65 through 77 removed outlier: 5.288A pdb=" N THRLj 69 " --> pdb=" O ARGLj 65 " (cutoff:3.500A) removed outlier: 3.884A 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 removed outlier: 3.652A pdb=" N ARGLk 17 " --> pdb=" O GLULk 13 " (cutoff:3.500A) Processing helix chain 'Lk' and resid 52 through 62 removed outlier: 3.974A pdb=" N GLNLk 60 " --> pdb=" O GLULk 56 " (cutoff:3.500A) Processing helix chain 'Ll' and resid 6 through 21 removed outlier: 5.236A pdb=" N ARGLl 21 " --> pdb=" O GLNLl 17 " (cutoff:3.500A) Processing helix chain 'Ll' and resid 24 through 30 removed outlier: 4.230A pdb=" N ARGLl 28 " --> pdb=" O PROLl 24 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEULl 29 " --> pdb=" O GLNLl 25 " (cutoff:3.500A) removed outlier: 3.809A 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: 3.779A pdb=" N LYSLp 28 " --> pdb=" O LYSLp 24 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLNLp 29 " --> pdb=" O LEULp 25 " (cutoff:3.500A) Processing helix chain 'Lp' and resid 73 through 92 Processing helix chain 'Lq' and resid 5 through 14 Processing helix chain 'Lq' and resid 44 through 49 removed outlier: 5.247A pdb=" N ASPLq 49 " --> pdb=" O GLYLq 45 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 86 through 102 removed outlier: 6.023A pdb=" N HISLq 101 " --> pdb=" O GLNLq 97 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLYLq 102 " --> pdb=" O ALALq 98 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 104 through 124 removed outlier: 4.356A pdb=" N ARGLq 108 " --> pdb=" O ARGLq 104 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLNLq 109 " --> pdb=" O ALALq 105 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ALALq 110 " --> pdb=" O ASPLq 106 " (cutoff:3.500A) Proline residue: Lq 124 - end of helix Processing helix chain 'Lq' and resid 135 through 140 Processing sheet with id= 1, first strand: chain 'CF' and resid 63 through 67 removed outlier: 6.834A pdb=" N VALCF 42 " --> pdb=" O LEUCF 224 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'CF' and resid 135 through 139 removed outlier: 6.935A pdb=" N VALCF 135 " --> pdb=" O ILECF 194 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N GLUCF 190 " --> pdb=" O PROCF 139 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'CF' and resid 172 through 175 Processing sheet with id= 4, first strand: chain 'CF' and resid 38 through 42 removed outlier: 8.254A pdb=" N GLNCF 38 " --> pdb=" O SERCF 229 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLYCF 225 " --> pdb=" O VALCF 42 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'CH' and resid 203 through 209 removed outlier: 5.009A pdb=" N ARGCH 167 " --> pdb=" O ARGCH 214 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THRCH 220 " --> pdb=" O VALCH 171 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLYCH 173 " --> pdb=" O THRCH 220 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N METCH 281 " --> pdb=" O ALACH 247 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'CK' and resid 148 through 151 Processing sheet with id= 7, first strand: chain 'CK' and resid 190 through 195 removed outlier: 3.661A pdb=" N VALCK 191 " --> pdb=" O HISCK 186 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASNCK 256 " --> pdb=" O THRCK 246 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N TYRCK 242 " --> pdb=" O LEUCK 260 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THRCK 219 " --> pdb=" O ILECK 245 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'CN' and resid 1 through 4 Processing sheet with id= 9, first strand: chain 'CN' and resid 23 through 27 Processing sheet with id= 10, first strand: chain 'CN' and resid 69 through 72 Processing sheet with id= 11, first strand: chain 'CN' and resid 158 through 161 Processing sheet with id= 12, first strand: chain 'CQ' and resid 3 through 6 removed outlier: 4.654A pdb=" N ARGCQ 11 " --> pdb=" O CYSCQ 6 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'CQ' and resid 18 through 23 removed outlier: 3.895A pdb=" N LYSCQ 27 " --> pdb=" O ARGCQ 23 " (cutoff:3.500A) Processing sheet with id= 14, 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= 15, first strand: chain 'Cd' and resid 293 through 297 removed outlier: 3.930A pdb=" N CYSCd 378 " --> pdb=" O LEUCd 331 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLYCd 333 " --> pdb=" O CYSCd 378 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILECd 373 " --> pdb=" O LEUCd 369 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'Cf' and resid 56 through 60 removed outlier: 5.597A pdb=" N ARGCf 34 " --> pdb=" O PHECf 60 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N SERCf 92 " --> pdb=" O GLYCf 35 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N SERCf 85 " --> pdb=" O METCf 105 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASNCf 93 " --> pdb=" O PROCf 97 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N HISCf 98 " --> pdb=" O LEUCf 118 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N LEUCf 111 " --> pdb=" O PROCf 263 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARGCf 259 " --> pdb=" O GLUCf 115 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'Cf' and resid 140 through 146 removed outlier: 6.789A pdb=" N VALCf 229 " --> pdb=" O HISCf 249 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'Cf' and resid 287 through 290 removed outlier: 4.817A pdb=" N ASPCf 294 " --> pdb=" O ASPCf 290 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'Cg' and resid 21 through 25 Processing sheet with id= 20, first strand: chain 'Cg' and resid 71 through 75 removed outlier: 4.383A pdb=" N THRCg 71 " --> pdb=" O THRCg 82 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'Cg' and resid 124 through 129 removed outlier: 8.658A pdb=" N ASNCg 124 " --> pdb=" O LYSCg 137 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYSCg 137 " --> pdb=" O ASNCg 124 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'Ch' and resid 52 through 56 removed outlier: 4.271A pdb=" N THRCh 121 " --> pdb=" O HISCh 88 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEUCh 94 " --> pdb=" O ILECh 89 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'Ch' and resid 139 through 143 removed outlier: 5.203A pdb=" N ALACh 511 " --> pdb=" O GLYCh 507 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLYCh 507 " --> pdb=" O ALACh 511 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N LEUCh 502 " --> pdb=" O ALACh 497 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'Ch' and resid 151 through 155 removed outlier: 6.346A pdb=" N ARGCh 161 " --> pdb=" O SERCh 155 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N SERCh 160 " --> pdb=" O THRCh 176 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THRCh 170 " --> pdb=" O SERCh 166 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILECh 173 " --> pdb=" O LYSCh 182 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'Ch' and resid 193 through 198 removed outlier: 5.613A pdb=" N TYRCh 203 " --> pdb=" O SERCh 198 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THRCh 212 " --> pdb=" O SERCh 208 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VALCh 215 " --> pdb=" O VALCh 224 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYSCh 222 " --> pdb=" O ASPCh 217 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'Ch' and resid 236 through 241 removed outlier: 5.932A pdb=" N ARGCh 252 " --> pdb=" O GLNCh 241 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALACh 251 " --> pdb=" O VALCh 267 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THRCh 261 " --> pdb=" O SERCh 257 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILECh 264 " --> pdb=" O GLUCh 273 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARGCh 271 " --> pdb=" O LEUCh 266 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'Ch' and resid 284 through 288 removed outlier: 3.982A pdb=" N SERCh 302 " --> pdb=" O SERCh 298 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VALCh 305 " --> pdb=" O VALCh 314 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'Ch' and resid 326 through 330 removed outlier: 3.560A pdb=" N HISCh 326 " --> pdb=" O ALACh 378 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARGCh 374 " --> pdb=" O SERCh 330 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THRCh 383 " --> pdb=" O SERCh 379 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALACh 398 " --> pdb=" O LEUCh 386 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'Ch' and resid 408 through 413 removed outlier: 5.792A pdb=" N LEUCh 418 " --> pdb=" O SERCh 413 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SERCh 427 " --> pdb=" O GLYCh 423 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYSCh 440 " --> pdb=" O LEUCh 430 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'Ch' and resid 451 through 455 removed outlier: 5.828A pdb=" N LEUCh 460 " --> pdb=" O SERCh 455 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ARGCh 459 " --> pdb=" O VALCh 475 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THRCh 469 " --> pdb=" O SERCh 465 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VALCh 472 " --> pdb=" O ALACh 481 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'Ch' and resid 170 through 173 Processing sheet with id= 32, first strand: chain 'Ch' and resid 261 through 264 removed outlier: 3.788A pdb=" N HISCh 274 " --> pdb=" O ILECh 264 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Ch' and resid 302 through 305 Processing sheet with id= 34, first strand: chain 'Ch' and resid 469 through 472 Processing sheet with id= 35, first strand: chain 'LA' and resid 47 through 50 removed outlier: 6.933A pdb=" N ARGLA 60 " --> pdb=" O LYSLA 46 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLNLA 86 " --> pdb=" O VALLA 45 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'LA' and resid 110 through 114 removed outlier: 4.385A pdb=" N THRLA 111 " --> pdb=" O VALLA 136 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ARGLA 147 " --> pdb=" O VALLA 137 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'LA' and resid 58 through 64 No H-bonds generated for sheet with id= 37 Processing sheet with id= 38, first strand: chain 'LA' and resid 145 through 150 removed outlier: 4.336A pdb=" N ALALA 154 " --> pdb=" O LEULA 150 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'LB' and resid 41 through 44 removed outlier: 6.746A pdb=" N GLNLB 183 " --> pdb=" O THRLB 44 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N HISLB 178 " --> pdb=" O THRLB 165 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N VALLB 159 " --> pdb=" O ILELB 184 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEULB 162 " --> pdb=" O VALLB 87 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYSLB 202 " --> pdb=" O VALLB 86 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'LB' and resid 53 through 58 removed outlier: 6.686A pdb=" N ILELB 78 " --> pdb=" O ALALB 51 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ARGLB 335 " --> pdb=" O LYSLB 50 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLULB 214 " --> pdb=" O ILELB 283 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'LB' and resid 98 through 102 removed outlier: 7.014A pdb=" N GLYLB 91 " --> pdb=" O LEULB 102 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THRLB 103 " --> pdb=" O GLYLB 91 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'LB' and resid 285 through 289 removed outlier: 3.842A pdb=" N GLYLB 289 " --> pdb=" O ASNLB 320 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ASNLB 320 " --> pdb=" O GLYLB 289 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'LB' and resid 76 through 80 Processing sheet with id= 44, first strand: chain 'LB' and resid 88 through 93 No H-bonds generated for sheet with id= 44 Processing sheet with id= 45, first strand: chain 'LC' and resid 5 through 9 removed outlier: 4.794A pdb=" N ALALC 19 " --> pdb=" O VALLC 9 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'LC' and resid 76 through 79 removed outlier: 4.395A pdb=" N GLNLC 88 " --> pdb=" O VALLC 78 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'LC' and resid 209 through 212 Processing sheet with id= 48, first strand: chain 'LD' and resid 60 through 66 Processing sheet with id= 49, first strand: chain 'LE' and resid 5 through 9 Processing sheet with id= 50, first strand: chain 'LE' and resid 56 through 61 removed outlier: 4.112A pdb=" N THRLE 56 " --> pdb=" O LEULE 72 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYSLE 68 " --> pdb=" O LEULE 60 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'LF' and resid 139 through 144 removed outlier: 7.573A pdb=" N TRPLF 139 " --> pdb=" O ILELF 95 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASNLF 119 " --> pdb=" O ARGLF 94 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ASNLF 118 " --> pdb=" O LEULF 213 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'LF' and resid 158 through 161 removed outlier: 6.419A pdb=" N GLYLF 158 " --> pdb=" O LEULF 169 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'LG' and resid 179 through 184 Processing sheet with id= 54, first strand: chain 'LH' and resid 5 through 12 removed outlier: 5.738A pdb=" N GLYLH 88 " --> pdb=" O VALLH 12 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'LH' and resid 54 through 57 Processing sheet with id= 56, first strand: chain 'LH' and resid 137 through 144 removed outlier: 3.780A pdb=" N CYSLH 148 " --> pdb=" O ASNLH 143 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TYRLH 149 " --> pdb=" O METLH 167 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'LH' and resid 171 through 176 removed outlier: 5.204A pdb=" N GLULH 182 " --> pdb=" O SERLH 176 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ASPLH 181 " --> pdb=" O TYRLH 129 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'LJ' and resid 46 through 50 removed outlier: 3.519A pdb=" N ALALJ 67 " --> pdb=" O SERLJ 49 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N SERLJ 23 " --> pdb=" O GLYLJ 125 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N GLYLJ 125 " --> pdb=" O SERLJ 23 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'LK' and resid 11 through 16 removed outlier: 4.162A pdb=" N THRLK 59 " --> pdb=" O VALLK 74 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'LM' and resid 18 through 22 removed outlier: 4.627A pdb=" N ARGLM 18 " --> pdb=" O ILELM 30 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SERLM 26 " --> pdb=" O LEULM 22 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEULM 40 " --> pdb=" O VALLM 31 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VALLM 39 " --> pdb=" O ILELM 56 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILELM 56 " --> pdb=" O VALLM 39 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALALM 41 " --> pdb=" O ARGLM 54 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ARGLM 54 " --> pdb=" O ALALM 41 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'LN' and resid 35 through 39 removed outlier: 6.319A pdb=" N VALLN 35 " --> pdb=" O ARGLN 65 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILELN 61 " --> pdb=" O ALALN 39 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLYLN 58 " --> pdb=" O ASPLN 136 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILELN 133 " --> pdb=" O LEULN 116 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'LN' and resid 117 through 121 removed outlier: 3.715A pdb=" N ASNLN 117 " --> pdb=" O ILELN 133 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N TYRLN 129 " --> pdb=" O VALLN 121 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'LO' and resid 7 through 11 Processing sheet with id= 64, first strand: chain 'LP' and resid 14 through 20 removed outlier: 6.624A pdb=" N ILELP 149 " --> pdb=" O LYSLP 115 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'LP' and resid 57 through 60 removed outlier: 5.532A pdb=" N ARGLP 80 " --> pdb=" O METLP 60 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'LP' and resid 116 through 122 Processing sheet with id= 67, first strand: chain 'LP' and resid 124 through 131 removed outlier: 4.274A pdb=" N ARGLP 127 " --> pdb=" O TYRLP 139 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARGLP 135 " --> pdb=" O ARGLP 131 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'LQ' and resid 106 through 110 Processing sheet with id= 69, first strand: chain 'LS' and resid 24 through 30 removed outlier: 6.714A pdb=" N ILELS 10 " --> pdb=" O VALLS 59 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'LS' and resid 89 through 95 removed outlier: 5.165A pdb=" N ASNLS 74 " --> pdb=" O LEULS 129 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'LS' and resid 6 through 10 removed outlier: 4.664A pdb=" N GLULS 6 " --> pdb=" O ILELS 64 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'LT' and resid 40 through 43 removed outlier: 3.778A pdb=" N LYSLT 60 " --> pdb=" O ILELT 42 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'LT' and resid 72 through 79 Processing sheet with id= 74, first strand: chain 'LU' and resid 60 through 64 removed outlier: 5.540A pdb=" N GLYLU 108 " --> pdb=" O LYSLU 20 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'LV' and resid 22 through 26 removed outlier: 4.241A pdb=" N ALALV 23 " --> pdb=" O ILELV 38 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'LV' and resid 58 through 62 removed outlier: 4.240A pdb=" N ASPLV 58 " --> pdb=" O ILELV 80 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASPLV 99 " --> pdb=" O ALALV 84 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALALV 84 " --> pdb=" O ASPLV 99 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'LV' and resid 86 through 89 removed outlier: 4.129A pdb=" N VALLV 93 " --> pdb=" O ARGLV 89 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'LX' and resid 93 through 99 removed outlier: 6.709A pdb=" N ASNLX 93 " --> pdb=" O LEULX 139 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYSLX 133 " --> pdb=" O VALLX 99 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THRLX 132 " --> pdb=" O ARGLX 128 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYSLX 122 " --> pdb=" O ARGLX 138 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'LY' and resid 55 through 58 removed outlier: 3.967A pdb=" N LYSLY 65 " --> pdb=" O ILELY 57 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'LY' and resid 85 through 88 removed outlier: 4.915A pdb=" N GLNLY 92 " --> pdb=" O LYSLY 88 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'LZ' and resid 9 through 13 removed outlier: 3.792A pdb=" N LYSLZ 20 " --> pdb=" O VALLZ 12 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'LZ' and resid 26 through 29 Processing sheet with id= 83, first strand: chain 'La' and resid 99 through 102 Processing sheet with id= 84, first strand: chain 'Lc' and resid 25 through 28 removed outlier: 5.957A pdb=" N LYSLc 25 " --> pdb=" O LEULc 96 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'Ld' and resid 56 through 59 removed outlier: 4.859A pdb=" N ASPLd 56 " --> pdb=" O LEULd 97 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ALALd 17 " --> pdb=" O VALLd 117 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'Le' and resid 72 through 78 Processing sheet with id= 87, first strand: chain 'Lf' and resid 12 through 17 removed outlier: 6.072A pdb=" N LYSLf 12 " --> pdb=" O GLULf 35 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEULf 31 " --> pdb=" O LEULf 16 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ARGLf 84 " --> pdb=" O THRLf 74 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LYSLf 65 " --> pdb=" O ALALf 57 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LYSLf 49 " --> pdb=" O ILELf 73 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ARGLf 50 " --> pdb=" O METLf 103 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'Lf' and resid 10 through 16 No H-bonds generated for sheet with id= 88 Processing sheet with id= 89, first strand: chain 'Lg' and resid 20 through 25 removed outlier: 4.556A pdb=" N ARGLg 20 " --> pdb=" O ILELg 36 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'Lk' and resid 2 through 5 removed outlier: 4.466A pdb=" N VALLk 48 " --> pdb=" O VALLk 5 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SERLk 22 " --> pdb=" O ARGLk 39 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LYSLk 27 " --> pdb=" O VALLk 71 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'Lp' and resid 47 through 50 removed outlier: 6.956A pdb=" N ILELp 54 " --> pdb=" O THRLp 50 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLYLp 53 " --> pdb=" O GLYLp 66 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYSLp 62 " --> pdb=" O CYSLp 57 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'Lq' and resid 20 through 23 removed outlier: 3.633A pdb=" N GLYLq 26 " --> pdb=" O GLNLq 23 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'Lq' and resid 51 through 56 removed outlier: 5.149A pdb=" N ALALq 51 " --> pdb=" O LYSLq 66 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N SERLq 77 " --> pdb=" O LYSLq 67 " (cutoff:3.500A) 3189 hydrogen bonds defined for protein. 9471 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2647 hydrogen bonds 4406 hydrogen bond angles 0 basepair planarities 1047 basepair parallelities 1883 stacking parallelities Total time for adding SS restraints: 216.77 Time building geometry restraints manager: 59.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 21158 1.33 - 1.45: 58015 1.45 - 1.57: 67961 1.57 - 1.70: 6677 1.70 - 1.82: 380 Bond restraints: 154191 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 2.32e+02 bond pdb=" C3' A2MC12289 " pdb=" C2' A2MC12289 " 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 848 " pdb=" C2' A2MC1 848 " 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 1.241 0.303 2.00e-02 2.50e+03 2.29e+02 bond pdb=" C3' A2MC1 637 " pdb=" C2' A2MC1 637 " ideal model delta sigma weight residual 1.544 1.242 0.302 2.00e-02 2.50e+03 2.28e+02 ... (remaining 154186 not shown) Histogram of bond angle deviations from ideal: 95.24 - 105.36: 16732 105.36 - 115.47: 105966 115.47 - 125.59: 88907 125.59 - 135.70: 12765 135.70 - 145.81: 8 Bond angle restraints: 224378 Sorted by residual: angle pdb=" CB ARGCQ 161 " pdb=" CG ARGCQ 161 " pdb=" CD ARGCQ 161 " ideal model delta sigma weight residual 111.30 128.99 -17.69 2.30e+00 1.89e-01 5.92e+01 angle pdb=" C1' OMGC1 385 " pdb=" N9 OMGC1 385 " pdb=" C4 OMGC1 385 " ideal model delta sigma weight residual 108.29 129.13 -20.84 3.00e+00 1.11e-01 4.83e+01 angle pdb=" C1' OMGC11433 " pdb=" N9 OMGC11433 " pdb=" C4 OMGC11433 " ideal model delta sigma weight residual 108.29 127.78 -19.49 3.00e+00 1.11e-01 4.22e+01 angle pdb=" C1' A2MC1 389 " pdb=" N9 A2MC1 389 " pdb=" C4 A2MC1 389 " ideal model delta sigma weight residual 126.51 145.81 -19.30 3.00e+00 1.11e-01 4.14e+01 angle pdb=" C1' A2MC1 637 " pdb=" N9 A2MC1 637 " pdb=" C4 A2MC1 637 " ideal model delta sigma weight residual 126.51 145.81 -19.30 3.00e+00 1.11e-01 4.14e+01 ... (remaining 224373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 89149 35.84 - 71.67: 7759 71.67 - 107.51: 960 107.51 - 143.34: 19 143.34 - 179.18: 37 Dihedral angle restraints: 97924 sinusoidal: 71311 harmonic: 26613 Sorted by residual: dihedral pdb=" C4' CC13324 " pdb=" C3' CC13324 " pdb=" C2' CC13324 " pdb=" C1' CC13324 " ideal model delta sinusoidal sigma weight residual -35.00 33.62 -68.62 1 8.00e+00 1.56e-02 9.53e+01 dihedral pdb=" C5' CC13324 " pdb=" C4' CC13324 " pdb=" C3' CC13324 " pdb=" O3' CC13324 " ideal model delta sinusoidal sigma weight residual 147.00 79.11 67.89 1 8.00e+00 1.56e-02 9.36e+01 dihedral pdb=" O4' UC12100 " pdb=" C1' UC12100 " pdb=" N1 UC12100 " pdb=" C2 UC12100 " ideal model delta sinusoidal sigma weight residual 200.00 34.85 165.15 1 1.50e+01 4.44e-03 8.39e+01 ... (remaining 97921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 25516 0.073 - 0.146: 1888 0.146 - 0.218: 136 0.218 - 0.291: 22 0.291 - 0.364: 4 Chirality restraints: 27566 Sorted by residual: chirality pdb=" C3' CC13324 " pdb=" C4' CC13324 " pdb=" O3' CC13324 " pdb=" C2' CC13324 " both_signs ideal model delta sigma weight residual False -2.74 -2.38 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" C3' CC11267 " pdb=" C4' CC11267 " pdb=" O3' CC11267 " pdb=" C2' CC11267 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.32 2.00e-01 2.50e+01 2.60e+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 -2.43 -0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 27563 not shown) Planarity restraints: 16159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMGC12578 " 0.060 2.00e-02 2.50e+03 5.86e-01 7.73e+03 pdb=" C4' OMGC12578 " 0.430 2.00e-02 2.50e+03 pdb=" O4' OMGC12578 " 0.607 2.00e-02 2.50e+03 pdb=" C3' OMGC12578 " -0.598 2.00e-02 2.50e+03 pdb=" O3' OMGC12578 " -0.619 2.00e-02 2.50e+03 pdb=" C2' OMGC12578 " -0.183 2.00e-02 2.50e+03 pdb=" O2' OMGC12578 " 0.963 2.00e-02 2.50e+03 pdb=" C1' OMGC12578 " 0.225 2.00e-02 2.50e+03 pdb=" N9 OMGC12578 " -0.885 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMCC11420 " -0.024 2.00e-02 2.50e+03 5.81e-01 7.60e+03 pdb=" C4' OMCC11420 " -0.443 2.00e-02 2.50e+03 pdb=" O4' OMCC11420 " -0.710 2.00e-02 2.50e+03 pdb=" C3' OMCC11420 " 0.595 2.00e-02 2.50e+03 pdb=" O3' OMCC11420 " 0.564 2.00e-02 2.50e+03 pdb=" C2' OMCC11420 " 0.233 2.00e-02 2.50e+03 pdb=" O2' OMCC11420 " -0.890 2.00e-02 2.50e+03 pdb=" C1' OMCC11420 " -0.207 2.00e-02 2.50e+03 pdb=" N1 OMCC11420 " 0.883 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMGC12876 " 0.026 2.00e-02 2.50e+03 5.75e-01 7.44e+03 pdb=" C4' OMGC12876 " 0.446 2.00e-02 2.50e+03 pdb=" O4' OMGC12876 " 0.666 2.00e-02 2.50e+03 pdb=" C3' OMGC12876 " -0.584 2.00e-02 2.50e+03 pdb=" O3' OMGC12876 " -0.566 2.00e-02 2.50e+03 pdb=" C2' OMGC12876 " -0.221 2.00e-02 2.50e+03 pdb=" O2' OMGC12876 " 0.894 2.00e-02 2.50e+03 pdb=" C1' OMGC12876 " 0.219 2.00e-02 2.50e+03 pdb=" N9 OMGC12876 " -0.881 2.00e-02 2.50e+03 ... (remaining 16156 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 6137 2.68 - 3.23: 119627 3.23 - 3.79: 278641 3.79 - 4.34: 371166 4.34 - 4.90: 518647 Nonbonded interactions: 1294218 Sorted by model distance: nonbonded pdb=" O2G GTPCd1000 " pdb="MG MGCd1002 " model vdw 2.121 2.170 nonbonded pdb=" OG1 THRCd 361 " pdb="MG MGCd1002 " model vdw 2.121 2.170 nonbonded pdb="MG MGCd1002 " pdb=" O HOHCd1101 " model vdw 2.154 2.170 nonbonded pdb=" OD1 ASNCd 336 " pdb="MG MGCd1001 " model vdw 2.193 2.170 nonbonded pdb=" O2 UC11685 " pdb=" O2' GC11766 " model vdw 2.199 2.440 ... (remaining 1294213 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 8.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 31.550 Check model and map are aligned: 0.510 Set scattering table: 0.980 Process input model: 533.340 Find NCS groups from input model: 3.650 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 589.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 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 154191 Z= 0.341 Angle : 0.733 20.839 224378 Z= 0.368 Chirality : 0.039 0.364 27566 Planarity : 0.020 0.586 16159 Dihedral : 21.284 179.179 80710 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.73 % Favored : 98.26 % Rotamer: Outliers : 0.01 % Allowed : 0.17 % Favored : 99.82 % 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: 0.06 (0.08), residues: 9079 helix: 0.38 (0.08), residues: 3395 sheet: 0.10 (0.14), residues: 1343 loop : -0.10 (0.09), residues: 4341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRPCQ 86 HIS 0.016 0.001 HISLB 244 PHE 0.033 0.002 PHELS 118 TYR 0.039 0.002 TYRLj 39 ARG 0.016 0.001 ARGCQ 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18158 Ramachandran restraints generated. 9079 Oldfield, 0 Emsley, 9079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18158 Ramachandran restraints generated. 9079 Oldfield, 0 Emsley, 9079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1259 residues out of total 7822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1259 time to evaluate : 8.019 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 52 TYR cc_start: 0.6145 (m-80) cc_final: 0.5861 (m-10) REVERT: CH 390 LEU cc_start: 0.7398 (pp) cc_final: 0.7162 (pp) REVERT: CQ 42 MET cc_start: 0.8663 (mtm) cc_final: 0.8456 (mtm) REVERT: Cf 138 MET cc_start: 0.8557 (ttm) cc_final: 0.8345 (ttp) REVERT: Cg 49 GLN cc_start: 0.8201 (tp-100) cc_final: 0.7992 (tp-100) REVERT: Ch 49 MET cc_start: 0.5980 (pmm) cc_final: 0.5600 (pmm) REVERT: LJ 58 PHE cc_start: 0.8073 (m-10) cc_final: 0.7808 (m-80) REVERT: LM 36 HIS cc_start: 0.6113 (p90) cc_final: 0.5782 (p-80) REVERT: LR 96 MET cc_start: 0.8627 (ttp) cc_final: 0.8372 (ttp) REVERT: LR 140 GLU cc_start: 0.6984 (pp20) cc_final: 0.6685 (pp20) REVERT: LT 114 GLU cc_start: 0.8021 (pp20) cc_final: 0.7806 (pp20) outliers start: 0 outliers final: 3 residues processed: 1259 average time/residue: 2.2729 time to fit residues: 4015.2883 Evaluate side-chains 898 residues out of total 7822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 895 time to evaluate : 7.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Cb residue 33 GLN Chi-restraints excluded: chain Ch residue 102 ASP Chi-restraints excluded: chain LG residue 67 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1230 random chunks: chunk 1038 optimal weight: 2.9990 chunk 932 optimal weight: 5.9990 chunk 517 optimal weight: 2.9990 chunk 318 optimal weight: 10.0000 chunk 628 optimal weight: 6.9990 chunk 498 optimal weight: 1.9990 chunk 964 optimal weight: 1.9990 chunk 373 optimal weight: 2.9990 chunk 586 optimal weight: 10.0000 chunk 717 optimal weight: 2.9990 chunk 1116 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 58 HIS CH 551 GLN CH 641 HIS CN 79 GLN CN 170 GLN Cd 159 ASN Cf 54 GLN ** Cg 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cg 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 141 ASN ** LB 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LB 379 GLN LC 324 GLN LE 35 GLN ** LF 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 148 ASN LH 208 ASN LJ 16 GLN LQ 86 ASN LQ 163 ASN LQ 172 ASN LR 130 ASN LU 24 ASN LX 92 GLN Ld 49 GLN ** Le 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lf 15 HIS Lp 45 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 154191 Z= 0.273 Angle : 0.699 16.847 224378 Z= 0.369 Chirality : 0.038 0.268 27566 Planarity : 0.007 0.132 16159 Dihedral : 22.839 179.272 62017 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.06 % Allowed : 8.94 % Favored : 88.99 % 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: 0.62 (0.08), residues: 9079 helix: 1.15 (0.09), residues: 3416 sheet: 0.03 (0.14), residues: 1362 loop : 0.08 (0.09), residues: 4301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRPCL 45 HIS 0.012 0.002 HISLB 244 PHE 0.023 0.002 PHECH 90 TYR 0.022 0.002 TYRLF 57 ARG 0.012 0.001 ARGCH 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18158 Ramachandran restraints generated. 9079 Oldfield, 0 Emsley, 9079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18158 Ramachandran restraints generated. 9079 Oldfield, 0 Emsley, 9079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1139 residues out of total 7822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 981 time to evaluate : 8.078 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: CF 8 ARG cc_start: 0.5127 (OUTLIER) cc_final: 0.4298 (pmt170) REVERT: CH 301 MET cc_start: 0.7405 (mmm) cc_final: 0.7043 (mmp) REVERT: CO 19 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7614 (tppt) REVERT: Cb 24 ARG cc_start: 0.7718 (mmm-85) cc_final: 0.7418 (mtp-110) REVERT: Cf 87 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7890 (mtt) REVERT: Cf 138 MET cc_start: 0.8505 (ttm) cc_final: 0.8297 (ttp) REVERT: Cz 76 ARG cc_start: 0.8870 (tpp-160) cc_final: 0.8555 (mmp80) REVERT: LA 46 LYS cc_start: 0.6931 (mmmt) cc_final: 0.6365 (tptp) REVERT: LA 64 ARG cc_start: 0.7635 (tpt-90) cc_final: 0.6218 (tpt170) REVERT: LA 83 TYR cc_start: 0.7810 (p90) cc_final: 0.7426 (p90) REVERT: LE 78 GLN cc_start: 0.7290 (mt0) cc_final: 0.7057 (mm110) REVERT: LG 41 GLN cc_start: 0.6864 (mm110) cc_final: 0.6433 (mm110) REVERT: LG 42 ASP cc_start: 0.7164 (t0) cc_final: 0.6711 (t70) REVERT: LK 124 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6792 (p0) REVERT: LL 200 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7721 (tmmm) REVERT: LM 36 HIS cc_start: 0.6262 (p90) cc_final: 0.5934 (p-80) REVERT: LM 137 LYS cc_start: 0.6682 (mmtt) cc_final: 0.6219 (mmtt) REVERT: LS 29 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8508 (mm) REVERT: LS 158 LYS cc_start: 0.7132 (mppt) cc_final: 0.6865 (mptt) REVERT: LU 31 ASP cc_start: 0.8077 (m-30) cc_final: 0.7824 (m-30) REVERT: LU 50 ASP cc_start: 0.8187 (p0) cc_final: 0.7688 (p0) REVERT: LU 52 ARG cc_start: 0.7282 (mtm-85) cc_final: 0.6846 (mtm-85) REVERT: LX 144 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7569 (t70) REVERT: LY 40 GLU cc_start: 0.7650 (pm20) cc_final: 0.7424 (pm20) REVERT: La 95 LYS cc_start: 0.5825 (ptmt) cc_final: 0.5599 (ptmt) REVERT: Lc 58 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6665 (mm-30) REVERT: Le 88 MET cc_start: 0.5206 (OUTLIER) cc_final: 0.4857 (mmm) REVERT: Lq 123 ARG cc_start: 0.6264 (mpt180) cc_final: 0.5837 (mpt180) outliers start: 158 outliers final: 62 residues processed: 1054 average time/residue: 2.1952 time to fit residues: 3309.3306 Evaluate side-chains 953 residues out of total 7822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 882 time to evaluate : 7.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CF residue 8 ARG Chi-restraints excluded: chain CH residue 446 VAL Chi-restraints excluded: chain CK residue 118 SER Chi-restraints excluded: chain CK residue 130 GLU Chi-restraints excluded: chain CN residue 78 ASP Chi-restraints excluded: chain CN residue 166 SER Chi-restraints excluded: chain CO residue 19 LYS Chi-restraints excluded: chain CQ residue 82 ASN Chi-restraints excluded: chain Cb residue 47 LEU Chi-restraints excluded: chain Cb residue 95 ILE Chi-restraints excluded: chain Cd residue 436 ILE Chi-restraints excluded: chain Cd residue 442 LEU Chi-restraints excluded: chain Cf residue 87 MET Chi-restraints excluded: chain Cg residue 71 THR Chi-restraints excluded: chain Cz residue 25 MET Chi-restraints excluded: chain Cz residue 83 ILE Chi-restraints excluded: chain Cz residue 111 LEU Chi-restraints excluded: chain LA residue 45 VAL Chi-restraints excluded: chain LA residue 49 ILE Chi-restraints excluded: chain LB residue 299 THR Chi-restraints excluded: chain LB residue 337 MET Chi-restraints excluded: chain LB residue 355 VAL Chi-restraints excluded: chain LC residue 265 LEU Chi-restraints excluded: chain LC residue 266 ASP Chi-restraints excluded: chain LC residue 294 THR Chi-restraints excluded: chain LE residue 6 THR Chi-restraints excluded: chain LE residue 122 VAL Chi-restraints excluded: chain LF residue 213 LEU Chi-restraints excluded: chain LH residue 166 VAL Chi-restraints excluded: chain LJ residue 23 SER Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 49 SER Chi-restraints excluded: chain LK residue 124 ASP Chi-restraints excluded: chain LL residue 200 LYS Chi-restraints excluded: chain LM residue 111 SER Chi-restraints excluded: chain LO residue 3 SER Chi-restraints excluded: chain LO residue 36 VAL Chi-restraints excluded: chain LP residue 169 SER Chi-restraints excluded: chain LQ residue 160 THR Chi-restraints excluded: chain LR residue 107 VAL Chi-restraints excluded: chain LR residue 112 SER Chi-restraints excluded: chain LS residue 29 ILE Chi-restraints excluded: chain LS residue 84 ARG Chi-restraints excluded: chain LS residue 87 THR Chi-restraints excluded: chain LS residue 164 ILE Chi-restraints excluded: chain LT residue 39 ILE Chi-restraints excluded: chain LT residue 140 THR Chi-restraints excluded: chain LU residue 30 SER Chi-restraints excluded: chain LV residue 117 THR Chi-restraints excluded: chain LX residue 144 ASP Chi-restraints excluded: chain LY residue 114 ARG Chi-restraints excluded: chain La residue 72 SER Chi-restraints excluded: chain Lc residue 58 GLU Chi-restraints excluded: chain Ld residue 52 MET Chi-restraints excluded: chain Le residue 11 VAL Chi-restraints excluded: chain Le residue 31 SER Chi-restraints excluded: chain Le residue 88 MET Chi-restraints excluded: chain Le residue 92 THR Chi-restraints excluded: chain Le residue 111 THR Chi-restraints excluded: chain Le residue 118 VAL Chi-restraints excluded: chain Lg residue 23 VAL Chi-restraints excluded: chain Lg residue 41 THR Chi-restraints excluded: chain Lh residue 76 LYS Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Li residue 46 THR Chi-restraints excluded: chain Lj residue 59 THR Chi-restraints excluded: chain Lk residue 5 VAL Chi-restraints excluded: chain Lk residue 46 THR Chi-restraints excluded: chain Lk residue 62 LEU Chi-restraints excluded: chain Lp residue 56 SER Chi-restraints excluded: chain Lq residue 7 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1230 random chunks: chunk 620 optimal weight: 0.7980 chunk 346 optimal weight: 0.8980 chunk 929 optimal weight: 0.7980 chunk 760 optimal weight: 1.9990 chunk 308 optimal weight: 5.9990 chunk 1118 optimal weight: 4.9990 chunk 1208 optimal weight: 4.9990 chunk 996 optimal weight: 0.0170 chunk 1109 optimal weight: 1.9990 chunk 381 optimal weight: 3.9990 chunk 897 optimal weight: 4.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CH 266 GLN CH 641 HIS CN 170 GLN ** Cg 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cg 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ch 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 141 ASN ** LB 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LB 379 GLN LD 42 ASN LF 10 ASN LH 202 GLN LH 208 ASN LL 142 GLN LQ 98 ASN LQ 163 ASN LQ 172 ASN ** LR 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LZ 75 ASN Ld 49 GLN ** Le 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lj 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lp 45 ASN ** Lq 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.089 154191 Z= 0.146 Angle : 0.610 16.929 224378 Z= 0.329 Chirality : 0.034 0.257 27566 Planarity : 0.006 0.126 16159 Dihedral : 22.758 178.998 62010 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.83 % Allowed : 11.40 % Favored : 86.77 % 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 (0.09), residues: 9079 helix: 1.59 (0.09), residues: 3419 sheet: -0.00 (0.14), residues: 1391 loop : 0.21 (0.09), residues: 4269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRPCL 45 HIS 0.009 0.001 HISLB 244 PHE 0.020 0.001 PHELJ 58 TYR 0.016 0.001 TYRLG 100 ARG 0.013 0.000 ARGCH 246 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18158 Ramachandran restraints generated. 9079 Oldfield, 0 Emsley, 9079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18158 Ramachandran restraints generated. 9079 Oldfield, 0 Emsley, 9079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1087 residues out of total 7822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 947 time to evaluate : 8.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CH 85 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: CH 301 MET cc_start: 0.7708 (mmm) cc_final: 0.7230 (mmp) REVERT: CH 360 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6512 (ttt-90) REVERT: CH 470 LYS cc_start: 0.8907 (ttmt) cc_final: 0.8597 (ptpt) REVERT: CL 45 TRP cc_start: 0.7619 (m-10) cc_final: 0.6938 (m-10) REVERT: CO 19 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7613 (tppt) REVERT: Cf 87 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7858 (mtt) REVERT: Cz 77 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8322 (mm-40) REVERT: Cz 103 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7316 (ppp) REVERT: LA 64 ARG cc_start: 0.7643 (tpt-90) cc_final: 0.6240 (tpt170) REVERT: LA 83 TYR cc_start: 0.7798 (p90) cc_final: 0.7483 (p90) REVERT: LE 22 GLU cc_start: 0.7402 (tp30) cc_final: 0.7011 (tm-30) REVERT: LE 78 GLN cc_start: 0.7195 (mt0) cc_final: 0.6966 (mm110) REVERT: LG 41 GLN cc_start: 0.6852 (mm110) cc_final: 0.6323 (mm110) REVERT: LG 42 ASP cc_start: 0.7112 (t0) cc_final: 0.6755 (t70) REVERT: LG 147 GLU cc_start: 0.6879 (tp30) cc_final: 0.6676 (tp30) REVERT: LK 124 ASP cc_start: 0.6961 (OUTLIER) cc_final: 0.6751 (p0) REVERT: LL 200 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7673 (tmmm) REVERT: LM 36 HIS cc_start: 0.6143 (p90) cc_final: 0.5807 (p-80) REVERT: LM 137 LYS cc_start: 0.6698 (mmtt) cc_final: 0.6465 (mmtt) REVERT: LR 140 GLU cc_start: 0.7616 (pp20) cc_final: 0.7196 (pp20) REVERT: LS 29 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8461 (mm) REVERT: LS 158 LYS cc_start: 0.7210 (mppt) cc_final: 0.6949 (mptt) REVERT: LU 50 ASP cc_start: 0.8157 (p0) cc_final: 0.7885 (p0) REVERT: LU 52 ARG cc_start: 0.7299 (mtm-85) cc_final: 0.7043 (mtm-85) REVERT: LX 144 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7537 (t70) REVERT: La 58 MET cc_start: 0.8701 (mtm) cc_final: 0.8430 (mtt) REVERT: Lg 30 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7318 (tt0) REVERT: Lk 4 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7461 (tt0) outliers start: 140 outliers final: 55 residues processed: 1013 average time/residue: 2.1198 time to fit residues: 3083.6831 Evaluate side-chains 942 residues out of total 7822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 876 time to evaluate : 7.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 360 ARG Chi-restraints excluded: chain CH residue 446 VAL Chi-restraints excluded: chain CK residue 118 SER Chi-restraints excluded: chain CN residue 166 SER Chi-restraints excluded: chain CO residue 19 LYS Chi-restraints excluded: chain CQ residue 82 ASN Chi-restraints excluded: chain CQ residue 163 GLU Chi-restraints excluded: chain Cb residue 47 LEU Chi-restraints excluded: chain Cb residue 95 ILE Chi-restraints excluded: chain Cd residue 436 ILE Chi-restraints excluded: chain Cd residue 442 LEU Chi-restraints excluded: chain Cf residue 87 MET Chi-restraints excluded: chain Cg residue 71 THR Chi-restraints excluded: chain Cz residue 103 MET Chi-restraints excluded: chain Cz residue 111 LEU Chi-restraints excluded: chain LA residue 49 ILE Chi-restraints excluded: chain LA residue 130 SER Chi-restraints excluded: chain LB residue 355 VAL Chi-restraints excluded: chain LC residue 266 ASP Chi-restraints excluded: chain LC residue 299 VAL Chi-restraints excluded: chain LE residue 6 THR Chi-restraints excluded: chain LG residue 223 GLU Chi-restraints excluded: chain LJ residue 23 SER Chi-restraints excluded: chain LJ residue 49 SER Chi-restraints excluded: chain LK residue 124 ASP Chi-restraints excluded: chain LL residue 166 THR Chi-restraints excluded: chain LL residue 200 LYS Chi-restraints excluded: chain LM residue 107 GLU Chi-restraints excluded: chain LM residue 111 SER Chi-restraints excluded: chain LO residue 3 SER Chi-restraints excluded: chain LO residue 36 VAL Chi-restraints excluded: chain LO residue 54 LYS Chi-restraints excluded: chain LP residue 169 SER Chi-restraints excluded: chain LQ residue 109 VAL Chi-restraints excluded: chain LQ residue 160 THR Chi-restraints excluded: chain LR residue 29 VAL Chi-restraints excluded: chain LR residue 107 VAL Chi-restraints excluded: chain LR residue 112 SER Chi-restraints excluded: chain LS residue 29 ILE Chi-restraints excluded: chain LS residue 84 ARG Chi-restraints excluded: chain LS residue 88 HIS Chi-restraints excluded: chain LT residue 39 ILE Chi-restraints excluded: chain LU residue 37 SER Chi-restraints excluded: chain LX residue 119 ASP Chi-restraints excluded: chain LX residue 144 ASP Chi-restraints excluded: chain LY residue 107 LYS Chi-restraints excluded: chain LY residue 114 ARG Chi-restraints excluded: chain La residue 72 SER Chi-restraints excluded: chain Ld residue 52 MET Chi-restraints excluded: chain Le residue 11 VAL Chi-restraints excluded: chain Le residue 31 SER Chi-restraints excluded: chain Le residue 92 THR Chi-restraints excluded: chain Le residue 118 VAL Chi-restraints excluded: chain Lf residue 66 ILE Chi-restraints excluded: chain Lg residue 30 GLN Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Li residue 46 THR Chi-restraints excluded: chain Li residue 77 ARG Chi-restraints excluded: chain Lk residue 4 GLU Chi-restraints excluded: chain Lk residue 5 VAL Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 70 ASP Chi-restraints excluded: chain Lp residue 56 SER Chi-restraints excluded: chain Lq residue 7 ASP Chi-restraints excluded: chain Lq residue 24 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1230 random chunks: chunk 1105 optimal weight: 9.9990 chunk 841 optimal weight: 20.0000 chunk 580 optimal weight: 0.6980 chunk 123 optimal weight: 7.9990 chunk 534 optimal weight: 4.9990 chunk 751 optimal weight: 3.9990 chunk 1123 optimal weight: 10.0000 chunk 1188 optimal weight: 0.9990 chunk 586 optimal weight: 10.0000 chunk 1064 optimal weight: 7.9990 chunk 320 optimal weight: 8.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CF 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CH 641 HIS ** CQ 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cd 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cg 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cg 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ch 517 ASN LB 141 ASN ** LB 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LB 379 GLN LC 315 GLN LF 10 ASN ** LF 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 240 HIS LH 208 ASN LJ 96 ASN LL 142 GLN LP 120 ASN LP 137 ASN LQ 172 ASN ** LR 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LU 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LZ 35 HIS LZ 39 HIS ** LZ 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** La 62 HIS Ld 49 GLN ** Le 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lg 84 ASN ** Lh 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lp 45 ASN Lq 97 GLN Lq 101 HIS ** Lq 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 154191 Z= 0.396 Angle : 0.756 17.272 224378 Z= 0.393 Chirality : 0.043 0.305 27566 Planarity : 0.007 0.138 16159 Dihedral : 22.835 178.620 62010 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.78 % Allowed : 12.21 % Favored : 85.01 % 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: 0.67 (0.09), residues: 9079 helix: 1.33 (0.09), residues: 3416 sheet: -0.25 (0.13), residues: 1373 loop : 0.08 (0.09), residues: 4290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRPCg 105 HIS 0.011 0.002 HISLB 244 PHE 0.025 0.003 PHELC 121 TYR 0.040 0.003 TYRLH 3 ARG 0.010 0.001 ARGCb 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18158 Ramachandran restraints generated. 9079 Oldfield, 0 Emsley, 9079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18158 Ramachandran restraints generated. 9079 Oldfield, 0 Emsley, 9079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1142 residues out of total 7822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 929 time to evaluate : 8.249 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 85 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.7767 (m-80) REVERT: CH 388 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8113 (mppt) REVERT: CL 45 TRP cc_start: 0.7950 (m-10) cc_final: 0.7401 (m-10) REVERT: CO 19 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7760 (tppt) REVERT: CQ 22 MET cc_start: 0.8391 (mmt) cc_final: 0.8075 (mmt) REVERT: Cd 53 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7675 (ttmt) REVERT: Cf 87 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7938 (mtt) REVERT: Cf 138 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7957 (ttt) REVERT: Cz 103 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7527 (ppp) REVERT: LA 64 ARG cc_start: 0.7628 (tpt-90) cc_final: 0.6302 (tpt170) REVERT: LA 83 TYR cc_start: 0.7753 (p90) cc_final: 0.7391 (p90) REVERT: LB 4 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7238 (ttm-80) REVERT: LB 303 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7976 (ttmm) REVERT: LG 41 GLN cc_start: 0.6919 (mm110) cc_final: 0.6332 (mm110) REVERT: LM 15 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7335 (pm20) REVERT: LM 36 HIS cc_start: 0.6419 (p90) cc_final: 0.6020 (p-80) REVERT: LM 105 GLN cc_start: 0.4984 (OUTLIER) cc_final: 0.4063 (tp40) REVERT: LO 102 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6673 (pm20) REVERT: LS 29 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8450 (mm) REVERT: LU 52 ARG cc_start: 0.7303 (mtm-85) cc_final: 0.7044 (mtm-85) REVERT: LV 29 ASP cc_start: 0.8193 (p0) cc_final: 0.7954 (p0) REVERT: LX 144 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7651 (t0) REVERT: La 58 MET cc_start: 0.8765 (mtm) cc_final: 0.8564 (mtt) REVERT: La 135 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7259 (tt0) REVERT: Lc 58 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6809 (tp30) REVERT: Lf 32 ILE cc_start: 0.6145 (OUTLIER) cc_final: 0.5804 (mm) REVERT: Lf 50 ARG cc_start: 0.5871 (OUTLIER) cc_final: 0.5247 (mpt180) REVERT: Lg 87 ARG cc_start: 0.6707 (ttm170) cc_final: 0.6137 (ttm170) outliers start: 213 outliers final: 122 residues processed: 1036 average time/residue: 2.1577 time to fit residues: 3205.0642 Evaluate side-chains 1001 residues out of total 7822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 861 time to evaluate : 7.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CF residue 28 SER Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 388 LYS Chi-restraints excluded: chain CH residue 446 VAL Chi-restraints excluded: chain CK residue 118 SER Chi-restraints excluded: chain CK residue 130 GLU Chi-restraints excluded: chain CK residue 185 THR Chi-restraints excluded: chain CN residue 166 SER Chi-restraints excluded: chain CO residue 19 LYS Chi-restraints excluded: chain CQ residue 82 ASN Chi-restraints excluded: chain CQ residue 163 GLU Chi-restraints excluded: chain Cb residue 47 LEU Chi-restraints excluded: chain Cb residue 95 ILE Chi-restraints excluded: chain Cd residue 12 LEU Chi-restraints excluded: chain Cd residue 53 LYS Chi-restraints excluded: chain Cd residue 206 VAL Chi-restraints excluded: chain Cd residue 436 ILE Chi-restraints excluded: chain Cd residue 442 LEU Chi-restraints excluded: chain Cf residue 87 MET Chi-restraints excluded: chain Cf residue 138 MET Chi-restraints excluded: chain Cg residue 71 THR Chi-restraints excluded: chain Cg residue 168 SER Chi-restraints excluded: chain Cg residue 188 MET Chi-restraints excluded: chain Cz residue 46 THR Chi-restraints excluded: chain Cz residue 83 ILE Chi-restraints excluded: chain Cz residue 103 MET Chi-restraints excluded: chain Cz residue 111 LEU Chi-restraints excluded: chain LA residue 49 ILE Chi-restraints excluded: chain LA residue 113 VAL Chi-restraints excluded: chain LA residue 130 SER Chi-restraints excluded: chain LA residue 135 THR Chi-restraints excluded: chain LA residue 146 THR Chi-restraints excluded: chain LA residue 183 SER Chi-restraints excluded: chain LB residue 4 ARG Chi-restraints excluded: chain LB residue 303 LYS Chi-restraints excluded: chain LB residue 337 MET Chi-restraints excluded: chain LB residue 355 VAL Chi-restraints excluded: chain LC residue 94 MET Chi-restraints excluded: chain LC residue 163 VAL Chi-restraints excluded: chain LC residue 265 LEU Chi-restraints excluded: chain LC residue 266 ASP Chi-restraints excluded: chain LC residue 294 THR Chi-restraints excluded: chain LC residue 299 VAL Chi-restraints excluded: chain LC residue 314 VAL Chi-restraints excluded: chain LC residue 326 MET Chi-restraints excluded: chain LC residue 354 VAL Chi-restraints excluded: chain LE residue 6 THR Chi-restraints excluded: chain LF residue 24 SER Chi-restraints excluded: chain LF residue 93 ILE Chi-restraints excluded: chain LF residue 126 THR Chi-restraints excluded: chain LF residue 170 THR Chi-restraints excluded: chain LF residue 213 LEU Chi-restraints excluded: chain LG residue 43 ILE Chi-restraints excluded: chain LH residue 94 ILE Chi-restraints excluded: chain LH residue 127 MET Chi-restraints excluded: chain LH residue 166 VAL Chi-restraints excluded: chain LJ residue 23 SER Chi-restraints excluded: chain LJ residue 31 LEU Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 49 SER Chi-restraints excluded: chain LK residue 90 ARG Chi-restraints excluded: chain LL residue 166 THR Chi-restraints excluded: chain LL residue 197 VAL Chi-restraints excluded: chain LM residue 15 GLU Chi-restraints excluded: chain LM residue 86 GLU Chi-restraints excluded: chain LM residue 105 GLN Chi-restraints excluded: chain LM residue 111 SER Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LO residue 3 SER Chi-restraints excluded: chain LO residue 36 VAL Chi-restraints excluded: chain LO residue 42 LEU Chi-restraints excluded: chain LO residue 53 LEU Chi-restraints excluded: chain LO residue 54 LYS Chi-restraints excluded: chain LO residue 102 GLU Chi-restraints excluded: chain LP residue 169 SER Chi-restraints excluded: chain LQ residue 50 ASP Chi-restraints excluded: chain LQ residue 109 VAL Chi-restraints excluded: chain LQ residue 160 THR Chi-restraints excluded: chain LR residue 29 VAL Chi-restraints excluded: chain LR residue 107 VAL Chi-restraints excluded: chain LR residue 112 SER Chi-restraints excluded: chain LR residue 140 GLU Chi-restraints excluded: chain LS residue 27 MET Chi-restraints excluded: chain LS residue 29 ILE Chi-restraints excluded: chain LS residue 39 SER Chi-restraints excluded: chain LS residue 84 ARG Chi-restraints excluded: chain LS residue 87 THR Chi-restraints excluded: chain LS residue 123 ILE Chi-restraints excluded: chain LS residue 154 HIS Chi-restraints excluded: chain LS residue 164 ILE Chi-restraints excluded: chain LT residue 39 ILE Chi-restraints excluded: chain LT residue 85 ILE Chi-restraints excluded: chain LT residue 140 THR Chi-restraints excluded: chain LT residue 151 LEU Chi-restraints excluded: chain LU residue 78 LEU Chi-restraints excluded: chain LV residue 58 ASP Chi-restraints excluded: chain LV residue 117 THR Chi-restraints excluded: chain LV residue 137 VAL Chi-restraints excluded: chain LX residue 119 ASP Chi-restraints excluded: chain LX residue 144 ASP Chi-restraints excluded: chain LY residue 107 LYS Chi-restraints excluded: chain LZ residue 53 THR Chi-restraints excluded: chain LZ residue 61 ILE Chi-restraints excluded: chain La residue 72 SER Chi-restraints excluded: chain La residue 135 GLU Chi-restraints excluded: chain Lc residue 28 LEU Chi-restraints excluded: chain Lc residue 58 GLU Chi-restraints excluded: chain Le residue 11 VAL Chi-restraints excluded: chain Le residue 31 SER Chi-restraints excluded: chain Le residue 92 THR Chi-restraints excluded: chain Le residue 111 THR Chi-restraints excluded: chain Le residue 118 VAL Chi-restraints excluded: chain Le residue 121 THR Chi-restraints excluded: chain Lf residue 11 VAL Chi-restraints excluded: chain Lf residue 30 SER Chi-restraints excluded: chain Lf residue 32 ILE Chi-restraints excluded: chain Lf residue 37 VAL Chi-restraints excluded: chain Lf residue 50 ARG Chi-restraints excluded: chain Lf residue 58 GLN Chi-restraints excluded: chain Lf residue 66 ILE Chi-restraints excluded: chain Lf residue 69 ILE Chi-restraints excluded: chain Lg residue 23 VAL Chi-restraints excluded: chain Lg residue 33 VAL Chi-restraints excluded: chain Lg residue 41 THR Chi-restraints excluded: chain Lh residue 32 SER Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Lh residue 109 THR Chi-restraints excluded: chain Li residue 46 THR Chi-restraints excluded: chain Li residue 77 ARG Chi-restraints excluded: chain Lj residue 59 THR Chi-restraints excluded: chain Lk residue 5 VAL Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 46 THR Chi-restraints excluded: chain Lk residue 62 LEU Chi-restraints excluded: chain Lk residue 70 ASP Chi-restraints excluded: chain Lp residue 30 GLU Chi-restraints excluded: chain Lp residue 56 SER Chi-restraints excluded: chain Lq residue 7 ASP Chi-restraints excluded: chain Lq residue 79 TYR Chi-restraints excluded: chain Lq residue 120 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1230 random chunks: chunk 990 optimal weight: 0.0030 chunk 674 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 885 optimal weight: 1.9990 chunk 490 optimal weight: 0.9980 chunk 1014 optimal weight: 5.9990 chunk 821 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 607 optimal weight: 10.0000 chunk 1067 optimal weight: 2.9990 chunk 300 optimal weight: 6.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CF 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CH 641 HIS CN 43 GLN CN 170 GLN ** CQ 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cd 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cd 422 HIS ** Cg 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cg 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LB 379 GLN LE 78 GLN ** LF 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LH 208 ASN LJ 96 ASN LL 142 GLN LM 5 ASN ** LO 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 120 ASN LQ 43 HIS LQ 163 ASN ** LQ 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LR 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LT 131 GLN ** LU 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LZ 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LZ 122 ASN Ld 49 GLN ** Le 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lp 45 ASN ** Lq 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 154191 Z= 0.266 Angle : 0.677 16.767 224378 Z= 0.359 Chirality : 0.038 0.280 27566 Planarity : 0.006 0.131 16159 Dihedral : 22.802 178.809 62010 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.65 % Allowed : 13.45 % Favored : 83.91 % 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: 0.75 (0.09), residues: 9079 helix: 1.44 (0.09), residues: 3439 sheet: -0.23 (0.14), residues: 1364 loop : 0.09 (0.09), residues: 4276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPCg 105 HIS 0.010 0.001 HISLB 244 PHE 0.022 0.002 PHELf 45 TYR 0.030 0.002 TYRLH 3 ARG 0.010 0.001 ARGLP 182 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18158 Ramachandran restraints generated. 9079 Oldfield, 0 Emsley, 9079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18158 Ramachandran restraints generated. 9079 Oldfield, 0 Emsley, 9079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1102 residues out of total 7822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 899 time to evaluate : 8.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CF 8 ARG cc_start: 0.5468 (OUTLIER) cc_final: 0.4532 (pmt170) REVERT: CH 85 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.7795 (m-80) REVERT: CH 388 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8121 (mppt) REVERT: CH 464 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6955 (pt0) REVERT: CL 45 TRP cc_start: 0.8023 (m-10) cc_final: 0.7528 (m-10) REVERT: CO 19 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7739 (tppt) REVERT: CQ 22 MET cc_start: 0.8416 (mmt) cc_final: 0.8133 (mmt) REVERT: CQ 82 ASN cc_start: 0.7975 (OUTLIER) cc_final: 0.7646 (t0) REVERT: Cd 53 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7671 (ttmt) REVERT: Cf 87 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7877 (mtt) REVERT: Cf 317 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8404 (mp) REVERT: Cz 77 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8214 (mm-40) REVERT: Cz 103 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7462 (ppp) REVERT: LA 64 ARG cc_start: 0.7579 (tpt-90) cc_final: 0.6383 (tpt170) REVERT: LA 83 TYR cc_start: 0.7747 (p90) cc_final: 0.7447 (p90) REVERT: LB 4 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7355 (ttm-80) REVERT: LB 337 MET cc_start: 0.6663 (OUTLIER) cc_final: 0.6279 (mtm) REVERT: LG 41 GLN cc_start: 0.6950 (mm110) cc_final: 0.6359 (mm110) REVERT: LH 188 ASN cc_start: 0.6607 (OUTLIER) cc_final: 0.6240 (m-40) REVERT: LH 216 ASP cc_start: 0.6963 (OUTLIER) cc_final: 0.6705 (m-30) REVERT: LJ 132 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7527 (mtm) REVERT: LM 36 HIS cc_start: 0.6255 (p90) cc_final: 0.5865 (p-80) REVERT: LO 102 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.6469 (pm20) REVERT: LS 29 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8428 (mm) REVERT: LU 50 ASP cc_start: 0.8150 (p0) cc_final: 0.7807 (p0) REVERT: LU 52 ARG cc_start: 0.7341 (mtm-85) cc_final: 0.7076 (mtm-85) REVERT: LV 29 ASP cc_start: 0.8120 (p0) cc_final: 0.7875 (p0) REVERT: LX 144 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7669 (t0) REVERT: La 135 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7262 (tt0) REVERT: Lc 58 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6758 (tp30) REVERT: Lp 84 ARG cc_start: 0.6419 (tpm170) cc_final: 0.6159 (tpm170) outliers start: 203 outliers final: 109 residues processed: 1006 average time/residue: 2.1644 time to fit residues: 3131.5860 Evaluate side-chains 983 residues out of total 7822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 855 time to evaluate : 8.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CF residue 8 ARG Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 361 LEU Chi-restraints excluded: chain CH residue 388 LYS Chi-restraints excluded: chain CH residue 446 VAL Chi-restraints excluded: chain CH residue 464 GLU Chi-restraints excluded: chain CH residue 490 GLN Chi-restraints excluded: chain CK residue 118 SER Chi-restraints excluded: chain CK residue 130 GLU Chi-restraints excluded: chain CK residue 185 THR Chi-restraints excluded: chain CN residue 78 ASP Chi-restraints excluded: chain CN residue 166 SER Chi-restraints excluded: chain CO residue 19 LYS Chi-restraints excluded: chain CQ residue 82 ASN Chi-restraints excluded: chain CQ residue 163 GLU Chi-restraints excluded: chain Cb residue 47 LEU Chi-restraints excluded: chain Cb residue 95 ILE Chi-restraints excluded: chain Cd residue 12 LEU Chi-restraints excluded: chain Cd residue 53 LYS Chi-restraints excluded: chain Cd residue 436 ILE Chi-restraints excluded: chain Cd residue 442 LEU Chi-restraints excluded: chain Cf residue 87 MET Chi-restraints excluded: chain Cf residue 317 LEU Chi-restraints excluded: chain Cg residue 71 THR Chi-restraints excluded: chain Cz residue 25 MET Chi-restraints excluded: chain Cz residue 103 MET Chi-restraints excluded: chain Cz residue 111 LEU Chi-restraints excluded: chain LA residue 49 ILE Chi-restraints excluded: chain LA residue 113 VAL Chi-restraints excluded: chain LA residue 130 SER Chi-restraints excluded: chain LA residue 135 THR Chi-restraints excluded: chain LA residue 183 SER Chi-restraints excluded: chain LB residue 4 ARG Chi-restraints excluded: chain LB residue 156 CYS Chi-restraints excluded: chain LB residue 337 MET Chi-restraints excluded: chain LB residue 355 VAL Chi-restraints excluded: chain LC residue 94 MET Chi-restraints excluded: chain LC residue 183 GLU Chi-restraints excluded: chain LC residue 266 ASP Chi-restraints excluded: chain LC residue 294 THR Chi-restraints excluded: chain LC residue 299 VAL Chi-restraints excluded: chain LC residue 314 VAL Chi-restraints excluded: chain LC residue 326 MET Chi-restraints excluded: chain LE residue 6 THR Chi-restraints excluded: chain LE residue 16 THR Chi-restraints excluded: chain LF residue 126 THR Chi-restraints excluded: chain LF residue 170 THR Chi-restraints excluded: chain LF residue 181 LYS Chi-restraints excluded: chain LF residue 213 LEU Chi-restraints excluded: chain LG residue 43 ILE Chi-restraints excluded: chain LG residue 223 GLU Chi-restraints excluded: chain LH residue 94 ILE Chi-restraints excluded: chain LH residue 166 VAL Chi-restraints excluded: chain LH residue 188 ASN Chi-restraints excluded: chain LH residue 216 ASP Chi-restraints excluded: chain LJ residue 23 SER Chi-restraints excluded: chain LJ residue 31 LEU Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 49 SER Chi-restraints excluded: chain LJ residue 132 MET Chi-restraints excluded: chain LL residue 146 GLU Chi-restraints excluded: chain LL residue 166 THR Chi-restraints excluded: chain LL residue 197 VAL Chi-restraints excluded: chain LM residue 86 GLU Chi-restraints excluded: chain LM residue 111 SER Chi-restraints excluded: chain LN residue 41 ARG Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LO residue 3 SER Chi-restraints excluded: chain LO residue 36 VAL Chi-restraints excluded: chain LO residue 42 LEU Chi-restraints excluded: chain LO residue 53 LEU Chi-restraints excluded: chain LO residue 54 LYS Chi-restraints excluded: chain LO residue 102 GLU Chi-restraints excluded: chain LP residue 169 SER Chi-restraints excluded: chain LQ residue 109 VAL Chi-restraints excluded: chain LQ residue 160 THR Chi-restraints excluded: chain LR residue 29 VAL Chi-restraints excluded: chain LR residue 107 VAL Chi-restraints excluded: chain LR residue 112 SER Chi-restraints excluded: chain LR residue 140 GLU Chi-restraints excluded: chain LS residue 29 ILE Chi-restraints excluded: chain LS residue 39 SER Chi-restraints excluded: chain LS residue 84 ARG Chi-restraints excluded: chain LS residue 87 THR Chi-restraints excluded: chain LS residue 154 HIS Chi-restraints excluded: chain LT residue 85 ILE Chi-restraints excluded: chain LT residue 140 THR Chi-restraints excluded: chain LT residue 151 LEU Chi-restraints excluded: chain LU residue 30 SER Chi-restraints excluded: chain LU residue 37 SER Chi-restraints excluded: chain LV residue 58 ASP Chi-restraints excluded: chain LV residue 137 VAL Chi-restraints excluded: chain LX residue 119 ASP Chi-restraints excluded: chain LX residue 144 ASP Chi-restraints excluded: chain LY residue 107 LYS Chi-restraints excluded: chain LZ residue 51 LYS Chi-restraints excluded: chain LZ residue 53 THR Chi-restraints excluded: chain La residue 72 SER Chi-restraints excluded: chain La residue 135 GLU Chi-restraints excluded: chain Lc residue 28 LEU Chi-restraints excluded: chain Ld residue 52 MET Chi-restraints excluded: chain Le residue 11 VAL Chi-restraints excluded: chain Le residue 31 SER Chi-restraints excluded: chain Le residue 83 VAL Chi-restraints excluded: chain Le residue 92 THR Chi-restraints excluded: chain Le residue 118 VAL Chi-restraints excluded: chain Le residue 121 THR Chi-restraints excluded: chain Lf residue 11 VAL Chi-restraints excluded: chain Lf residue 30 SER Chi-restraints excluded: chain Lf residue 37 VAL Chi-restraints excluded: chain Lf residue 58 GLN Chi-restraints excluded: chain Lf residue 66 ILE Chi-restraints excluded: chain Lg residue 23 VAL Chi-restraints excluded: chain Lg residue 41 THR Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Li residue 46 THR Chi-restraints excluded: chain Li residue 77 ARG Chi-restraints excluded: chain Lj residue 15 THR Chi-restraints excluded: chain Lj residue 55 ARG Chi-restraints excluded: chain Lj residue 59 THR Chi-restraints excluded: chain Lk residue 5 VAL Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 46 THR Chi-restraints excluded: chain Lk residue 62 LEU Chi-restraints excluded: chain Lk residue 70 ASP Chi-restraints excluded: chain Lp residue 56 SER Chi-restraints excluded: chain Lq residue 7 ASP Chi-restraints excluded: chain Lq residue 79 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1230 random chunks: chunk 400 optimal weight: 0.0010 chunk 1070 optimal weight: 0.8980 chunk 235 optimal weight: 8.9990 chunk 698 optimal weight: 0.5980 chunk 293 optimal weight: 10.0000 chunk 1190 optimal weight: 2.9990 chunk 987 optimal weight: 0.9990 chunk 551 optimal weight: 4.9990 chunk 98 optimal weight: 50.0000 chunk 393 optimal weight: 4.9990 chunk 624 optimal weight: 5.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: