Starting phenix.real_space_refine on Sun Mar 3 05:45:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv2_17951/03_2024/8pv2_17951_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv2_17951/03_2024/8pv2_17951.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv2_17951/03_2024/8pv2_17951_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv2_17951/03_2024/8pv2_17951_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv2_17951/03_2024/8pv2_17951_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv2_17951/03_2024/8pv2_17951.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv2_17951/03_2024/8pv2_17951.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv2_17951/03_2024/8pv2_17951_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv2_17951/03_2024/8pv2_17951_updated.pdb" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.018 sd= 0.155 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 3334 5.49 5 Mg 3 5.21 5 S 256 5.16 5 C 85230 2.51 5 N 28880 2.21 5 O 38173 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "CF TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF ASP 123": "OD1" <-> "OD2" Residue "CF TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH GLU 229": "OE1" <-> "OE2" Residue "CH TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH ASP 298": "OD1" <-> "OD2" Residue "CH PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH GLU 385": "OE1" <-> "OE2" Residue "CH ASP 453": "OD1" <-> "OD2" Residue "CH PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH GLU 505": "OE1" <-> "OE2" Residue "CH ASP 540": "OD1" <-> "OD2" Residue "CK GLU 31": "OE1" <-> "OE2" Residue "CK ASP 92": "OD1" <-> "OD2" Residue "CK ASP 227": "OD1" <-> "OD2" Residue "CK ASP 252": "OD1" <-> "OD2" Residue "CL ASP 52": "OD1" <-> "OD2" Residue "CL GLU 63": "OE1" <-> "OE2" Residue "CN TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CN TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CN PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CN ASP 120": "OD1" <-> "OD2" Residue "CN ASP 131": "OD1" <-> "OD2" Residue "CN ASP 171": "OD1" <-> "OD2" Residue "CN ASP 201": "OD1" <-> "OD2" Residue "CN ASP 209": "OD1" <-> "OD2" Residue "CO GLU 12": "OE1" <-> "OE2" Residue "CQ PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CQ ASP 66": "OD1" <-> "OD2" Residue "CQ PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CQ TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cb TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cb ASP 100": "OD1" <-> "OD2" Residue "Cd GLU 139": "OE1" <-> "OE2" Residue "Cd ASP 162": "OD1" <-> "OD2" Residue "Cd PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cd ASP 312": "OD1" <-> "OD2" Residue "Cd GLU 360": "OE1" <-> "OE2" Residue "Cd GLU 408": "OE1" <-> "OE2" Residue "Cd GLU 481": "OE1" <-> "OE2" Residue "Cf GLU 17": "OE1" <-> "OE2" Residue "Cf GLU 247": "OE1" <-> "OE2" Residue "Cf GLU 270": "OE1" <-> "OE2" Residue "Cf ASP 290": "OD1" <-> "OD2" Residue "Cg ASP 24": "OD1" <-> "OD2" Residue "Cg ASP 32": "OD1" <-> "OD2" Residue "Cg ASP 43": "OD1" <-> "OD2" Residue "Cg ASP 77": "OD1" <-> "OD2" Residue "Cg GLU 135": "OE1" <-> "OE2" Residue "Cg GLU 176": "OE1" <-> "OE2" Residue "Cg GLU 197": "OE1" <-> "OE2" Residue "Ch TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ch ASP 248": "OD1" <-> "OD2" Residue "Ch PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA GLU 74": "OE1" <-> "OE2" Residue "LA ASP 122": "OD1" <-> "OD2" Residue "LB PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB GLU 194": "OE1" <-> "OE2" Residue "LB ASP 213": "OD1" <-> "OD2" Residue "LB GLU 356": "OE1" <-> "OE2" Residue "LC ASP 13": "OD1" <-> "OD2" Residue "LC GLU 55": "OE1" <-> "OE2" Residue "LC ASP 266": "OD1" <-> "OD2" Residue "LC TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC ASP 286": "OD1" <-> "OD2" Residue "LD TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD ASP 232": "OD1" <-> "OD2" Residue "LD ASP 233": "OD1" <-> "OD2" Residue "LD GLU 241": "OE1" <-> "OE2" Residue "LE GLU 22": "OE1" <-> "OE2" Residue "LE ASP 32": "OD1" <-> "OD2" Residue "LE GLU 121": "OE1" <-> "OE2" Residue "LE TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE ASP 177": "OD1" <-> "OD2" Residue "LF ASP 11": "OD1" <-> "OD2" Residue "LF ASP 171": "OD1" <-> "OD2" Residue "LF GLU 177": "OE1" <-> "OE2" Residue "LG ASP 86": "OD1" <-> "OD2" Residue "LH ASP 74": "OD1" <-> "OD2" Residue "LH ASP 101": "OD1" <-> "OD2" 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 ASP 112": "OD1" <-> "OD2" Residue "LK GLU 87": "OE1" <-> "OE2" Residue "LK ASP 91": "OD1" <-> "OD2" Residue "LK GLU 156": "OE1" <-> "OE2" Residue "LK GLU 159": "OE1" <-> "OE2" Residue "LK ASP 164": "OD1" <-> "OD2" Residue "LL ASP 52": "OD1" <-> "OD2" Residue "LL ASP 137": "OD1" <-> "OD2" Residue "LL GLU 158": "OE1" <-> "OE2" Residue "LM ASP 91": "OD1" <-> "OD2" Residue "LM GLU 96": "OE1" <-> "OE2" Residue "LM GLU 107": "OE1" <-> "OE2" Residue "LN ASP 17": "OD1" <-> "OD2" Residue "LN ASP 124": "OD1" <-> "OD2" Residue "LN PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO GLU 5": "OE1" <-> "OE2" Residue "LO TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO GLU 102": "OE1" <-> "OE2" Residue "LO ASP 153": "OD1" <-> "OD2" Residue "LP ASP 53": "OD1" <-> "OD2" Residue "LP GLU 99": "OE1" <-> "OE2" Residue "LP ASP 108": "OD1" <-> "OD2" Residue "LP GLU 147": "OE1" <-> "OE2" Residue "LQ PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LQ GLU 104": "OE1" <-> "OE2" Residue "LQ GLU 127": "OE1" <-> "OE2" Residue "LR GLU 31": "OE1" <-> "OE2" Residue "LR ASP 47": "OD1" <-> "OD2" Residue "LR TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS GLU 6": "OE1" <-> "OE2" Residue "LS TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS GLU 34": "OE1" <-> "OE2" Residue "LS TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS GLU 96": "OE1" <-> "OE2" Residue "LS PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS GLU 133": "OE1" <-> "OE2" Residue "LS PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT ASP 104": "OD1" <-> "OD2" Residue "LT GLU 137": "OE1" <-> "OE2" Residue "LU ASP 31": "OD1" <-> "OD2" Residue "LU PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU ASP 35": "OD1" <-> "OD2" Residue "LU ASP 77": "OD1" <-> "OD2" Residue "LU TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LV PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LV PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LV GLU 126": "OE1" <-> "OE2" Residue "LX GLU 90": "OE1" <-> "OE2" Residue "LX PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX ASP 100": "OD1" <-> "OD2" Residue "LX ASP 119": "OD1" <-> "OD2" Residue "LX ASP 147": "OD1" <-> "OD2" Residue "LY GLU 54": "OE1" <-> "OE2" Residue "LY ASP 64": "OD1" <-> "OD2" Residue "LY ASP 111": "OD1" <-> "OD2" Residue "LZ PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ ASP 29": "OD1" <-> "OD2" Residue "LZ TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ GLU 87": "OE1" <-> "OE2" Residue "La TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "La GLU 140": "OE1" <-> "OE2" Residue "La GLU 146": "OE1" <-> "OE2" Residue "Lc GLU 58": "OE1" <-> "OE2" Residue "Ld GLU 43": "OE1" <-> "OE2" Residue "Ld TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Le PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lf TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lg GLU 62": "OE1" <-> "OE2" Residue "Lg TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lg GLU 97": "OE1" <-> "OE2" Residue "Lg GLU 98": "OE1" <-> "OE2" Residue "Lh GLU 26": "OE1" <-> "OE2" Residue "Lh GLU 100": "OE1" <-> "OE2" Residue "Lh GLU 107": "OE1" <-> "OE2" Residue "Li PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lj GLU 51": "OE1" <-> "OE2" Residue "Lk ASP 70": "OD1" <-> "OD2" Residue "Ll TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lp GLU 30": "OE1" <-> "OE2" Residue "Lp TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lq GLU 11": "OE1" <-> "OE2" Residue "Lq ASP 49": "OD1" <-> "OD2" Residue "CC GLU 437": "OE1" <-> "OE2" Residue "CC PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC ASP 601": "OD1" <-> "OD2" Residue "CC PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CD TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CD ASP 111": "OD1" <-> "OD2" Residue "CD TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CD TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CD PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ ASP 32": "OD1" <-> "OD2" Residue "CJ TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 155881 Number of models: 1 Model: "" Number of chains: 66 Chain: "C1" Number of atoms: 65414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3056, 65414 Classifications: {'RNA': 3056} Modifications used: {'rna2p': 1, 'rna2p_pur': 316, 'rna2p_pyr': 216, 'rna3p': 25, 'rna3p_pur': 1347, 'rna3p_pyr': 1143} Link IDs: {'rna2p': 533, 'rna3p': 2522} Chain breaks: 9 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 18 Chain: "C2" Number of atoms: 3259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3259 Classifications: {'RNA': 153} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 9, 'rna3p_pur': 63, 'rna3p_pyr': 64} Link IDs: {'rna2p': 26, 'rna3p': 126} 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: 5036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5036 Classifications: {'peptide': 627} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 26, 'TRANS': 600} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 19 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: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1889 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 223} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "LH" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1495 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain: "LJ" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1357 Classifications: {'peptide': 169} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 163} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "LK" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1184 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 149} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "LL" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1587 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 189} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 21 Chain: "LM" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1126 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "LN" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1704 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain: "LO" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1611 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 192} Chain: "LP" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1343 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 164} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "LQ" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1200 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "LR" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1241 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 151} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "LS" Number of atoms: 1426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1426 Classifications: {'peptide': 174} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 163} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "LT" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1027 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 121} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "LU" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 846 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "LV" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 991 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 125} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "LX" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 967 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 113} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 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: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 951 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} 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: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1073 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 6, 'TRANS': 132} Chain: "CC" Number of atoms: 3890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3890 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 450} Chain breaks: 2 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 7, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 85 Chain: "CD" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3390 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 25, 'TRANS': 427} Chain breaks: 5 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "CJ" Number of atoms: 3577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3577 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 463} Chain breaks: 4 Unresolved non-hydrogen bonds: 466 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 369 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 11, 'PHE:plan': 8, 'GLU:plan': 23, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 293 Chain: "CM" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 685 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 416 Unresolved non-hydrogen angles: 531 Unresolved non-hydrogen dihedrals: 344 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 14, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 5, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 228 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 83075 SG CYSCQ 6 146.191 178.694 101.021 1.00 25.58 S ATOM 83103 SG CYSCQ 9 149.796 179.757 101.655 1.00 25.68 S ATOM 83288 SG CYSCQ 32 149.163 176.548 99.856 1.00 22.46 S ATOM 83320 SG CYSCQ 36 148.313 176.949 103.607 1.00 22.22 S ATOM 84932 SG CYSCb 52 127.629 185.504 123.488 1.00 36.41 S ATOM 84955 SG CYSCb 55 130.750 183.670 123.616 1.00 37.14 S ATOM A0TME SG CYSLg 45 142.481 158.545 199.581 1.00 24.34 S ATOM A0TMW SG CYSLg 48 140.073 160.388 197.423 1.00 27.65 S ATOM A0TU4 SG CYSLg 82 141.976 162.375 200.080 1.00 25.91 S ATOM A0TUM SG CYSLg 85 139.283 160.004 201.095 1.00 28.00 S ATOM A0VJ3 SG CYSLj 19 164.062 111.631 172.348 1.00 16.88 S ATOM A0VJV SG CYSLj 22 164.842 109.376 169.373 1.00 16.52 S ATOM A0VML SG CYSLj 34 161.342 110.743 169.873 1.00 14.70 S ATOM A0VN2 SG CYSLj 37 162.748 108.120 172.325 1.00 16.68 S ATOM A0X0S SG CYSLp 39 123.635 160.995 192.801 1.00 34.54 S ATOM A0X1G SG CYSLp 42 125.365 164.358 193.207 1.00 35.12 S ATOM A0X4L SG CYSLp 57 126.726 162.067 190.655 1.00 33.84 S ATOM A0X56 SG CYSLp 60 127.042 161.051 194.311 1.00 35.27 S Time building chain proxies: 61.10, per 1000 atoms: 0.39 Number of scatterers: 155881 At special positions: 0 Unit cell: (235.125, 251.845, 288.42, 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 256 16.00 P 3334 15.00 Mg 3 11.99 O 38173 8.00 N 28880 7.00 C 85230 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: 56.22 Conformation dependent library (CDL) restraints added in 13.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNCQ1000 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 9 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 6 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 36 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 32 " pdb=" ZNCb1000 " pdb="ZN ZNCb1000 " - pdb=" ND1 HISCb 74 " pdb="ZN ZNCb1000 " - pdb=" NE2 HISCb 68 " pdb="ZN ZNCb1000 " - pdb=" SG CYSCb 52 " pdb="ZN ZNCb1000 " - pdb=" SG CYSCb 55 " pdb=" ZNLg1000 " pdb="ZN ZNLg1000 " - pdb=" SG CYSLg 48 " pdb="ZN ZNLg1000 " - pdb=" SG CYSLg 85 " pdb="ZN ZNLg1000 " - pdb=" SG CYSLg 82 " pdb="ZN ZNLg1000 " - pdb=" SG CYSLg 45 " pdb=" ZNLj1000 " pdb="ZN ZNLj1000 " - pdb=" SG CYSLj 37 " pdb="ZN ZNLj1000 " - pdb=" SG CYSLj 19 " pdb="ZN ZNLj1000 " - pdb=" SG CYSLj 22 " pdb="ZN ZNLj1000 " - pdb=" SG CYSLj 34 " pdb=" ZNLp 101 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 42 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 60 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 39 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 57 " Number of angles added : 26 21252 Ramachandran restraints generated. 10626 Oldfield, 0 Emsley, 10626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 20168 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: 373 helices and 119 sheets defined 42.6% alpha, 16.2% beta 1050 base pairs and 1851 stacking pairs defined. Time for finding SS restraints: 90.40 Creating SS restraints... Processing helix chain 'CF' and resid 19 through 37 removed outlier: 3.853A pdb=" N LYSCF 23 " --> pdb=" O GLYCF 19 " (cutoff:3.500A) Proline residue: CF 35 - end of helix Processing helix chain 'CF' and resid 50 through 61 removed outlier: 5.105A pdb=" N LYSCF 54 " --> pdb=" O ASNCF 50 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ASPCF 55 " --> pdb=" O ASNCF 51 " (cutoff:3.500A) removed outlier: 3.634A 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: 3.880A pdb=" N LEUCF 92 " --> pdb=" O GLYCF 88 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ARGCF 94 " --> pdb=" O HISCF 90 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N TYRCF 95 " --> pdb=" O ARGCF 91 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEUCF 96 " --> pdb=" O LEUCF 92 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N THRCF 97 " --> pdb=" O THRCF 93 " (cutoff:3.500A) Processing helix chain 'CF' and resid 108 through 119 Processing helix chain 'CF' and resid 150 through 155 removed outlier: 4.684A pdb=" N VALCF 155 " --> pdb=" O PROCF 151 " (cutoff:3.500A) Processing helix chain 'CF' and resid 158 through 169 removed outlier: 4.334A pdb=" N GLUCF 162 " --> pdb=" O SERCF 158 " (cutoff:3.500A) Proline residue: CF 163 - end of helix Processing helix chain 'CF' and resid 202 through 213 Processing helix chain 'CF' and resid 237 through 243 removed outlier: 3.740A 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 65 Processing helix chain 'CH' and resid 69 through 74 removed outlier: 3.638A pdb=" N GLNCH 73 " --> pdb=" O VALCH 69 " (cutoff:3.500A) removed outlier: 6.062A 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: 4.041A pdb=" N TYRCH 117 " --> pdb=" O ARGCH 113 " (cutoff:3.500A) Processing helix chain 'CH' and resid 120 through 143 removed outlier: 3.991A pdb=" N LEUCH 142 " --> pdb=" O LEUCH 138 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYSCH 143 " --> pdb=" O ILECH 139 " (cutoff:3.500A) Processing helix chain 'CH' and resid 144 through 159 Processing helix chain 'CH' and resid 178 through 187 Processing helix chain 'CH' and resid 227 through 232 removed outlier: 3.658A pdb=" N METCH 231 " --> pdb=" O PROCH 227 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ASNCH 232 " --> pdb=" O LEUCH 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'CH' and resid 227 through 232' Processing helix chain 'CH' and resid 233 through 244 removed outlier: 3.938A 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: 4.043A pdb=" N ALACH 278 " --> pdb=" O LYSCH 274 " (cutoff:3.500A) Processing helix chain 'CH' and resid 298 through 311 removed outlier: 3.566A pdb=" N THRCH 309 " --> pdb=" O ILECH 305 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N SERCH 311 " --> pdb=" O ASPCH 307 " (cutoff:3.500A) Processing helix chain 'CH' and resid 326 through 351 removed outlier: 4.871A pdb=" N GLYCH 350 " --> pdb=" O LYSCH 346 " (cutoff:3.500A) removed outlier: 4.546A 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: 4.740A pdb=" N LYSCH 388 " --> pdb=" O PROCH 384 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASNCH 389 " --> pdb=" O GLUCH 385 " (cutoff:3.500A) Processing helix chain 'CH' and resid 403 through 412 Processing helix chain 'CH' and resid 445 through 450 removed outlier: 3.675A pdb=" N TYRCH 449 " --> pdb=" O ASNCH 445 " (cutoff:3.500A) Processing helix chain 'CH' and resid 453 through 472 removed outlier: 3.835A 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: 4.039A pdb=" N VALCH 523 " --> pdb=" O PROCH 519 " (cutoff:3.500A) removed outlier: 5.439A 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: 3.652A pdb=" N ILECH 544 " --> pdb=" O ASPCH 540 " (cutoff:3.500A) Processing helix chain 'CH' and resid 582 through 597 Processing helix chain 'CH' and resid 609 through 631 removed outlier: 3.877A pdb=" N GLNCH 624 " --> pdb=" O ALACH 620 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARGCH 625 " --> pdb=" O LYSCH 621 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LYSCH 626 " --> pdb=" O LEUCH 622 " (cutoff:3.500A) removed outlier: 5.434A 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: 4.657A pdb=" N GLYCK 32 " --> pdb=" O ALACK 28 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N HISCK 33 " --> pdb=" O ALACK 29 " (cutoff:3.500A) Processing helix chain 'CK' and resid 44 through 71 Processing helix chain 'CK' and resid 128 through 133 Processing helix chain 'CK' and resid 174 through 179 removed outlier: 3.595A pdb=" N ARGCK 178 " --> pdb=" O PROCK 174 " (cutoff:3.500A) removed outlier: 6.017A 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: 3.859A pdb=" N PHECN 16 " --> pdb=" O GLUCN 12 " (cutoff:3.500A) Processing helix chain 'CN' and resid 32 through 43 removed outlier: 3.704A pdb=" N PHECN 38 " --> pdb=" O PHECN 34 " (cutoff:3.500A) removed outlier: 3.806A 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: 4.528A pdb=" N ILECN 233 " --> pdb=" O GLYCN 229 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASNCN 234 " --> pdb=" O PROCN 230 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THRCN 235 " --> pdb=" O GLYCN 231 " (cutoff:3.500A) Processing helix chain 'CN' and resid 237 through 245 Processing helix chain 'CO' and resid 7 through 21 Processing helix chain 'CO' and resid 22 through 43 Processing helix chain 'CO' and resid 83 through 88 Processing helix chain 'CQ' and resid 33 through 43 Processing helix chain 'CQ' and resid 45 through 50 removed outlier: 5.314A 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: 4.376A pdb=" N GLNCQ 70 " --> pdb=" O ASPCQ 66 " (cutoff:3.500A) removed outlier: 4.673A 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: 6.030A pdb=" N GLYCQ 114 " --> pdb=" O LYSCQ 110 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LYSCQ 115 " --> pdb=" O ARGCQ 111 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ARGCQ 116 " --> pdb=" O METCQ 112 " (cutoff:3.500A) removed outlier: 5.284A 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: 4.811A pdb=" N LYSCQ 171 " --> pdb=" O LEUCQ 167 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 5 through 10 removed outlier: 3.720A pdb=" N METCb 9 " --> pdb=" O ALACb 5 " (cutoff:3.500A) removed outlier: 5.257A 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: 3.753A pdb=" N LYSCb 39 " --> pdb=" O TYRCb 35 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ALACb 40 " --> pdb=" O LYSCb 36 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 61 through 72 removed outlier: 3.765A pdb=" N LYSCb 70 " --> pdb=" O VALCb 66 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLYCb 71 " --> pdb=" O GLYCb 67 " (cutoff:3.500A) removed outlier: 5.172A 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: 3.696A 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: 3.990A pdb=" N LEUCd 41 " --> pdb=" O THRCd 37 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYSCd 42 " --> pdb=" O LEUCd 38 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 73 through 79 removed outlier: 4.703A pdb=" N PHECd 77 " --> pdb=" O ASNCd 73 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THRCd 78 " --> pdb=" O ARGCd 74 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ASNCd 79 " --> pdb=" O LYSCd 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cd' and resid 73 through 79' Processing helix chain 'Cd' and resid 84 through 98 Processing helix chain 'Cd' and resid 113 through 118 removed outlier: 3.541A pdb=" N ILECd 117 " --> pdb=" O PROCd 113 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 122 through 140 removed outlier: 4.076A pdb=" N HISCd 130 " --> pdb=" O GLYCd 126 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALACd 132 " --> pdb=" O LYSCd 128 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LYSCd 133 " --> pdb=" O LYSCd 129 " (cutoff:3.500A) Proline residue: Cd 140 - end of helix Processing helix chain 'Cd' and resid 160 through 185 Processing helix chain 'Cd' and resid 211 through 216 removed outlier: 4.295A pdb=" N ASNCd 215 " --> pdb=" O GLUCd 211 " (cutoff:3.500A) removed outlier: 4.108A 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: 4.410A 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: 3.987A pdb=" N LYSCd 290 " --> pdb=" O ARGCd 286 " (cutoff:3.500A) removed outlier: 4.479A 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: 4.026A pdb=" N VALCd 404 " --> pdb=" O ARGCd 400 " (cutoff:3.500A) removed outlier: 6.117A 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 406 through 419 removed outlier: 4.819A pdb=" N TYRCd 410 " --> pdb=" O HISCd 406 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILECd 411 " --> pdb=" O PROCd 407 " (cutoff:3.500A) Proline residue: Cd 412 - end of helix removed outlier: 5.112A 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: 3.719A 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: 4.289A pdb=" N PHECf 129 " --> pdb=" O SERCf 125 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LYSCf 130 " --> pdb=" O ILECf 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cf' and resid 125 through 130' Processing helix chain 'Cf' and resid 155 through 169 Processing helix chain 'Cf' and resid 264 through 273 Processing helix chain 'Cf' and resid 314 through 319 removed outlier: 3.823A pdb=" N LYSCf 318 " --> pdb=" O METCf 314 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ARGCf 319 " --> pdb=" O LYSCf 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cf' and resid 314 through 319' Processing helix chain 'Cf' and resid 177 through 182 removed outlier: 3.842A pdb=" N LEUCf 181 " --> pdb=" O VALCf 178 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ARGCf 182 " --> pdb=" O GLUCf 179 " (cutoff:3.500A) Processing helix chain 'Cg' and resid 43 through 69 Processing helix chain 'Cg' and resid 103 through 113 Processing helix chain 'Cg' and resid 118 through 123 removed outlier: 3.678A pdb=" N ARGCg 123 " --> pdb=" O ARGCg 119 " (cutoff:3.500A) Processing helix chain 'Cg' and resid 156 through 163 Processing helix chain 'Cg' and resid 168 through 198 removed outlier: 4.222A pdb=" N ASPCg 172 " --> pdb=" O SERCg 168 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYSCg 173 " --> pdb=" O VALCg 169 " (cutoff:3.500A) removed outlier: 5.399A 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: 3.924A 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 39 Processing helix chain 'LA' and resid 103 through 108 removed outlier: 3.781A 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: 4.127A pdb=" N VALLA 191 " --> pdb=" O HISLA 187 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYSLA 192 " --> pdb=" O LYSLA 188 " (cutoff:3.500A) Processing helix chain 'LA' and resid 200 through 205 removed outlier: 3.766A pdb=" N METLA 204 " --> pdb=" O ARGLA 200 " (cutoff:3.500A) removed outlier: 5.155A 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 'LA' and resid 173 through 178 removed outlier: 3.769A pdb=" N LYSLA 177 " --> pdb=" O ARGLA 174 " (cutoff:3.500A) Proline residue: LA 178 - end of helix Processing helix chain 'LB' and resid 13 through 18 removed outlier: 4.957A pdb=" N LEULB 17 " --> pdb=" O SERLB 13 " (cutoff:3.500A) Proline residue: LB 18 - end of helix No H-bonds generated for 'chain 'LB' and resid 13 through 18' Processing helix chain 'LB' and resid 111 through 120 removed outlier: 3.982A pdb=" N ARGLB 117 " --> pdb=" O GLULB 113 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHELB 118 " --> pdb=" O VALLB 114 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYRLB 119 " --> pdb=" O LYSLB 115 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LYSLB 120 " --> pdb=" O ARGLB 116 " (cutoff:3.500A) Processing helix chain 'LB' and resid 130 through 140 removed outlier: 3.757A pdb=" N LYSLB 135 " --> pdb=" O THRLB 131 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYSLB 136 " --> pdb=" O LYSLB 132 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TYRLB 137 " --> pdb=" O TYRLB 133 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALALB 138 " --> pdb=" O ALALB 134 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ASNLB 140 " --> pdb=" O LYSLB 136 " (cutoff:3.500A) Processing helix chain 'LB' and resid 142 through 155 Processing helix chain 'LB' and resid 166 through 171 removed outlier: 4.240A 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: 4.012A 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: 3.966A pdb=" N LEULB 352 " --> pdb=" O SERLB 348 " (cutoff:3.500A) Processing helix chain 'LB' and resid 373 through 382 Processing helix chain 'LB' and resid 384 through 390 removed outlier: 3.586A pdb=" N LEULB 388 " --> pdb=" O LEULB 384 " (cutoff:3.500A) Processing helix chain 'LC' and resid 24 through 30 removed outlier: 4.570A pdb=" N SERLC 28 " --> pdb=" O PROLC 24 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALALC 29 " --> pdb=" O LYSLC 25 " (cutoff:3.500A) Proline residue: LC 30 - end of helix No H-bonds generated for 'chain 'LC' and resid 24 through 30' Processing helix chain 'LC' and resid 32 through 47 removed outlier: 3.971A pdb=" N LYSLC 45 " --> pdb=" O THRLC 41 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASNLC 46 " --> pdb=" O GLYLC 42 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LYSLC 47 " --> pdb=" O METLC 43 " (cutoff:3.500A) Processing helix chain 'LC' and resid 115 through 133 removed outlier: 3.560A pdb=" N ALALC 131 " --> pdb=" O LEULC 127 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VALLC 132 " --> pdb=" O ALALC 128 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ALALC 133 " --> pdb=" O ALALC 129 " (cutoff:3.500A) Processing helix chain 'LC' and resid 134 through 140 removed outlier: 3.588A pdb=" N GLYLC 140 " --> pdb=" O LEULC 136 " (cutoff:3.500A) Processing helix chain 'LC' and resid 154 through 159 removed outlier: 3.951A pdb=" N VALLC 158 " --> pdb=" O ASPLC 154 " (cutoff:3.500A) Processing helix chain 'LC' and resid 165 through 177 Processing helix chain 'LC' and resid 178 through 189 removed outlier: 4.017A pdb=" N LYSLC 189 " --> pdb=" O VALLC 185 " (cutoff:3.500A) Processing helix chain 'LC' and resid 194 through 200 removed outlier: 4.741A pdb=" N METLC 198 " --> pdb=" O GLYLC 194 " (cutoff:3.500A) Processing helix chain 'LC' and resid 220 through 228 removed outlier: 4.035A pdb=" N LYSLC 224 " --> pdb=" O LYSLC 220 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASNLC 228 " --> pdb=" O LYSLC 224 " (cutoff:3.500A) Processing helix chain 'LC' and resid 241 through 247 Proline residue: LC 247 - end of helix Processing helix chain 'LC' and resid 258 through 272 removed outlier: 4.907A pdb=" N ASPLC 266 " --> pdb=" O ILELC 262 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALALC 267 " --> pdb=" O LYSLC 263 " (cutoff:3.500A) removed outlier: 3.648A 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: 4.316A pdb=" N VALLC 299 " --> pdb=" O GLULC 295 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEULC 300 " --> pdb=" O ILELC 296 " (cutoff:3.500A) Processing helix chain 'LC' and resid 318 through 323 removed outlier: 4.599A 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: 4.507A pdb=" N THRLC 335 " --> pdb=" O PROLC 331 " (cutoff:3.500A) Processing helix chain 'LC' and resid 355 through 364 Processing helix chain 'LC' and resid 214 through 219 removed outlier: 3.825A 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: 3.843A pdb=" N ARGLD 35 " --> pdb=" O TYRLD 31 " (cutoff:3.500A) Processing helix chain 'LD' and resid 79 through 87 removed outlier: 4.215A pdb=" N LEULD 83 " --> pdb=" O TYRLD 79 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ARGLD 84 " --> pdb=" O SERLD 80 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ALALD 85 " --> pdb=" O HISLD 81 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYRLD 86 " --> pdb=" O GLULD 82 " (cutoff:3.500A) Processing helix chain 'LD' and resid 94 through 114 Processing helix chain 'LD' and resid 130 through 136 Processing helix chain 'LD' and resid 160 through 173 removed outlier: 3.697A pdb=" N GLYLD 164 " --> pdb=" O ALALD 160 " (cutoff:3.500A) Processing helix chain 'LD' and resid 194 through 204 Processing helix chain 'LD' and resid 205 through 218 Processing helix chain 'LD' and resid 219 through 227 Processing helix chain 'LD' and resid 228 through 233 Processing helix chain 'LD' and resid 235 through 253 removed outlier: 4.104A pdb=" N LEULD 239 " --> pdb=" O GLULD 235 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLULD 240 " --> pdb=" O ALALD 236 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLULD 241 " --> pdb=" O ASPLD 237 " (cutoff:3.500A) Processing helix chain 'LD' and resid 266 through 278 removed outlier: 3.809A 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: 3.876A pdb=" N VALLE 102 " --> pdb=" O ASNLE 98 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILELE 103 " --> pdb=" O ALALE 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'LE' and resid 98 through 103' Processing helix chain 'LE' and resid 115 through 124 Processing helix chain 'LE' and resid 131 through 140 Processing helix chain 'LE' and resid 155 through 174 removed outlier: 4.967A pdb=" N ALALE 168 " --> pdb=" O ALALE 164 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEULE 169 " --> pdb=" O ILELE 165 " (cutoff:3.500A) Processing helix chain 'LE' and resid 178 through 186 removed outlier: 5.290A 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: 5.359A pdb=" N GLULF 31 " --> pdb=" O LYSLF 27 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ARGLF 32 " --> pdb=" O ALALF 28 " (cutoff:3.500A) Processing helix chain 'LF' and resid 35 through 79 removed outlier: 3.600A pdb=" N GLULF 45 " --> pdb=" O GLNLF 41 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLNLF 48 " --> pdb=" O LYSLF 44 " (cutoff:3.500A) Processing helix chain 'LF' and resid 102 through 113 Processing helix chain 'LF' and resid 126 through 137 removed outlier: 4.136A pdb=" N METLF 132 " --> pdb=" O ALALF 128 " (cutoff:3.500A) Processing helix chain 'LF' and resid 146 through 156 Processing helix chain 'LF' and resid 171 through 179 removed outlier: 4.058A 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: 5.143A pdb=" N TRPLF 209 " --> pdb=" O ALALF 205 " (cutoff:3.500A) Processing helix chain 'LF' and resid 240 through 249 removed outlier: 3.947A 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: 5.107A pdb=" N PHELG 81 " --> pdb=" O ALALG 77 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLNLG 82 " --> pdb=" O ILELG 78 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYRLG 83 " --> pdb=" O ALALG 79 " (cutoff:3.500A) Processing helix chain 'LG' and resid 86 through 101 removed outlier: 3.618A pdb=" N LEULG 96 " --> pdb=" O GLNLG 92 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYSLG 99 " --> pdb=" O LYSLG 95 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYRLG 100 " --> pdb=" O LEULG 96 " (cutoff:3.500A) Processing helix chain 'LG' and resid 104 through 122 Processing helix chain 'LG' and resid 124 through 129 Processing helix chain 'LG' and resid 138 through 149 Processing helix chain 'LG' and resid 162 through 177 removed outlier: 4.882A pdb=" N VALLG 166 " --> pdb=" O PROLG 162 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N PHELG 168 " --> pdb=" O GLULG 164 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEULG 169 " --> pdb=" O LEULG 165 " (cutoff:3.500A) Proline residue: LG 170 - end of helix Processing helix chain 'LG' and resid 185 through 194 Processing helix chain 'LG' and resid 207 through 233 removed outlier: 4.822A pdb=" N ASNLG 212 " --> pdb=" O SERLG 208 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLULG 213 " --> pdb=" O GLULG 209 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLULG 227 " --> pdb=" O GLULG 223 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYSLG 228 " --> pdb=" O GLYLG 224 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASPLG 231 " --> pdb=" O GLULG 227 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N THRLG 232 " --> pdb=" O LYSLG 228 " (cutoff:3.500A) Processing helix chain 'LG' and resid 242 through 259 Processing helix chain 'LH' and resid 98 through 121 removed outlier: 3.959A pdb=" N LEULH 105 " --> pdb=" O ASPLH 101 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARGLH 106 " --> pdb=" O VALLH 102 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THRLH 107 " --> pdb=" O ALALH 103 " (cutoff:3.500A) Processing helix chain 'LH' and resid 189 through 205 removed outlier: 3.773A pdb=" N CYSLH 204 " --> pdb=" O ILELH 200 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LYSLH 205 " --> pdb=" O GLNLH 201 " (cutoff:3.500A) Processing helix chain 'LH' and resid 210 through 215 removed outlier: 4.894A 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 109 through 114 removed outlier: 4.987A pdb=" N LEULJ 113 " --> pdb=" O GLULJ 109 " (cutoff:3.500A) removed outlier: 4.514A 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: 3.804A pdb=" N LYSLJ 141 " --> pdb=" O GLULJ 137 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 150 through 155 removed outlier: 5.820A 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 32 removed outlier: 4.819A pdb=" N ALALK 27 " --> pdb=" O GLYLK 23 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEULK 28 " --> pdb=" O ALALK 24 " (cutoff:3.500A) Proline residue: LK 30 - end of helix Processing helix chain 'LK' and resid 38 through 51 Processing helix chain 'LK' and resid 76 through 86 removed outlier: 3.988A pdb=" N LYSLK 86 " --> pdb=" O ILELK 82 " (cutoff:3.500A) Processing helix chain 'LK' and resid 105 through 118 removed outlier: 5.023A pdb=" N PHELK 118 " --> pdb=" O ARGLK 114 " (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: 4.484A pdb=" N ARGLL 21 " --> pdb=" O HISLL 17 " (cutoff:3.500A) removed outlier: 3.584A 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: 3.762A pdb=" N GLYLL 94 " --> pdb=" O ALALL 90 " (cutoff:3.500A) Processing helix chain 'LL' and resid 105 through 123 removed outlier: 3.795A pdb=" N LEULL 109 " --> pdb=" O SERLL 105 " (cutoff:3.500A) Processing helix chain 'LL' and resid 139 through 144 removed outlier: 4.483A pdb=" N THRLL 144 " --> pdb=" O LYSLL 140 " (cutoff:3.500A) Processing helix chain 'LL' and resid 150 through 155 Processing helix chain 'LL' and resid 180 through 195 Processing helix chain 'LL' and resid 196 through 213 Processing helix chain 'LM' and resid 58 through 63 removed outlier: 3.699A pdb=" N ALALM 62 " --> pdb=" O PROLM 58 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEULM 63 " --> pdb=" O LEULM 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'LM' and resid 58 through 63' Processing helix chain 'LM' and resid 77 through 89 Processing helix chain 'LM' and resid 90 through 98 removed outlier: 5.411A pdb=" N ASNLM 98 " --> pdb=" O TRPLM 94 " (cutoff:3.500A) Processing helix chain 'LM' and resid 99 through 112 removed outlier: 3.702A 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: 4.483A pdb=" N TYRLN 6 " --> pdb=" O GLYLN 2 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYSLN 13 " --> pdb=" O GLULN 9 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LYSLN 14 " --> pdb=" O LEULN 10 " (cutoff:3.500A) Processing helix chain 'LN' and resid 16 through 34 removed outlier: 4.843A 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: 3.795A 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: 4.473A pdb=" N CYSLN 152 " --> pdb=" O ILELN 148 " (cutoff:3.500A) removed outlier: 4.300A 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: 3.571A pdb=" N ARGLN 162 " --> pdb=" O HISLN 158 " (cutoff:3.500A) Processing helix chain 'LN' and resid 165 through 173 Processing helix chain 'LN' and resid 186 through 196 Processing helix chain 'LO' and resid 16 through 31 Processing helix chain 'LO' and resid 47 through 61 removed outlier: 3.558A pdb=" N ALALO 51 " --> pdb=" O GLULO 47 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYSLO 61 " --> pdb=" O ALALO 57 " (cutoff:3.500A) Processing helix chain 'LO' and resid 77 through 91 removed outlier: 3.808A pdb=" N METLO 89 " --> pdb=" O ALALO 85 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILELO 90 " --> pdb=" O VALLO 86 " (cutoff:3.500A) Proline residue: LO 91 - end of helix Processing helix chain 'LO' and resid 94 through 105 removed outlier: 3.680A pdb=" N ARGLO 103 " --> pdb=" O ALALO 99 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEULO 104 " --> pdb=" O ALALO 100 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LYSLO 105 " --> pdb=" O LEULO 101 " (cutoff:3.500A) Processing helix chain 'LO' and resid 112 through 118 removed outlier: 7.987A pdb=" N LYSLO 116 " --> pdb=" O PROLO 112 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYSLO 117 " --> pdb=" O PROLO 113 " (cutoff:3.500A) removed outlier: 5.398A 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: 4.268A 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: 4.910A 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: 4.083A pdb=" N LYSLQ 74 " --> pdb=" O ALALQ 70 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N METLQ 82 " --> pdb=" O ARGLQ 78 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N SERLQ 83 " --> pdb=" O ARGLQ 79 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 91 through 100 removed outlier: 3.920A 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: 3.685A pdb=" N VALLR 22 " --> pdb=" O GLYLR 18 " (cutoff:3.500A) removed outlier: 5.965A 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: 3.746A pdb=" N ALALR 35 " --> pdb=" O GLULR 31 " (cutoff:3.500A) removed outlier: 5.305A 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: 5.742A 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: 6.751A pdb=" N VALLR 93 " --> pdb=" O METLR 89 " (cutoff:3.500A) Processing helix chain 'LR' and resid 116 through 130 Processing helix chain 'LR' and resid 134 through 156 Processing helix chain 'LS' and resid 33 through 49 Processing helix chain 'LS' and resid 98 through 114 Processing helix chain 'LS' and resid 117 through 122 removed outlier: 3.829A pdb=" N ILELS 121 " --> pdb=" O ARGLS 117 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N HISLS 122 " --> pdb=" O PHELS 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'LS' and resid 117 through 122' Processing helix chain 'LS' and resid 137 through 145 removed outlier: 4.475A pdb=" N LEULS 143 " --> pdb=" O TYRLS 139 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALALS 145 " --> pdb=" O LYSLS 141 " (cutoff:3.500A) Processing helix chain 'LT' and resid 92 through 97 removed outlier: 3.830A pdb=" N VALLT 96 " --> pdb=" O ARGLT 92 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LYSLT 97 " --> pdb=" O ILELT 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'LT' and resid 92 through 97' Processing helix chain 'LT' and resid 102 through 123 Processing helix chain 'LT' and resid 155 through 160 Processing helix chain 'LT' and resid 46 through 51 removed outlier: 4.000A pdb=" N GLNLT 49 " --> pdb=" O GLYLT 46 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYSLT 50 " --> pdb=" O ALALT 47 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLYLT 51 " --> pdb=" O VALLT 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'LT' and resid 46 through 51' 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 73 removed outlier: 3.773A pdb=" N ARGLV 72 " --> pdb=" O LYSLV 68 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYSLV 73 " --> pdb=" O PROLV 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'LV' and resid 68 through 73' Processing helix chain 'LV' and resid 121 through 129 Proline residue: LV 129 - end of helix Processing helix chain 'LV' and resid 130 through 135 Processing helix chain 'LX' and resid 71 through 76 removed outlier: 4.422A pdb=" N ILELX 76 " --> pdb=" O GLULX 72 " (cutoff:3.500A) Processing helix chain 'LX' and resid 82 through 92 removed outlier: 4.208A 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: 3.672A pdb=" N VALLY 28 " --> pdb=" O SERLY 24 " (cutoff:3.500A) removed outlier: 4.246A 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: 4.022A pdb=" N VALLY 103 " --> pdb=" O HISLY 99 " (cutoff:3.500A) removed outlier: 5.218A 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: 3.506A pdb=" N SERLZ 65 " --> pdb=" O ILELZ 61 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYSLZ 66 " --> pdb=" O GLULZ 62 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 75 through 80 removed outlier: 3.689A pdb=" N LEULZ 79 " --> pdb=" O ASNLZ 75 " (cutoff:3.500A) removed outlier: 5.377A 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 Proline residue: LZ 103 - end of helix Processing helix chain 'LZ' and resid 104 through 124 removed outlier: 3.532A pdb=" N LYSLZ 111 " --> pdb=" O GLULZ 107 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THRLZ 112 " --> pdb=" O GLULZ 108 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 126 through 132 Proline residue: LZ 132 - end of helix Processing helix chain 'La' and resid 6 through 12 removed outlier: 3.993A pdb=" N LYSLa 10 " --> pdb=" O SERLa 6 " (cutoff:3.500A) Processing helix chain 'La' and resid 64 through 69 removed outlier: 4.167A pdb=" N TYRLa 68 " --> pdb=" O LEULa 64 " (cutoff:3.500A) Processing helix chain 'La' and resid 74 through 83 removed outlier: 3.628A pdb=" N LEULa 78 " --> pdb=" O ASNLa 74 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N TRPLa 79 " --> pdb=" O ILELa 75 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N SERLa 80 " --> pdb=" O ASPLa 76 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEULa 81 " --> pdb=" O LYSLa 77 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VALLa 82 " --> pdb=" O LEULa 78 " (cutoff:3.500A) Proline residue: La 83 - end of helix No H-bonds generated for 'chain 'La' and resid 74 through 83' Processing helix chain 'La' and resid 84 through 93 Processing helix chain 'La' and resid 103 through 108 removed outlier: 3.724A 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: 4.004A 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: 4.968A 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 55 through 60 removed outlier: 4.376A pdb=" N GLYLe 59 " --> pdb=" O SERLe 55 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N SERLe 60 " --> pdb=" O ILELe 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'Le' and resid 55 through 60' Processing helix chain 'Le' and resid 79 through 88 removed outlier: 3.732A pdb=" N LEULe 85 " --> pdb=" O LYSLe 81 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEULe 86 " --> pdb=" O ASPLe 82 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEULe 87 " --> pdb=" O VALLe 83 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N METLe 88 " --> pdb=" O GLULe 84 " (cutoff:3.500A) Processing helix chain 'Le' and resid 102 through 117 Processing helix chain 'Lf' and resid 39 through 47 removed outlier: 3.952A pdb=" N PHELf 45 " --> pdb=" O ALALf 41 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYRLf 46 " --> pdb=" O ALALf 42 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEULf 47 " --> pdb=" O ALALf 43 " (cutoff:3.500A) Processing helix chain 'Lg' and resid 59 through 67 removed outlier: 3.961A pdb=" N TYRLg 63 " --> pdb=" O ARGLg 59 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALALg 64 " --> pdb=" O PROLg 60 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THRLg 65 " --> pdb=" O ARGLg 61 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILELg 66 " --> pdb=" O GLULg 62 " (cutoff:3.500A) removed outlier: 5.777A 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: 4.117A pdb=" N SERLh 14 " --> pdb=" O GLYLh 10 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYSLh 15 " --> pdb=" O GLNLh 11 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ASNLh 16 " --> pdb=" O LEULh 12 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 17 through 35 Processing helix chain 'Lh' and resid 43 through 76 removed outlier: 4.144A pdb=" N ASNLh 47 " --> pdb=" O GLYLh 43 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 82 through 87 Proline residue: Lh 87 - end of helix Processing helix chain 'Lh' and resid 90 through 96 Processing helix chain 'Lh' and resid 98 through 104 Processing helix chain 'Lh' and resid 106 through 116 Processing helix chain 'Li' and resid 34 through 39 removed outlier: 4.149A pdb=" N ARGLi 38 " --> pdb=" O ARGLi 34 " (cutoff:3.500A) removed outlier: 4.847A 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: 3.671A pdb=" N GLYLj 9 " --> pdb=" O THRLj 5 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYSLj 10 " --> pdb=" O SERLj 6 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARGLj 11 " --> pdb=" O SERLj 7 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 50 through 58 removed outlier: 3.808A pdb=" N LYSLj 57 " --> pdb=" O ALALj 53 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 65 through 77 removed outlier: 5.380A pdb=" N THRLj 69 " --> pdb=" O ARGLj 65 " (cutoff:3.500A) removed outlier: 3.853A 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 18 removed outlier: 5.609A pdb=" N LYSLk 18 " --> pdb=" O ILELk 14 " (cutoff:3.500A) Processing helix chain 'Lk' and resid 52 through 62 removed outlier: 4.523A pdb=" N GLULk 56 " --> pdb=" O SERLk 52 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLNLk 60 " --> pdb=" O GLULk 56 " (cutoff:3.500A) Processing helix chain 'Ll' and resid 6 through 21 removed outlier: 5.345A pdb=" N ARGLl 21 " --> pdb=" O GLNLl 17 " (cutoff:3.500A) Processing helix chain 'Ll' and resid 24 through 30 removed outlier: 4.355A pdb=" N ARGLl 28 " --> pdb=" O PROLl 24 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEULl 29 " --> pdb=" O GLNLl 25 " (cutoff:3.500A) removed outlier: 3.941A 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: 3.694A pdb=" N LYSLp 28 " --> pdb=" O LYSLp 24 " (cutoff:3.500A) removed outlier: 4.000A 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: 5.405A pdb=" N ASPLq 49 " --> pdb=" O GLYLq 45 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 86 through 99 Processing helix chain 'Lq' and resid 104 through 123 removed outlier: 4.004A pdb=" N ARGLq 108 " --> pdb=" O ARGLq 104 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLNLq 109 " --> pdb=" O ALALq 105 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ALALq 110 " --> pdb=" O ASPLq 106 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARGLq 123 " --> pdb=" O LEULq 119 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 135 through 140 removed outlier: 4.424A pdb=" N ARGLq 139 " --> pdb=" O GLYLq 135 " (cutoff:3.500A) Processing helix chain 'CC' and resid 284 through 301 Processing helix chain 'CC' and resid 308 through 316 Processing helix chain 'CC' and resid 363 through 373 Processing helix chain 'CC' and resid 389 through 394 Proline residue: CC 394 - end of helix Processing helix chain 'CC' and resid 398 through 412 removed outlier: 3.635A pdb=" N TYRCC 411 " --> pdb=" O CYSCC 407 " (cutoff:3.500A) Processing helix chain 'CC' and resid 424 through 430 removed outlier: 4.490A pdb=" N LEUCC 428 " --> pdb=" O ASPCC 424 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEUCC 429 " --> pdb=" O PROCC 425 " (cutoff:3.500A) Proline residue: CC 430 - end of helix No H-bonds generated for 'chain 'CC' and resid 424 through 430' Processing helix chain 'CC' and resid 434 through 439 removed outlier: 3.681A pdb=" N LEUCC 438 " --> pdb=" O SERCC 434 " (cutoff:3.500A) Processing helix chain 'CC' and resid 532 through 545 Processing helix chain 'CC' and resid 573 through 580 Processing helix chain 'CD' and resid 29 through 34 removed outlier: 4.567A pdb=" N GLNCD 34 " --> pdb=" O GLUCD 30 " (cutoff:3.500A) Processing helix chain 'CD' and resid 42 through 52 Processing helix chain 'CD' and resid 75 through 84 removed outlier: 4.228A pdb=" N GLYCD 84 " --> pdb=" O LEUCD 80 " (cutoff:3.500A) Processing helix chain 'CD' and resid 124 through 132 Processing helix chain 'CD' and resid 255 through 260 removed outlier: 3.513A pdb=" N ALACD 259 " --> pdb=" O SERCD 255 " (cutoff:3.500A) Proline residue: CD 260 - end of helix No H-bonds generated for 'chain 'CD' and resid 255 through 260' Processing helix chain 'CD' and resid 263 through 268 Proline residue: CD 268 - end of helix Processing helix chain 'CD' and resid 443 through 450 Processing helix chain 'CJ' and resid 11 through 16 Processing helix chain 'CJ' and resid 18 through 27 Processing helix chain 'CJ' and resid 29 through 41 Processing helix chain 'CJ' and resid 49 through 54 removed outlier: 3.537A pdb=" N VALCJ 53 " --> pdb=" O ASPCJ 49 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 65 through 76 Proline residue: CJ 76 - end of helix Processing helix chain 'CJ' and resid 77 through 98 Processing helix chain 'CJ' and resid 99 through 111 removed outlier: 3.627A pdb=" N ALACJ 103 " --> pdb=" O ASPCJ 99 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASNCJ 109 " --> pdb=" O ARGCJ 105 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 112 through 117 Processing helix chain 'CJ' and resid 123 through 132 Proline residue: CJ 132 - end of helix Processing helix chain 'CJ' and resid 133 through 154 removed outlier: 4.072A pdb=" N LEUCJ 141 " --> pdb=" O ALACJ 137 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ASPCJ 142 " --> pdb=" O LEUCJ 138 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ASPCJ 143 " --> pdb=" O ARGCJ 139 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N CYSCJ 144 " --> pdb=" O ASPCJ 140 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 161 through 183 Processing helix chain 'CJ' and resid 225 through 250 Processing helix chain 'CJ' and resid 258 through 265 Processing helix chain 'CJ' and resid 267 through 272 removed outlier: 5.134A pdb=" N SERCJ 272 " --> pdb=" O LEUCJ 268 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 362 through 368 removed outlier: 5.499A pdb=" N PHECJ 367 " --> pdb=" O PROCJ 363 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALACJ 368 " --> pdb=" O SERCJ 364 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 379 through 391 Processing helix chain 'CJ' and resid 457 through 468 Processing helix chain 'CJ' and resid 472 through 477 removed outlier: 4.277A pdb=" N TYRCJ 476 " --> pdb=" O PROCJ 472 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 502 through 507 removed outlier: 3.970A pdb=" N GLNCJ 507 " --> pdb=" O LEUCJ 503 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 508 through 522 Processing helix chain 'CJ' and resid 582 through 594 Processing helix chain 'CJ' and resid 606 through 639 removed outlier: 5.506A pdb=" N SERCJ 639 " --> pdb=" O LYSCJ 635 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 640 through 673 Processing helix chain 'CM' and resid 102 through 113 Processing helix chain 'CM' and resid 126 through 137 Processing helix chain 'CM' and resid 146 through 157 Processing helix chain 'CM' and resid 171 through 180 removed outlier: 3.955A pdb=" N ILECM 175 " --> pdb=" O ASPCM 171 " (cutoff:3.500A) Processing helix chain 'CM' and resid 186 through 197 removed outlier: 4.340A pdb=" N VALCM 197 " --> pdb=" O GLUCM 193 " (cutoff:3.500A) Processing helix chain 'CM' and resid 200 through 209 removed outlier: 5.156A pdb=" N TRPCM 209 " --> pdb=" O ALACM 205 " (cutoff:3.500A) Processing helix chain 'CM' and resid 240 through 249 removed outlier: 3.600A pdb=" N LEUCM 244 " --> pdb=" O HISCM 240 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'CF' and resid 63 through 67 removed outlier: 6.799A 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: 6.715A pdb=" N VALCF 135 " --> pdb=" O ILECF 194 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N GLUCF 190 " --> pdb=" O PROCF 139 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'CF' and resid 38 through 42 removed outlier: 8.417A pdb=" N GLNCF 38 " --> pdb=" O SERCF 229 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLYCF 225 " --> pdb=" O VALCF 42 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'CH' and resid 203 through 209 removed outlier: 4.789A pdb=" N ARGCH 167 " --> pdb=" O ARGCH 214 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THRCH 220 " --> pdb=" O VALCH 171 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLYCH 173 " --> pdb=" O THRCH 220 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLYCH 222 " --> pdb=" O GLYCH 173 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHECH 174 " --> pdb=" O PHECH 252 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ASPCH 254 " --> pdb=" O PHECH 174 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N METCH 281 " --> pdb=" O ALACH 247 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'CK' and resid 148 through 151 Processing sheet with id= 6, first strand: chain 'CK' and resid 190 through 195 removed outlier: 3.629A pdb=" N VALCK 191 " --> pdb=" O HISCK 186 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASNCK 256 " --> pdb=" O THRCK 246 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N TYRCK 242 " --> pdb=" O LEUCK 260 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THRCK 219 " --> pdb=" O ILECK 245 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'CN' and resid 1 through 4 Processing sheet with id= 8, first strand: chain 'CN' and resid 23 through 27 Processing sheet with id= 9, first strand: chain 'CN' and resid 69 through 73 Processing sheet with id= 10, first strand: chain 'CN' and resid 114 through 117 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: 4.682A 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: 4.101A 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: 4.577A 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: 3.959A pdb=" N CYSCd 378 " --> pdb=" O LEUCd 331 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLYCd 333 " --> pdb=" O CYSCd 378 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILECd 373 " --> pdb=" O LEUCd 369 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VALCd 363 " --> pdb=" O PROCd 379 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'Cf' and resid 56 through 60 removed outlier: 5.787A pdb=" N ARGCf 34 " --> pdb=" O PHECf 60 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N SERCf 92 " --> pdb=" O GLYCf 35 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N HISCf 98 " --> pdb=" O LEUCf 118 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N LEUCf 111 " --> pdb=" O PROCf 263 " (cutoff:3.500A) removed outlier: 4.715A 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: 6.860A 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: 4.754A 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: 4.322A 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: 8.575A pdb=" N ASNCg 124 " --> pdb=" O LYSCg 137 " (cutoff:3.500A) removed outlier: 4.389A 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: 4.279A pdb=" N THRCh 121 " --> pdb=" O HISCh 88 " (cutoff:3.500A) removed outlier: 4.583A 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: 5.073A pdb=" N ALACh 511 " --> pdb=" O GLYCh 507 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLYCh 507 " --> pdb=" O ALACh 511 " (cutoff:3.500A) removed outlier: 5.795A 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: 6.339A pdb=" N ARGCh 161 " --> pdb=" O SERCh 155 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SERCh 160 " --> pdb=" O THRCh 176 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THRCh 170 " --> pdb=" O SERCh 166 " (cutoff:3.500A) removed outlier: 6.552A 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: 5.519A pdb=" N TYRCh 203 " --> pdb=" O SERCh 198 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THRCh 212 " --> pdb=" O SERCh 208 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VALCh 215 " --> pdb=" O VALCh 224 " (cutoff:3.500A) removed outlier: 3.643A 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: 5.861A pdb=" N ARGCh 252 " --> pdb=" O GLNCh 241 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THRCh 261 " --> pdb=" O SERCh 257 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N HISCh 274 " --> pdb=" O ILECh 264 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'Ch' and resid 284 through 289 removed outlier: 3.562A pdb=" N CYSCh 285 " --> pdb=" O GLYCh 297 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEUCh 293 " --> pdb=" O GLYCh 289 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ASPCh 292 " --> pdb=" O ALACh 308 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SERCh 302 " --> pdb=" O SERCh 298 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VALCh 305 " --> pdb=" O VALCh 314 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THRCh 312 " --> pdb=" O ASPCh 307 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'Ch' and resid 326 through 330 removed outlier: 3.513A pdb=" N HISCh 326 " --> pdb=" O ALACh 378 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ARGCh 374 " --> pdb=" O SERCh 330 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THRCh 383 " --> pdb=" O SERCh 379 " (cutoff:3.500A) removed outlier: 3.567A 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: 5.688A pdb=" N LEUCh 418 " --> pdb=" O SERCh 413 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THRCh 417 " --> pdb=" O ALACh 433 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SERCh 427 " --> pdb=" O GLYCh 423 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THRCh 428 " --> pdb=" O ASNCh 441 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ASNCh 441 " --> pdb=" O THRCh 428 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEUCh 430 " --> pdb=" O ILECh 439 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYSCh 437 " --> pdb=" O ASNCh 432 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'Ch' and resid 450 through 455 removed outlier: 5.804A pdb=" N LEUCh 460 " --> pdb=" O SERCh 455 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ARGCh 459 " --> pdb=" O VALCh 475 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THRCh 469 " --> pdb=" O SERCh 465 " (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 302 through 305 Processing sheet with id= 33, first strand: chain 'LA' and resid 47 through 50 removed outlier: 3.588A pdb=" N GLULA 47 " --> pdb=" O ARGLA 60 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ARGLA 60 " --> pdb=" O LYSLA 46 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLNLA 86 " --> pdb=" O VALLA 45 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'LA' and resid 110 through 114 removed outlier: 4.273A pdb=" N THRLA 111 " --> pdb=" O VALLA 136 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARGLA 147 " --> pdb=" O VALLA 137 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'LA' and resid 58 through 64 No H-bonds generated for sheet with id= 35 Processing sheet with id= 36, first strand: chain 'LA' and resid 145 through 150 removed outlier: 4.111A pdb=" N ALALA 154 " --> pdb=" O LEULA 150 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'LB' and resid 41 through 44 removed outlier: 6.429A pdb=" N GLNLB 183 " --> pdb=" O THRLB 44 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N HISLB 178 " --> pdb=" O THRLB 165 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N VALLB 159 " --> pdb=" O ILELB 184 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N GLYLB 186 " --> pdb=" O THRLB 157 " (cutoff:3.500A) removed outlier: 11.092A pdb=" N THRLB 157 " --> pdb=" O GLYLB 186 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLYLB 91 " --> pdb=" O LEULB 102 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'LB' and resid 53 through 58 removed outlier: 6.699A pdb=" N ILELB 78 " --> pdb=" O ALALB 51 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARGLB 335 " --> pdb=" O LYSLB 50 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ILELB 336 " --> pdb=" O VALLB 221 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N VALLB 221 " --> pdb=" O ILELB 336 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N HISLB 274 " --> pdb=" O THRLB 222 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'LB' and resid 285 through 289 removed outlier: 3.674A pdb=" N ARGLB 285 " --> pdb=" O METLB 324 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLYLB 289 " --> pdb=" O ASNLB 320 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ASNLB 320 " --> pdb=" O GLYLB 289 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'LB' and resid 76 through 80 Processing sheet with id= 41, first strand: chain 'LB' and resid 87 through 91 removed outlier: 8.059A pdb=" N VALLB 87 " --> pdb=" O ALALB 107 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THRLB 103 " --> pdb=" O GLYLB 91 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'LB' and resid 84 through 87 removed outlier: 3.751A pdb=" N LYSLB 202 " --> pdb=" O VALLB 86 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'LB' and resid 214 through 217 removed outlier: 4.315A pdb=" N GLULB 214 " --> pdb=" O ILELB 283 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'LC' and resid 5 through 9 removed outlier: 4.803A pdb=" N ALALC 19 " --> pdb=" O VALLC 9 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'LC' and resid 231 through 235 removed outlier: 5.295A pdb=" N PHELC 254 " --> pdb=" O GLYLC 208 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'LD' and resid 60 through 66 Processing sheet with id= 47, first strand: chain 'LE' and resid 5 through 9 Processing sheet with id= 48, first strand: chain 'LE' and resid 56 through 61 removed outlier: 3.966A pdb=" N THRLE 56 " --> pdb=" O LEULE 72 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYSLE 68 " --> pdb=" O LEULE 60 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'LF' and resid 139 through 144 removed outlier: 7.622A pdb=" N TRPLF 139 " --> pdb=" O ILELF 95 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LYSLF 88 " --> pdb=" O VALLF 125 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASNLF 119 " --> pdb=" O ARGLF 94 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ASNLF 118 " --> pdb=" O LEULF 213 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'LF' and resid 158 through 162 removed outlier: 6.385A pdb=" N GLYLF 158 " --> pdb=" O LEULF 169 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'LG' and resid 179 through 184 Processing sheet with id= 52, first strand: chain 'LH' and resid 5 through 12 removed outlier: 5.797A pdb=" N GLYLH 88 " --> pdb=" O VALLH 12 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'LH' and resid 54 through 57 Processing sheet with id= 54, first strand: chain 'LH' and resid 137 through 144 removed outlier: 3.910A pdb=" N CYSLH 148 " --> pdb=" O ASNLH 143 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N TYRLH 149 " --> pdb=" O METLH 167 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'LH' and resid 171 through 176 removed outlier: 5.278A pdb=" N GLULH 182 " --> pdb=" O SERLH 176 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASPLH 181 " --> pdb=" O TYRLH 129 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'LJ' and resid 46 through 49 removed outlier: 3.588A pdb=" N ALALJ 67 " --> pdb=" O SERLJ 49 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYSLJ 17 " --> pdb=" O CYSLJ 131 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N SERLJ 23 " --> pdb=" O GLYLJ 125 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N GLYLJ 125 " --> pdb=" O SERLJ 23 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'LJ' and resid 90 through 93 Processing sheet with id= 58, first strand: chain 'LK' and resid 11 through 16 removed outlier: 4.353A pdb=" N THRLK 59 " --> pdb=" O VALLK 74 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'LL' and resid 56 through 59 Processing sheet with id= 60, first strand: chain 'LM' and resid 18 through 21 removed outlier: 4.633A pdb=" N ARGLM 18 " --> pdb=" O ILELM 30 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEULM 40 " --> pdb=" O VALLM 31 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'LN' and resid 35 through 39 removed outlier: 6.361A pdb=" N VALLN 35 " --> pdb=" O ARGLN 65 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILELN 61 " --> pdb=" O ALALN 39 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLYLN 58 " --> pdb=" O ASPLN 136 " (cutoff:3.500A) removed outlier: 6.911A 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: 3.587A pdb=" N ASNLN 117 " --> pdb=" O ILELN 133 " (cutoff:3.500A) removed outlier: 6.762A 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: 6.599A 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: 5.385A 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: 4.044A pdb=" N ARGLP 127 " --> pdb=" O TYRLP 139 " (cutoff:3.500A) removed outlier: 3.811A 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 'LQ' and resid 126 through 129 Processing sheet with id= 70, first strand: chain 'LS' and resid 24 through 30 removed outlier: 6.578A pdb=" N ILELS 10 " --> pdb=" O VALLS 59 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N THRLS 55 " --> pdb=" O LEULS 14 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'LS' and resid 87 through 96 removed outlier: 5.132A pdb=" N ASNLS 74 " --> pdb=" O LEULS 129 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'LS' and resid 6 through 10 removed outlier: 4.516A pdb=" N GLULS 6 " --> pdb=" O ILELS 64 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'LT' and resid 40 through 43 removed outlier: 3.744A pdb=" N LYSLT 60 " --> pdb=" O ILELT 42 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'LT' and resid 72 through 79 Processing sheet with id= 75, first strand: chain 'LU' and resid 60 through 65 removed outlier: 6.193A pdb=" N LYSLU 69 " --> pdb=" O ILELU 65 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLYLU 108 " --> pdb=" O LYSLU 20 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'LV' and resid 35 through 38 removed outlier: 4.422A pdb=" N ALALV 23 " --> pdb=" O ILELV 38 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASNLV 100 " --> pdb=" O ILELV 24 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ILELV 104 " --> pdb=" O ALALV 28 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASPLV 58 " --> pdb=" O ILELV 80 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'LV' and resid 86 through 89 removed outlier: 4.041A pdb=" N VALLV 93 " --> pdb=" O ARGLV 89 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'LV' and resid 81 through 84 removed outlier: 3.810A pdb=" N ALALV 84 " --> pdb=" O ASPLV 99 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASPLV 99 " --> pdb=" O ALALV 84 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'LX' and resid 77 through 80 removed outlier: 5.708A pdb=" N VALLX 96 " --> pdb=" O LEULX 80 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASNLX 93 " --> pdb=" O LEULX 139 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYSLX 133 " --> pdb=" O VALLX 99 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THRLX 132 " --> pdb=" O ARGLX 128 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYSLX 122 " --> pdb=" O ARGLX 138 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'LY' and resid 55 through 58 removed outlier: 4.066A pdb=" N LYSLY 65 " --> pdb=" O ILELY 57 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'LY' and resid 71 through 74 removed outlier: 3.623A pdb=" N SERLY 71 " --> pdb=" O HISLY 80 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'LY' and resid 85 through 88 removed outlier: 5.030A pdb=" N GLNLY 92 " --> pdb=" O LYSLY 88 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'LZ' and resid 9 through 13 removed outlier: 4.007A pdb=" N LYSLZ 20 " --> pdb=" O VALLZ 12 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'LZ' and resid 26 through 29 Processing sheet with id= 85, first strand: chain 'La' and resid 99 through 102 Processing sheet with id= 86, first strand: chain 'Lc' and resid 25 through 28 removed outlier: 6.162A pdb=" N LYSLc 25 " --> pdb=" O LEULc 96 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'Ld' and resid 56 through 59 removed outlier: 4.922A pdb=" N ASPLd 56 " --> pdb=" O LEULd 97 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ALALd 17 " --> pdb=" O VALLd 117 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'Le' and resid 72 through 78 Processing sheet with id= 89, first strand: chain 'Lf' and resid 12 through 17 removed outlier: 5.892A pdb=" N LYSLf 12 " --> pdb=" O GLULf 35 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEULf 31 " --> pdb=" O LEULf 16 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ARGLf 84 " --> pdb=" O THRLf 74 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LYSLf 65 " --> pdb=" O ALALf 57 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYSLf 49 " --> pdb=" O ILELf 73 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ARGLf 50 " --> pdb=" O METLf 103 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'Lf' and resid 10 through 16 removed outlier: 4.148A pdb=" N ALALf 98 " --> pdb=" O HISLf 15 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'Lg' and resid 20 through 25 removed outlier: 4.543A pdb=" N ARGLg 20 " --> pdb=" O ILELg 36 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'Lk' and resid 2 through 5 removed outlier: 4.087A pdb=" N VALLk 48 " --> pdb=" O VALLk 5 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LYSLk 27 " --> pdb=" O VALLk 71 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'Lp' and resid 46 through 50 removed outlier: 8.377A pdb=" N SERLp 46 " --> pdb=" O LYSLp 58 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILELp 54 " --> pdb=" O THRLp 50 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLYLp 53 " --> pdb=" O GLYLp 66 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYSLp 62 " --> pdb=" O CYSLp 57 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'Lq' and resid 19 through 22 removed outlier: 6.828A pdb=" N PHELq 19 " --> pdb=" O ARGLq 30 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'Lq' and resid 51 through 56 removed outlier: 5.296A pdb=" N ALALq 51 " --> pdb=" O LYSLq 66 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N SERLq 77 " --> pdb=" O LYSLq 67 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'CC' and resid 447 through 450 removed outlier: 4.554A pdb=" N THRCC 796 " --> pdb=" O GLYCC 792 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N TRPCC 787 " --> pdb=" O HISCC 782 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASPCC 778 " --> pdb=" O ALACC 791 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'CC' and resid 458 through 462 removed outlier: 5.412A pdb=" N ALACC 467 " --> pdb=" O ASPCC 462 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VALCC 479 " --> pdb=" O VALCC 488 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARGCC 486 " --> pdb=" O GLUCC 481 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'CC' and resid 501 through 505 removed outlier: 3.812A pdb=" N THRCC 501 " --> pdb=" O ALACC 516 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ILECC 512 " --> pdb=" O ARGCC 505 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'CC' and resid 592 through 597 removed outlier: 5.668A pdb=" N HISCC 602 " --> pdb=" O HISCC 597 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N ASPCC 601 " --> pdb=" O LEUCC 620 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SERCC 614 " --> pdb=" O SERCC 607 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'CC' and resid 638 through 642 removed outlier: 5.470A pdb=" N LEUCC 647 " --> pdb=" O HISCC 642 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N CYSCC 658 " --> pdb=" O VALCC 667 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'CC' and resid 679 through 683 removed outlier: 5.578A pdb=" N ASNCC 688 " --> pdb=" O HISCC 683 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N ASPCC 687 " --> pdb=" O LEUCC 703 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARGCC 697 " --> pdb=" O SERCC 693 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'CC' and resid 722 through 726 removed outlier: 5.717A pdb=" N LEUCC 732 " --> pdb=" O HISCC 726 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILECC 744 " --> pdb=" O VALCC 762 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 'CC' and resid 475 through 479 removed outlier: 8.692A pdb=" N GLYCC 475 " --> pdb=" O LEUCC 493 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'CC' and resid 655 through 658 Processing sheet with id=105, first strand: chain 'CC' and resid 741 through 744 Processing sheet with id=106, first strand: chain 'CD' and resid 35 through 39 removed outlier: 8.202A pdb=" N ALACD 13 " --> pdb=" O ALACD 39 " (cutoff:3.500A) Processing sheet with id=107, first strand: chain 'CD' and resid 116 through 121 removed outlier: 5.338A pdb=" N LEUCD 155 " --> pdb=" O SERCD 168 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALACD 166 " --> pdb=" O ILECD 157 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain 'CD' and resid 182 through 186 removed outlier: 6.434A pdb=" N ARGCD 190 " --> pdb=" O LEUCD 186 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ASPCD 189 " --> pdb=" O TYRCD 205 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VALCD 202 " --> pdb=" O THRCD 218 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THRCD 212 " --> pdb=" O SERCD 208 " (cutoff:3.500A) Processing sheet with id=109, first strand: chain 'CD' and resid 229 through 235 removed outlier: 8.673A pdb=" N LYSCD 238 " --> pdb=" O ALACD 254 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALACD 248 " --> pdb=" O SERCD 244 " (cutoff:3.500A) Processing sheet with id=110, first strand: chain 'CD' and resid 285 through 288 Processing sheet with id=111, first strand: chain 'CD' and resid 302 through 305 removed outlier: 4.183A pdb=" N THRCD 321 " --> pdb=" O SERCD 317 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N HISCD 320 " --> pdb=" O LEUCD 338 " (cutoff:3.500A) Processing sheet with id=112, first strand: chain 'CD' and resid 344 through 349 removed outlier: 3.541A pdb=" N SERCD 344 " --> pdb=" O GLYCD 361 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N HISCD 366 " --> pdb=" O THRCD 362 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N METCD 382 " --> pdb=" O METCD 369 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLYCD 433 " --> pdb=" O VALCD 381 " (cutoff:3.500A) Processing sheet with id=113, first strand: chain 'CD' and resid 392 through 397 removed outlier: 5.858A pdb=" N SERCD 403 " --> pdb=" O SERCD 397 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SERCD 408 " --> pdb=" O THRCD 412 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N THRCD 412 " --> pdb=" O SERCD 408 " (cutoff:3.500A) Processing sheet with id=114, first strand: chain 'CD' and resid 465 through 468 Processing sheet with id=115, first strand: chain 'CD' and resid 102 through 108 removed outlier: 6.553A pdb=" N VALCD 484 " --> pdb=" O GLUCD 105 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SERCD 107 " --> pdb=" O VALCD 482 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VALCD 482 " --> pdb=" O SERCD 107 " (cutoff:3.500A) Processing sheet with id=116, first strand: chain 'CD' and resid 199 through 202 Processing sheet with id=117, first strand: chain 'CJ' and resid 186 through 191 Processing sheet with id=118, first strand: chain 'CJ' and resid 394 through 397 removed outlier: 3.790A pdb=" N PHECJ 372 " --> pdb=" O ARGCJ 394 " (cutoff:3.500A) Processing sheet with id=119, first strand: chain 'CM' and resid 118 through 121 removed outlier: 5.667A pdb=" N ASNCM 118 " --> pdb=" O LEUCM 213 " (cutoff:3.500A) 3793 hydrogen bonds defined for protein. 11241 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2654 hydrogen bonds 4408 hydrogen bond angles 0 basepair planarities 1050 basepair parallelities 1851 stacking parallelities Total time for adding SS restraints: 232.78 Time building geometry restraints manager: 61.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 20853 1.32 - 1.45: 61543 1.45 - 1.57: 76444 1.57 - 1.69: 6671 1.69 - 1.82: 425 Bond restraints: 165936 Sorted by residual: bond pdb=" C3' A2MC12289 " pdb=" C2' A2MC12289 " ideal model delta sigma weight residual 1.544 1.236 0.308 2.00e-02 2.50e+03 2.38e+02 bond pdb=" C3' A2MC1 858 " pdb=" C2' A2MC1 858 " ideal model delta sigma weight residual 1.544 1.236 0.308 2.00e-02 2.50e+03 2.37e+02 bond pdb=" C3' A2MC1 848 " pdb=" C2' A2MC1 848 " ideal model delta sigma weight residual 1.544 1.242 0.302 2.00e-02 2.50e+03 2.28e+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 bond pdb=" C3' A2MC11223 " pdb=" C2' A2MC11223 " ideal model delta sigma weight residual 1.544 1.242 0.302 2.00e-02 2.50e+03 2.28e+02 ... (remaining 165931 not shown) Histogram of bond angle deviations from ideal: 93.37 - 103.84: 10751 103.84 - 114.30: 113080 114.30 - 124.77: 102064 124.77 - 135.24: 14465 135.24 - 145.70: 9 Bond angle restraints: 240369 Sorted by residual: angle pdb=" C1' OMGC1 385 " pdb=" N9 OMGC1 385 " pdb=" C4 OMGC1 385 " ideal model delta sigma weight residual 108.29 129.60 -21.31 3.00e+00 1.11e-01 5.05e+01 angle pdb=" C1' A2MC12289 " pdb=" N9 A2MC12289 " pdb=" C8 A2MC12289 " ideal model delta sigma weight residual 88.50 108.69 -20.19 3.00e+00 1.11e-01 4.53e+01 angle pdb=" C1' OMGC12881 " pdb=" N9 OMGC12881 " pdb=" C4 OMGC12881 " ideal model delta sigma weight residual 108.29 128.21 -19.92 3.00e+00 1.11e-01 4.41e+01 angle pdb=" C1' OMGC12876 " pdb=" N9 OMGC12876 " pdb=" C4 OMGC12876 " ideal model delta sigma weight residual 108.29 127.79 -19.50 3.00e+00 1.11e-01 4.22e+01 angle pdb=" C1' A2MC1 848 " pdb=" N9 A2MC1 848 " pdb=" C8 A2MC1 848 " ideal model delta sigma weight residual 88.50 107.85 -19.35 3.00e+00 1.11e-01 4.16e+01 ... (remaining 240364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 96144 35.86 - 71.72: 7834 71.72 - 107.58: 958 107.58 - 143.44: 20 143.44 - 179.30: 34 Dihedral angle restraints: 104990 sinusoidal: 73820 harmonic: 31170 Sorted by residual: dihedral pdb=" O4' CC13338 " pdb=" C1' CC13338 " pdb=" N1 CC13338 " pdb=" C2 CC13338 " ideal model delta sinusoidal sigma weight residual 200.00 38.81 161.19 1 1.50e+01 4.44e-03 8.31e+01 dihedral pdb=" O4' CC1 961 " pdb=" C1' CC1 961 " pdb=" N1 CC1 961 " pdb=" C2 CC1 961 " ideal model delta sinusoidal sigma weight residual 200.00 42.05 157.95 1 1.50e+01 4.44e-03 8.22e+01 dihedral pdb=" O4' UC12100 " pdb=" C1' UC12100 " pdb=" N1 UC12100 " pdb=" C2 UC12100 " ideal model delta sinusoidal sigma weight residual 200.00 45.87 154.13 1 1.50e+01 4.44e-03 8.11e+01 ... (remaining 104987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 26111 0.068 - 0.137: 2987 0.137 - 0.205: 213 0.205 - 0.273: 42 0.273 - 0.341: 11 Chirality restraints: 29364 Sorted by residual: chirality pdb=" CB ILELH 157 " pdb=" CA ILELH 157 " pdb=" CG1 ILELH 157 " pdb=" CG2 ILELH 157 " both_signs ideal model delta sigma weight residual False 2.64 2.99 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" C3' UC11537 " pdb=" C4' UC11537 " pdb=" O3' UC11537 " pdb=" C2' UC11537 " both_signs ideal model delta sigma weight residual False -2.74 -2.41 -0.34 2.00e-01 2.50e+01 2.83e+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 -2.15 -0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 29361 not shown) Planarity restraints: 18265 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMGC12358 " -0.076 2.00e-02 2.50e+03 6.18e-01 8.59e+03 pdb=" C4' OMGC12358 " -0.438 2.00e-02 2.50e+03 pdb=" O4' OMGC12358 " -0.658 2.00e-02 2.50e+03 pdb=" C3' OMGC12358 " 0.606 2.00e-02 2.50e+03 pdb=" O3' OMGC12358 " 0.670 2.00e-02 2.50e+03 pdb=" C2' OMGC12358 " 0.166 2.00e-02 2.50e+03 pdb=" O2' OMGC12358 " -1.009 2.00e-02 2.50e+03 pdb=" C1' OMGC12358 " -0.211 2.00e-02 2.50e+03 pdb=" N9 OMGC12358 " 0.949 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMGC12578 " 0.078 2.00e-02 2.50e+03 6.13e-01 8.47e+03 pdb=" C4' OMGC12578 " 0.436 2.00e-02 2.50e+03 pdb=" O4' OMGC12578 " 0.629 2.00e-02 2.50e+03 pdb=" C3' OMGC12578 " -0.601 2.00e-02 2.50e+03 pdb=" O3' OMGC12578 " -0.675 2.00e-02 2.50e+03 pdb=" C2' OMGC12578 " -0.160 2.00e-02 2.50e+03 pdb=" O2' OMGC12578 " 1.013 2.00e-02 2.50e+03 pdb=" C1' OMGC12578 " 0.217 2.00e-02 2.50e+03 pdb=" N9 OMGC12578 " -0.938 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMGC1 627 " 0.081 2.00e-02 2.50e+03 6.00e-01 8.09e+03 pdb=" C4' OMGC1 627 " 0.417 2.00e-02 2.50e+03 pdb=" O4' OMGC1 627 " 0.596 2.00e-02 2.50e+03 pdb=" C3' OMGC1 627 " -0.613 2.00e-02 2.50e+03 pdb=" O3' OMGC1 627 " -0.652 2.00e-02 2.50e+03 pdb=" C2' OMGC1 627 " -0.164 2.00e-02 2.50e+03 pdb=" O2' OMGC1 627 " 1.009 2.00e-02 2.50e+03 pdb=" C1' OMGC1 627 " 0.224 2.00e-02 2.50e+03 pdb=" N9 OMGC1 627 " -0.897 2.00e-02 2.50e+03 ... (remaining 18262 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 2715 2.63 - 3.20: 122061 3.20 - 3.77: 294986 3.77 - 4.33: 406998 4.33 - 4.90: 569194 Nonbonded interactions: 1395954 Sorted by model distance: nonbonded pdb=" OG SERCd 340 " pdb="MG MGCd1002 " model vdw 2.067 2.170 nonbonded pdb=" O2G GTPCd1000 " pdb="MG MGCd1002 " model vdw 2.069 2.170 nonbonded pdb=" OG1 THRCd 361 " pdb="MG MGCd1002 " model vdw 2.084 2.170 nonbonded pdb=" O THRCC 510 " pdb=" OG SERCC 539 " model vdw 2.119 2.440 nonbonded pdb=" O1B GTPCH 701 " pdb="MG MGCH 702 " model vdw 2.127 2.170 ... (remaining 1395949 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: 9.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 29.020 Check model and map are aligned: 1.780 Set scattering table: 1.040 Process input model: 584.280 Find NCS groups from input model: 3.920 Set up NCS constraints: 0.400 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:13.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 643.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 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 : 0.007 0.308 165936 Z= 0.411 Angle : 0.777 21.309 240369 Z= 0.395 Chirality : 0.044 0.341 29364 Planarity : 0.019 0.618 18265 Dihedral : 20.893 179.296 84822 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.02 % Allowed : 0.19 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % 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: 0.24 (0.07), residues: 10626 helix: 0.63 (0.08), residues: 3871 sheet: 0.17 (0.12), residues: 1755 loop : -0.09 (0.08), residues: 5000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.002 TRPLD 95 HIS 0.013 0.002 HISCN 118 PHE 0.042 0.002 PHELC 121 TYR 0.042 0.002 TYRCd 366 ARG 0.015 0.001 ARGCJ 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21252 Ramachandran restraints generated. 10626 Oldfield, 0 Emsley, 10626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21252 Ramachandran restraints generated. 10626 Oldfield, 0 Emsley, 10626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1231 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1230 time to evaluate : 9.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: CH 298 ASP cc_start: 0.8031 (p0) cc_final: 0.7491 (p0) REVERT: CH 490 GLN cc_start: 0.7815 (tm-30) cc_final: 0.7607 (tm-30) REVERT: CL 21 ARG cc_start: 0.8358 (mtm-85) cc_final: 0.8057 (mtt90) REVERT: CQ 63 MET cc_start: 0.8585 (ttp) cc_final: 0.8249 (ttp) REVERT: Cf 159 MET cc_start: 0.8700 (ttm) cc_final: 0.8464 (ttm) REVERT: Cz 76 ARG cc_start: 0.8152 (ttt-90) cc_final: 0.7856 (ttt-90) REVERT: LF 248 MET cc_start: 0.8872 (mtp) cc_final: 0.8600 (mtm) REVERT: LH 199 ASP cc_start: 0.8462 (m-30) cc_final: 0.8253 (m-30) REVERT: LJ 132 MET cc_start: 0.8697 (mmm) cc_final: 0.8423 (mmm) REVERT: LM 15 GLU cc_start: 0.8887 (pm20) cc_final: 0.8676 (pm20) REVERT: LM 103 GLN cc_start: 0.8448 (tt0) cc_final: 0.8243 (tt0) REVERT: LM 107 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7816 (mt-10) REVERT: LY 30 MET cc_start: 0.9057 (mtp) cc_final: 0.8790 (mtp) REVERT: La 136 ARG cc_start: 0.8834 (tmm160) cc_final: 0.8556 (tmm160) REVERT: Lc 66 SER cc_start: 0.8700 (p) cc_final: 0.8480 (t) REVERT: Lh 16 ASN cc_start: 0.8699 (p0) cc_final: 0.8194 (p0) REVERT: CD 19 PHE cc_start: 0.8931 (m-10) cc_final: 0.8675 (m-10) REVERT: CD 35 LEU cc_start: 0.8282 (mm) cc_final: 0.7960 (mm) outliers start: 1 outliers final: 2 residues processed: 1231 average time/residue: 2.4833 time to fit residues: 4274.3213 Evaluate side-chains 985 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 983 time to evaluate : 9.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CH residue 307 ASP Chi-restraints excluded: chain LX residue 147 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 1169 optimal weight: 2.9990 chunk 1049 optimal weight: 0.9990 chunk 582 optimal weight: 7.9990 chunk 358 optimal weight: 3.9990 chunk 708 optimal weight: 0.4980 chunk 560 optimal weight: 3.9990 chunk 1085 optimal weight: 9.9990 chunk 420 optimal weight: 3.9990 chunk 660 optimal weight: 3.9990 chunk 807 optimal weight: 4.9990 chunk 1257 optimal weight: 8.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 29 ASN CF 153 HIS CH 533 HIS CH 633 GLN CK 53 GLN CK 57 GLN CK 190 ASN CQ 87 GLN CQ 130 ASN ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 101 ASN Cd 9 ASN Cd 326 GLN Cd 406 HIS ** Cf 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ch 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ch 517 ASN Cz 56 GLN LB 379 GLN LC 118 GLN LC 241 ASN LC 264 GLN LD 39 GLN LE 172 ASN LF 10 ASN ** LF 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 78 GLN LF 163 ASN LG 27 ASN ** LG 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 64 GLN LG 158 ASN LG 212 ASN LG 246 GLN LH 179 GLN LH 201 GLN LH 202 GLN LJ 40 GLN LJ 96 ASN LJ 110 HIS LP 125 GLN LP 170 HIS LQ 101 ASN LR 91 GLN LS 147 ASN LT 90 ASN LU 55 ASN LX 92 GLN LY 116 ASN Le 50 ASN Lg 30 GLN Lh 77 ASN ** Li 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Li 72 ASN CC 623 HIS CD 340 HIS CJ 109 ASN CJ 457 GLN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.0711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 165936 Z= 0.275 Angle : 0.677 18.362 240369 Z= 0.358 Chirality : 0.039 0.271 29364 Planarity : 0.007 0.138 18265 Dihedral : 22.571 179.940 63652 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.31 % Allowed : 6.76 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % 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: 0.87 (0.08), residues: 10626 helix: 1.50 (0.08), residues: 3895 sheet: 0.19 (0.12), residues: 1761 loop : 0.10 (0.08), residues: 4970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRPCC 396 HIS 0.012 0.001 HISCd 238 PHE 0.020 0.002 PHELX 136 TYR 0.029 0.002 TYRCd 366 ARG 0.009 0.001 ARGLU 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21252 Ramachandran restraints generated. 10626 Oldfield, 0 Emsley, 10626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21252 Ramachandran restraints generated. 10626 Oldfield, 0 Emsley, 10626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1143 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1029 time to evaluate : 8.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CF 241 LYS cc_start: 0.8103 (mtpp) cc_final: 0.7873 (mmmt) REVERT: CH 298 ASP cc_start: 0.7687 (p0) cc_final: 0.7453 (p0) REVERT: CH 360 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7298 (ttt180) REVERT: CH 362 GLN cc_start: 0.8196 (mt0) cc_final: 0.7939 (mt0) REVERT: CH 490 GLN cc_start: 0.7765 (tm-30) cc_final: 0.7467 (tm-30) REVERT: CL 21 ARG cc_start: 0.8357 (mtm-85) cc_final: 0.7935 (mtt90) REVERT: CO 19 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8623 (ttmt) REVERT: CQ 63 MET cc_start: 0.8652 (ttp) cc_final: 0.8245 (ttp) REVERT: Cd 16 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.6879 (ttm110) REVERT: LA 80 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: LE 31 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: LF 248 MET cc_start: 0.8933 (mtp) cc_final: 0.8635 (mtm) REVERT: LG 252 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7192 (mtm-85) REVERT: LJ 127 ASP cc_start: 0.6984 (m-30) cc_final: 0.6756 (m-30) REVERT: LJ 132 MET cc_start: 0.8732 (mmm) cc_final: 0.8510 (mmm) REVERT: LK 87 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.8021 (mt-10) REVERT: LM 103 GLN cc_start: 0.8490 (tt0) cc_final: 0.8254 (tt0) REVERT: LN 13 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8233 (mmtt) REVERT: LO 197 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: LS 104 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7545 (mt-10) REVERT: LU 55 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8143 (t0) REVERT: LY 56 GLN cc_start: 0.8674 (tt0) cc_final: 0.8396 (tt0) REVERT: LY 127 GLN cc_start: 0.9005 (tm-30) cc_final: 0.8801 (tm-30) REVERT: Lc 66 SER cc_start: 0.8667 (p) cc_final: 0.8438 (t) REVERT: Le 124 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7033 (mmtt) REVERT: Lh 16 ASN cc_start: 0.8681 (p0) cc_final: 0.8335 (p0) REVERT: Lk 41 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.7065 (tm-30) REVERT: CC 396 TRP cc_start: 0.6816 (m-10) cc_final: 0.6508 (m-90) REVERT: CC 408 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7701 (mtp) REVERT: CD 19 PHE cc_start: 0.8945 (m-10) cc_final: 0.8679 (m-10) REVERT: CD 35 LEU cc_start: 0.8240 (mm) cc_final: 0.7848 (mm) REVERT: CJ 142 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7379 (m-30) outliers start: 114 outliers final: 39 residues processed: 1072 average time/residue: 2.4856 time to fit residues: 3769.4392 Evaluate side-chains 1019 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 966 time to evaluate : 8.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CF residue 55 ASP Chi-restraints excluded: chain CH residue 291 ILE Chi-restraints excluded: chain CH residue 307 ASP Chi-restraints excluded: chain CH residue 360 ARG Chi-restraints excluded: chain CH residue 459 GLN Chi-restraints excluded: chain CN residue 51 THR Chi-restraints excluded: chain CO residue 19 LYS Chi-restraints excluded: chain Cb residue 38 THR Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cd residue 16 ARG Chi-restraints excluded: chain Cd residue 86 ASP Chi-restraints excluded: chain LA residue 80 GLU Chi-restraints excluded: chain LA residue 96 LEU Chi-restraints excluded: chain LA residue 114 SER Chi-restraints excluded: chain LD residue 188 ILE Chi-restraints excluded: chain LE residue 31 GLU Chi-restraints excluded: chain LE residue 162 GLN Chi-restraints excluded: chain LF residue 8 THR Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LG residue 88 ASN Chi-restraints excluded: chain LG residue 252 ARG Chi-restraints excluded: chain LJ residue 13 LEU Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 147 SER Chi-restraints excluded: chain LK residue 87 GLU Chi-restraints excluded: chain LK residue 107 ASP Chi-restraints excluded: chain LL residue 130 SER Chi-restraints excluded: chain LL residue 190 SER Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LM residue 86 GLU Chi-restraints excluded: chain LN residue 13 LYS Chi-restraints excluded: chain LN residue 15 GLN Chi-restraints excluded: chain LO residue 197 GLU Chi-restraints excluded: chain LQ residue 32 ILE Chi-restraints excluded: chain LQ residue 50 ASP Chi-restraints excluded: chain LQ residue 136 LYS Chi-restraints excluded: chain LU residue 37 SER Chi-restraints excluded: chain LU residue 55 ASN Chi-restraints excluded: chain LU residue 79 SER Chi-restraints excluded: chain LY residue 6 THR Chi-restraints excluded: chain La residue 75 ILE Chi-restraints excluded: chain Le residue 124 LYS Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lg residue 105 VAL Chi-restraints excluded: chain Lh residue 105 VAL Chi-restraints excluded: chain Lk residue 7 ASP Chi-restraints excluded: chain Lk residue 41 GLN Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 70 THR Chi-restraints excluded: chain CC residue 408 MET Chi-restraints excluded: chain CC residue 510 THR Chi-restraints excluded: chain CJ residue 142 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 698 optimal weight: 7.9990 chunk 390 optimal weight: 0.2980 chunk 1046 optimal weight: 6.9990 chunk 856 optimal weight: 7.9990 chunk 346 optimal weight: 10.0000 chunk 1259 optimal weight: 5.9990 chunk 1361 optimal weight: 20.0000 chunk 1122 optimal weight: 9.9990 chunk 1249 optimal weight: 0.9990 chunk 429 optimal weight: 2.9990 chunk 1010 optimal weight: 3.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 29 ASN CF 153 HIS CH 633 GLN CK 53 GLN CK 57 GLN CK 190 ASN CQ 130 ASN ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cd 409 GLN ** Cf 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ch 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cz 56 GLN LA 115 ASN LB 244 HIS LB 379 GLN LC 264 GLN LE 35 GLN LE 172 ASN LF 10 ASN LF 41 GLN LF 163 ASN LG 27 ASN ** LG 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 158 ASN LH 179 GLN LH 201 GLN LH 202 GLN LJ 40 GLN LJ 44 GLN LL 142 GLN LO 74 HIS LP 175 GLN LQ 101 ASN LR 91 GLN LS 147 ASN LU 55 ASN LY 116 ASN Lh 77 ASN ** Li 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Li 72 ASN Ll 11 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 165936 Z= 0.308 Angle : 0.676 18.794 240369 Z= 0.358 Chirality : 0.040 0.273 29364 Planarity : 0.007 0.137 18265 Dihedral : 22.526 179.888 63650 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.54 % Allowed : 8.37 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.08), residues: 10626 helix: 1.71 (0.08), residues: 3925 sheet: 0.19 (0.12), residues: 1722 loop : 0.15 (0.08), residues: 4979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPCC 396 HIS 0.015 0.001 HISCd 238 PHE 0.025 0.002 PHECh 37 TYR 0.032 0.002 TYRCd 366 ARG 0.008 0.001 ARGCd 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21252 Ramachandran restraints generated. 10626 Oldfield, 0 Emsley, 10626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21252 Ramachandran restraints generated. 10626 Oldfield, 0 Emsley, 10626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1018 time to evaluate : 9.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CF 241 LYS cc_start: 0.8132 (mtpp) cc_final: 0.7899 (mmmt) REVERT: CH 304 GLU cc_start: 0.7417 (tp30) cc_final: 0.7128 (tp30) REVERT: CH 360 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7295 (ttt180) REVERT: CH 362 GLN cc_start: 0.8236 (mt0) cc_final: 0.7937 (mt0) REVERT: CH 490 GLN cc_start: 0.7761 (tm-30) cc_final: 0.7408 (tm-30) REVERT: CL 21 ARG cc_start: 0.8379 (mtm-85) cc_final: 0.8160 (mtt90) REVERT: CO 19 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8675 (ttmt) REVERT: CQ 63 MET cc_start: 0.8674 (ttp) cc_final: 0.8297 (ttp) REVERT: Cd 16 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.6926 (ttm110) REVERT: Cd 386 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7383 (pm20) REVERT: Cf 87 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.7864 (mtm) REVERT: LA 80 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8308 (tt0) REVERT: LE 31 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7477 (mp0) REVERT: LF 248 MET cc_start: 0.8916 (mtp) cc_final: 0.8701 (mtm) REVERT: LG 252 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7269 (mtm-85) REVERT: LH 109 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7626 (ttp-170) REVERT: LJ 132 MET cc_start: 0.8747 (mmm) cc_final: 0.8524 (mmm) REVERT: LM 15 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.7854 (pm20) REVERT: LM 103 GLN cc_start: 0.8518 (tt0) cc_final: 0.8293 (tt0) REVERT: LN 13 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8270 (mmtt) REVERT: LO 131 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8794 (mt) REVERT: LO 197 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7859 (mp0) REVERT: LT 111 GLU cc_start: 0.7612 (mp0) cc_final: 0.7354 (mp0) REVERT: LU 55 ASN cc_start: 0.8369 (OUTLIER) cc_final: 0.8030 (t0) REVERT: LV 139 MET cc_start: 0.8569 (mtp) cc_final: 0.8340 (mtt) REVERT: LY 30 MET cc_start: 0.9058 (mtp) cc_final: 0.8813 (mtp) REVERT: Lc 25 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8058 (tttm) REVERT: Lc 66 SER cc_start: 0.8719 (p) cc_final: 0.8493 (t) REVERT: Lh 16 ASN cc_start: 0.8604 (p0) cc_final: 0.8311 (p0) REVERT: Lk 41 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.7036 (tm-30) REVERT: CC 293 LYS cc_start: 0.8037 (mppt) cc_final: 0.7822 (mmtm) REVERT: CC 396 TRP cc_start: 0.6992 (m-10) cc_final: 0.6693 (m-90) REVERT: CC 768 HIS cc_start: 0.7870 (OUTLIER) cc_final: 0.7309 (t70) REVERT: CD 19 PHE cc_start: 0.8969 (m-10) cc_final: 0.8725 (m-10) REVERT: CD 35 LEU cc_start: 0.8337 (mm) cc_final: 0.7854 (mm) REVERT: CD 212 THR cc_start: 0.9067 (m) cc_final: 0.8771 (p) REVERT: CD 286 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8596 (mt0) REVERT: CJ 142 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7380 (m-30) REVERT: CJ 669 ARG cc_start: 0.8247 (mmm-85) cc_final: 0.8035 (mmm-85) outliers start: 134 outliers final: 56 residues processed: 1081 average time/residue: 2.4437 time to fit residues: 3736.7165 Evaluate side-chains 1047 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 972 time to evaluate : 8.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CF residue 55 ASP Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 291 ILE Chi-restraints excluded: chain CH residue 360 ARG Chi-restraints excluded: chain CN residue 51 THR Chi-restraints excluded: chain CN residue 75 THR Chi-restraints excluded: chain CN residue 127 GLU Chi-restraints excluded: chain CN residue 233 ILE Chi-restraints excluded: chain CO residue 19 LYS Chi-restraints excluded: chain CQ residue 64 VAL Chi-restraints excluded: chain Cb residue 38 THR Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cd residue 16 ARG Chi-restraints excluded: chain Cd residue 86 ASP Chi-restraints excluded: chain Cd residue 386 GLN Chi-restraints excluded: chain Cf residue 16 LEU Chi-restraints excluded: chain Cf residue 87 MET Chi-restraints excluded: chain LA residue 80 GLU Chi-restraints excluded: chain LA residue 96 LEU Chi-restraints excluded: chain LA residue 114 SER Chi-restraints excluded: chain LA residue 161 SER Chi-restraints excluded: chain LB residue 79 ILE Chi-restraints excluded: chain LB residue 90 VAL Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LD residue 93 THR Chi-restraints excluded: chain LD residue 181 ASN Chi-restraints excluded: chain LD residue 188 ILE Chi-restraints excluded: chain LE residue 31 GLU Chi-restraints excluded: chain LE residue 165 ILE Chi-restraints excluded: chain LF residue 8 THR Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LG residue 88 ASN Chi-restraints excluded: chain LG residue 252 ARG Chi-restraints excluded: chain LH residue 109 ARG Chi-restraints excluded: chain LJ residue 13 LEU Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 147 SER Chi-restraints excluded: chain LL residue 130 SER Chi-restraints excluded: chain LL residue 190 SER Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 10 SER Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LM residue 15 GLU Chi-restraints excluded: chain LN residue 13 LYS Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LO residue 131 LEU Chi-restraints excluded: chain LO residue 160 GLU Chi-restraints excluded: chain LO residue 197 GLU Chi-restraints excluded: chain LQ residue 32 ILE Chi-restraints excluded: chain LQ residue 136 LYS Chi-restraints excluded: chain LT residue 33 THR Chi-restraints excluded: chain LT residue 93 ILE Chi-restraints excluded: chain LU residue 37 SER Chi-restraints excluded: chain LU residue 55 ASN Chi-restraints excluded: chain LU residue 79 SER Chi-restraints excluded: chain LV residue 98 GLU Chi-restraints excluded: chain LY residue 6 THR Chi-restraints excluded: chain LZ residue 99 THR Chi-restraints excluded: chain La residue 75 ILE Chi-restraints excluded: chain Lc residue 25 LYS Chi-restraints excluded: chain Lc residue 43 LYS Chi-restraints excluded: chain Lf residue 51 VAL Chi-restraints excluded: chain Lh residue 19 GLU Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Lh residue 105 VAL Chi-restraints excluded: chain Lk residue 7 ASP Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 41 GLN Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 70 THR Chi-restraints excluded: chain CC residue 510 THR Chi-restraints excluded: chain CC residue 713 MET Chi-restraints excluded: chain CC residue 768 HIS Chi-restraints excluded: chain CD residue 286 GLN Chi-restraints excluded: chain CJ residue 142 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 1244 optimal weight: 0.9990 chunk 947 optimal weight: 2.9990 chunk 653 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 601 optimal weight: 10.0000 chunk 846 optimal weight: 1.9990 chunk 1264 optimal weight: 10.0000 chunk 1338 optimal weight: 8.9990 chunk 660 optimal weight: 1.9990 chunk 1198 optimal weight: 4.9990 chunk 360 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 29 ASN CF 153 HIS CH 633 GLN CK 53 GLN CK 57 GLN CK 190 ASN CQ 24 ASN CQ 87 GLN CQ 130 ASN ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 101 ASN Cf 26 ASN ** Cf 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ch 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cz 56 GLN ** LA 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 379 GLN LC 264 GLN LE 53 GLN LE 78 GLN LE 172 ASN LF 10 ASN LF 163 ASN LF 200 ASN LG 27 ASN ** LG 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 212 ASN LH 179 GLN LH 201 GLN LJ 40 GLN LQ 101 ASN LR 91 GLN LS 147 ASN LU 55 ASN LY 116 ASN Lh 77 ASN Lh 118 GLN Li 72 ASN Ll 11 GLN CC 537 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 165936 Z= 0.207 Angle : 0.628 17.841 240369 Z= 0.338 Chirality : 0.037 0.267 29364 Planarity : 0.006 0.132 18265 Dihedral : 22.484 179.771 63648 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.39 % Allowed : 9.72 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.08), residues: 10626 helix: 1.93 (0.08), residues: 3926 sheet: 0.20 (0.12), residues: 1736 loop : 0.23 (0.09), residues: 4964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPCg 105 HIS 0.008 0.001 HISCd 252 PHE 0.020 0.001 PHECD 65 TYR 0.020 0.001 TYRCJ 71 ARG 0.010 0.000 ARGCd 178 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21252 Ramachandran restraints generated. 10626 Oldfield, 0 Emsley, 10626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21252 Ramachandran restraints generated. 10626 Oldfield, 0 Emsley, 10626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1136 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1015 time to evaluate : 9.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: CF 241 LYS cc_start: 0.8090 (mtpp) cc_final: 0.7846 (mmmt) REVERT: CH 360 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7166 (ttt180) REVERT: CH 362 GLN cc_start: 0.8309 (mt0) cc_final: 0.8074 (mt0) REVERT: CH 490 GLN cc_start: 0.7751 (tm-30) cc_final: 0.7388 (tm-30) REVERT: CO 19 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8653 (ttmt) REVERT: CQ 63 MET cc_start: 0.8604 (ttp) cc_final: 0.8228 (ttp) REVERT: Cd 16 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.6836 (ttm110) REVERT: Cf 290 ASP cc_start: 0.7734 (p0) cc_final: 0.7516 (p0) REVERT: Ch 344 LYS cc_start: 0.8338 (mmmt) cc_final: 0.8070 (mptp) REVERT: Cz 76 ARG cc_start: 0.8202 (ttt-90) cc_final: 0.7948 (ttp-170) REVERT: LA 80 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: LA 199 THR cc_start: 0.7657 (OUTLIER) cc_final: 0.7315 (t) REVERT: LE 31 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7525 (mp0) REVERT: LF 248 MET cc_start: 0.8888 (mtp) cc_final: 0.8663 (mtm) REVERT: LH 109 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7617 (ttp-170) REVERT: LJ 132 MET cc_start: 0.8716 (mmm) cc_final: 0.8417 (mmm) REVERT: LM 15 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.7697 (pm20) REVERT: LM 103 GLN cc_start: 0.8479 (tt0) cc_final: 0.8267 (tt0) REVERT: LM 107 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7752 (mt-10) REVERT: LN 13 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8209 (mmtt) REVERT: LO 197 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7831 (mp0) REVERT: LS 109 ASP cc_start: 0.8347 (t70) cc_final: 0.8135 (t0) REVERT: LT 111 GLU cc_start: 0.7622 (mp0) cc_final: 0.7363 (mp0) REVERT: LY 30 MET cc_start: 0.9049 (mtp) cc_final: 0.8751 (mtp) REVERT: LY 56 GLN cc_start: 0.8670 (tt0) cc_final: 0.8383 (tt0) REVERT: La 136 ARG cc_start: 0.8825 (tmm160) cc_final: 0.8596 (tmm160) REVERT: Lc 66 SER cc_start: 0.8649 (p) cc_final: 0.8424 (t) REVERT: Le 53 MET cc_start: 0.9040 (mtm) cc_final: 0.8718 (mtp) REVERT: Lk 41 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.6994 (tm-30) REVERT: CC 396 TRP cc_start: 0.6957 (m-10) cc_final: 0.6704 (m-90) REVERT: CC 735 ASP cc_start: 0.7539 (t0) cc_final: 0.7118 (p0) REVERT: CC 768 HIS cc_start: 0.7978 (OUTLIER) cc_final: 0.7406 (t70) REVERT: CD 19 PHE cc_start: 0.8974 (m-10) cc_final: 0.8750 (m-10) REVERT: CD 35 LEU cc_start: 0.8364 (mm) cc_final: 0.7830 (mm) REVERT: CD 185 PHE cc_start: 0.7846 (m-80) cc_final: 0.7645 (m-10) REVERT: CD 212 THR cc_start: 0.9058 (m) cc_final: 0.8765 (p) REVERT: CD 286 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8586 (mt0) REVERT: CJ 142 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7358 (m-30) outliers start: 121 outliers final: 63 residues processed: 1073 average time/residue: 2.4544 time to fit residues: 3727.5288 Evaluate side-chains 1048 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 971 time to evaluate : 9.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CF residue 55 ASP Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 360 ARG Chi-restraints excluded: chain CL residue 68 GLN Chi-restraints excluded: chain CN residue 51 THR Chi-restraints excluded: chain CN residue 127 GLU Chi-restraints excluded: chain CN residue 233 ILE Chi-restraints excluded: chain CO residue 19 LYS Chi-restraints excluded: chain CQ residue 64 VAL Chi-restraints excluded: chain Cb residue 38 THR Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cd residue 16 ARG Chi-restraints excluded: chain Cd residue 86 ASP Chi-restraints excluded: chain Cd residue 123 LEU Chi-restraints excluded: chain Cf residue 16 LEU Chi-restraints excluded: chain Ch residue 37 PHE Chi-restraints excluded: chain Ch residue 142 ILE Chi-restraints excluded: chain Ch residue 517 ASN Chi-restraints excluded: chain LA residue 80 GLU Chi-restraints excluded: chain LA residue 96 LEU Chi-restraints excluded: chain LA residue 114 SER Chi-restraints excluded: chain LA residue 161 SER Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LD residue 181 ASN Chi-restraints excluded: chain LD residue 188 ILE Chi-restraints excluded: chain LE residue 31 GLU Chi-restraints excluded: chain LE residue 35 GLN Chi-restraints excluded: chain LE residue 165 ILE Chi-restraints excluded: chain LF residue 8 THR Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LG residue 88 ASN Chi-restraints excluded: chain LH residue 109 ARG Chi-restraints excluded: chain LJ residue 13 LEU Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 147 SER Chi-restraints excluded: chain LL residue 130 SER Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LM residue 15 GLU Chi-restraints excluded: chain LN residue 13 LYS Chi-restraints excluded: chain LN residue 15 GLN Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LO residue 160 GLU Chi-restraints excluded: chain LO residue 175 LEU Chi-restraints excluded: chain LO residue 197 GLU Chi-restraints excluded: chain LQ residue 32 ILE Chi-restraints excluded: chain LQ residue 50 ASP Chi-restraints excluded: chain LQ residue 136 LYS Chi-restraints excluded: chain LR residue 107 VAL Chi-restraints excluded: chain LT residue 93 ILE Chi-restraints excluded: chain LU residue 37 SER Chi-restraints excluded: chain LU residue 79 SER Chi-restraints excluded: chain LV residue 98 GLU Chi-restraints excluded: chain LY residue 6 THR Chi-restraints excluded: chain La residue 58 MET Chi-restraints excluded: chain La residue 75 ILE Chi-restraints excluded: chain Lc residue 43 LYS Chi-restraints excluded: chain Lc residue 64 MET Chi-restraints excluded: chain Ld residue 96 LYS Chi-restraints excluded: chain Ld residue 108 ASN Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lg residue 65 THR Chi-restraints excluded: chain Lg residue 105 VAL Chi-restraints excluded: chain Lh residue 19 GLU Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Lh residue 105 VAL Chi-restraints excluded: chain Lh residue 113 LEU Chi-restraints excluded: chain Lk residue 7 ASP Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 41 GLN Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 70 THR Chi-restraints excluded: chain CC residue 713 MET Chi-restraints excluded: chain CC residue 768 HIS Chi-restraints excluded: chain CD residue 286 GLN Chi-restraints excluded: chain CJ residue 142 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 1114 optimal weight: 6.9990 chunk 759 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 996 optimal weight: 5.9990 chunk 552 optimal weight: 2.9990 chunk 1142 optimal weight: 9.9990 chunk 925 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 683 optimal weight: 1.9990 chunk 1201 optimal weight: 10.0000 chunk 337 optimal weight: 0.0060 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 29 ASN CF 153 HIS CH 633 GLN CK 53 GLN CK 57 GLN CK 67 GLN CK 190 ASN CQ 87 GLN CQ 130 ASN ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ch 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ch 64 ASN Ch 88 HIS Cz 56 GLN LA 115 ASN LB 379 GLN LC 264 GLN LD 39 GLN LE 53 GLN LE 78 GLN LE 172 ASN LF 10 ASN LF 163 ASN LG 27 ASN LG 36 ASN LG 41 GLN LH 179 GLN LH 201 GLN LJ 40 GLN LQ 43 HIS LR 91 GLN LS 147 ASN ** LU 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 92 GLN LY 116 ASN Lh 77 ASN Ll 11 GLN CD 483 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 165936 Z= 0.301 Angle : 0.666 18.524 240369 Z= 0.353 Chirality : 0.040 0.268 29364 Planarity : 0.006 0.138 18265 Dihedral : 22.463 179.965 63648 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.73 % Allowed : 9.97 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.08), residues: 10626 helix: 1.91 (0.08), residues: 3925 sheet: 0.20 (0.12), residues: 1725 loop : 0.20 (0.09), residues: 4976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPCD 468 HIS 0.009 0.001 HISCd 252 PHE 0.019 0.002 PHECD 65 TYR 0.022 0.002 TYRLC 269 ARG 0.010 0.001 ARGCQ 161 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21252 Ramachandran restraints generated. 10626 Oldfield, 0 Emsley, 10626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21252 Ramachandran restraints generated. 10626 Oldfield, 0 Emsley, 10626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1151 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1000 time to evaluate : 9.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CF 153 HIS cc_start: 0.8221 (OUTLIER) cc_final: 0.8008 (m170) REVERT: CF 241 LYS cc_start: 0.8139 (mtpp) cc_final: 0.7876 (mmmt) REVERT: CH 360 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7212 (ttt180) REVERT: CH 490 GLN cc_start: 0.7776 (tm-30) cc_final: 0.7405 (tm-30) REVERT: CL 21 ARG cc_start: 0.8379 (mtm-85) cc_final: 0.8142 (mtt90) REVERT: CN 188 ARG cc_start: 0.8346 (mtm-85) cc_final: 0.8130 (mtm-85) REVERT: CO 19 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8679 (ttmt) REVERT: CQ 63 MET cc_start: 0.8642 (ttp) cc_final: 0.8225 (ttp) REVERT: Cd 16 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.6885 (ttm110) REVERT: Cd 386 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7391 (pm20) REVERT: Cf 87 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.7922 (mtm) REVERT: Ch 344 LYS cc_start: 0.8364 (mmmt) cc_final: 0.8103 (mptp) REVERT: LA 80 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8315 (tt0) REVERT: LA 199 THR cc_start: 0.7772 (OUTLIER) cc_final: 0.7434 (t) REVERT: LE 31 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: LF 152 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7405 (mp0) REVERT: LF 248 MET cc_start: 0.8908 (mtp) cc_final: 0.8703 (mtm) REVERT: LH 109 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7616 (ttp-170) REVERT: LJ 112 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7799 (p0) REVERT: LJ 132 MET cc_start: 0.8722 (mmm) cc_final: 0.8495 (mmm) REVERT: LM 15 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.7823 (pm20) REVERT: LM 103 GLN cc_start: 0.8489 (tt0) cc_final: 0.8265 (tt0) REVERT: LN 13 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8231 (mmtt) REVERT: LO 131 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8793 (mt) REVERT: LO 197 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7849 (mp0) REVERT: LS 109 ASP cc_start: 0.8396 (t70) cc_final: 0.8179 (t0) REVERT: LT 111 GLU cc_start: 0.7606 (mp0) cc_final: 0.7364 (mp0) REVERT: LV 139 MET cc_start: 0.8600 (mtp) cc_final: 0.8322 (mtt) REVERT: LY 30 MET cc_start: 0.9062 (mtp) cc_final: 0.8799 (mtp) REVERT: La 136 ARG cc_start: 0.8838 (tmm160) cc_final: 0.8592 (tmm160) REVERT: Lc 66 SER cc_start: 0.8642 (p) cc_final: 0.8372 (t) REVERT: Lk 41 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: CC 396 TRP cc_start: 0.6903 (m-10) cc_final: 0.6665 (m-90) REVERT: CC 735 ASP cc_start: 0.7568 (t0) cc_final: 0.7134 (p0) REVERT: CC 768 HIS cc_start: 0.8140 (OUTLIER) cc_final: 0.7632 (t70) REVERT: CD 19 PHE cc_start: 0.8999 (m-10) cc_final: 0.8793 (m-10) REVERT: CD 35 LEU cc_start: 0.8419 (mm) cc_final: 0.7854 (mm) REVERT: CD 185 PHE cc_start: 0.7907 (m-80) cc_final: 0.7698 (m-10) REVERT: CD 212 THR cc_start: 0.9015 (m) cc_final: 0.8684 (p) REVERT: CD 216 LYS cc_start: 0.8660 (tptt) cc_final: 0.8455 (tptt) REVERT: CJ 142 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7340 (m-30) outliers start: 151 outliers final: 82 residues processed: 1078 average time/residue: 2.4625 time to fit residues: 3759.2264 Evaluate side-chains 1079 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 978 time to evaluate : 9.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CF residue 55 ASP Chi-restraints excluded: chain CF residue 153 HIS Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 297 LEU Chi-restraints excluded: chain CH residue 338 LEU Chi-restraints excluded: chain CH residue 360 ARG Chi-restraints excluded: chain CK residue 118 SER Chi-restraints excluded: chain CL residue 68 GLN Chi-restraints excluded: chain CN residue 51 THR Chi-restraints excluded: chain CN residue 75 THR Chi-restraints excluded: chain CN residue 127 GLU Chi-restraints excluded: chain CN residue 233 ILE Chi-restraints excluded: chain CO residue 19 LYS Chi-restraints excluded: chain CQ residue 24 ASN Chi-restraints excluded: chain CQ residue 64 VAL Chi-restraints excluded: chain Cb residue 38 THR Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cd residue 16 ARG Chi-restraints excluded: chain Cd residue 86 ASP Chi-restraints excluded: chain Cd residue 123 LEU Chi-restraints excluded: chain Cd residue 386 GLN Chi-restraints excluded: chain Cf residue 16 LEU Chi-restraints excluded: chain Cf residue 87 MET Chi-restraints excluded: chain Cf residue 306 LEU Chi-restraints excluded: chain Ch residue 142 ILE Chi-restraints excluded: chain Ch residue 517 ASN Chi-restraints excluded: chain LA residue 80 GLU Chi-restraints excluded: chain LA residue 96 LEU Chi-restraints excluded: chain LA residue 114 SER Chi-restraints excluded: chain LA residue 161 SER Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LB residue 79 ILE Chi-restraints excluded: chain LB residue 90 VAL Chi-restraints excluded: chain LB residue 336 ILE Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 354 VAL Chi-restraints excluded: chain LD residue 93 THR Chi-restraints excluded: chain LD residue 181 ASN Chi-restraints excluded: chain LD residue 188 ILE Chi-restraints excluded: chain LE residue 16 THR Chi-restraints excluded: chain LE residue 31 GLU Chi-restraints excluded: chain LE residue 35 GLN Chi-restraints excluded: chain LE residue 165 ILE Chi-restraints excluded: chain LF residue 8 THR Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 152 GLU Chi-restraints excluded: chain LG residue 86 ASP Chi-restraints excluded: chain LG residue 88 ASN Chi-restraints excluded: chain LH residue 109 ARG Chi-restraints excluded: chain LJ residue 13 LEU Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 112 ASP Chi-restraints excluded: chain LJ residue 147 SER Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LL residue 130 SER Chi-restraints excluded: chain LL residue 190 SER Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 10 SER Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LM residue 15 GLU Chi-restraints excluded: chain LN residue 13 LYS Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LO residue 131 LEU Chi-restraints excluded: chain LO residue 160 GLU Chi-restraints excluded: chain LO residue 197 GLU Chi-restraints excluded: chain LP residue 75 GLN Chi-restraints excluded: chain LQ residue 32 ILE Chi-restraints excluded: chain LQ residue 50 ASP Chi-restraints excluded: chain LQ residue 136 LYS Chi-restraints excluded: chain LR residue 107 VAL Chi-restraints excluded: chain LT residue 33 THR Chi-restraints excluded: chain LT residue 93 ILE Chi-restraints excluded: chain LU residue 37 SER Chi-restraints excluded: chain LU residue 79 SER Chi-restraints excluded: chain LU residue 98 ASP Chi-restraints excluded: chain LV residue 98 GLU Chi-restraints excluded: chain LY residue 6 THR Chi-restraints excluded: chain LY residue 110 LEU Chi-restraints excluded: chain LZ residue 99 THR Chi-restraints excluded: chain La residue 58 MET Chi-restraints excluded: chain La residue 75 ILE Chi-restraints excluded: chain Lc residue 43 LYS Chi-restraints excluded: chain Lc residue 64 MET Chi-restraints excluded: chain Ld residue 96 LYS Chi-restraints excluded: chain Lf residue 51 VAL Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lg residue 65 THR Chi-restraints excluded: chain Lg residue 105 VAL Chi-restraints excluded: chain Lh residue 19 GLU Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Lh residue 105 VAL Chi-restraints excluded: chain Lj residue 84 LYS Chi-restraints excluded: chain Lk residue 7 ASP Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 41 GLN Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 70 THR Chi-restraints excluded: chain CC residue 713 MET Chi-restraints excluded: chain CC residue 768 HIS Chi-restraints excluded: chain CJ residue 142 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 450 optimal weight: 3.9990 chunk 1205 optimal weight: 3.9990 chunk 264 optimal weight: 6.9990 chunk 786 optimal weight: 4.9990 chunk 330 optimal weight: 10.0000 chunk 1340 optimal weight: 0.9980 chunk 1112 optimal weight: 3.9990 chunk 620 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 443 optimal weight: 7.9990 chunk 703 optimal weight: 5.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 29 ASN CF 153 HIS CH 633 GLN CK 53 GLN CK 57 GLN CK 67 GLN CK 190 ASN CQ 87 GLN CQ 130 ASN ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ch 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ch 88 HIS Cz 56 GLN LA 115 ASN LB 379 GLN LC 264 GLN LE 53 GLN LE 78 GLN LE 172 ASN LF 10 ASN LF 163 ASN LG 27 ASN LG 212 ASN LH 179 GLN LH 201 GLN LJ 40 GLN ** LU 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 92 GLN LY 116 ASN ** Lh 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 77 ASN Lh 118 GLN Ll 11 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 165936 Z= 0.301 Angle : 0.667 18.404 240369 Z= 0.354 Chirality : 0.040 0.270 29364 Planarity : 0.006 0.137 18265 Dihedral : 22.461 179.680 63648 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.71 % Allowed : 10.48 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.08), residues: 10626 helix: 1.91 (0.08), residues: 3925 sheet: 0.17 (0.12), residues: 1734 loop : 0.20 (0.09), residues: 4967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPCD 468 HIS 0.025 0.001 HISCF 153 PHE 0.018 0.002 PHECH 90 TYR 0.022 0.002 TYRLC 269 ARG 0.012 0.001 ARGCz 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21252 Ramachandran restraints generated. 10626 Oldfield, 0 Emsley, 10626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21252 Ramachandran restraints generated. 10626 Oldfield, 0 Emsley, 10626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1143 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 994 time to evaluate : 9.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CF 241 LYS cc_start: 0.8169 (mtpp) cc_final: 0.7914 (mmmt) REVERT: CH 360 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7214 (ttt180) REVERT: CH 362 GLN cc_start: 0.8168 (mt0) cc_final: 0.7921 (mt0) REVERT: CH 490 GLN cc_start: 0.7765 (tm-30) cc_final: 0.7395 (tm-30) REVERT: CL 21 ARG cc_start: 0.8379 (mtm-85) cc_final: 0.8095 (mtm110) REVERT: CO 19 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8666 (ttmt) REVERT: CQ 63 MET cc_start: 0.8633 (ttp) cc_final: 0.8218 (ttp) REVERT: Cb 6 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8547 (ttmp) REVERT: Cd 16 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.6826 (ttm110) REVERT: Cd 381 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8778 (pt) REVERT: Cf 87 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.7981 (mtm) REVERT: Ch 344 LYS cc_start: 0.8376 (mmmt) cc_final: 0.8117 (mptp) REVERT: Cz 76 ARG cc_start: 0.8145 (ttt-90) cc_final: 0.7906 (ttp-170) REVERT: LA 80 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8317 (tt0) REVERT: LA 165 MET cc_start: 0.8634 (ttm) cc_final: 0.8263 (ttm) REVERT: LA 199 THR cc_start: 0.7775 (OUTLIER) cc_final: 0.7447 (t) REVERT: LE 31 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: LH 109 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7613 (ttp-170) REVERT: LJ 112 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7804 (p0) REVERT: LJ 132 MET cc_start: 0.8696 (mmm) cc_final: 0.8495 (mmm) REVERT: LM 15 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.7791 (pm20) REVERT: LM 86 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7434 (mt-10) REVERT: LM 103 GLN cc_start: 0.8490 (tt0) cc_final: 0.8250 (tt0) REVERT: LM 107 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7703 (mt-10) REVERT: LN 13 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8218 (mmtt) REVERT: LO 131 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8792 (mt) REVERT: LO 197 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: LP 181 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7568 (ttt-90) REVERT: LS 119 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7302 (pmm150) REVERT: LT 111 GLU cc_start: 0.7613 (mp0) cc_final: 0.7371 (mp0) REVERT: LY 30 MET cc_start: 0.9075 (mtp) cc_final: 0.8777 (mtp) REVERT: La 136 ARG cc_start: 0.8825 (tmm160) cc_final: 0.8575 (tmm160) REVERT: Lc 66 SER cc_start: 0.8727 (p) cc_final: 0.8467 (t) REVERT: Lj 64 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8493 (mmm) REVERT: Lk 41 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.7058 (tm-30) REVERT: CC 396 TRP cc_start: 0.7007 (OUTLIER) cc_final: 0.6791 (m-90) REVERT: CC 735 ASP cc_start: 0.7579 (t0) cc_final: 0.7162 (p0) REVERT: CC 768 HIS cc_start: 0.8211 (OUTLIER) cc_final: 0.7713 (t70) REVERT: CD 19 PHE cc_start: 0.9019 (m-10) cc_final: 0.8796 (m-10) REVERT: CD 35 LEU cc_start: 0.8455 (mm) cc_final: 0.7868 (mm) REVERT: CD 212 THR cc_start: 0.8999 (m) cc_final: 0.8658 (p) REVERT: CJ 142 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7466 (m-30) REVERT: CJ 611 LYS cc_start: 0.8931 (mtmm) cc_final: 0.8690 (mttt) outliers start: 149 outliers final: 85 residues processed: 1068 average time/residue: 2.4848 time to fit residues: 3776.0714 Evaluate side-chains 1081 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 973 time to evaluate : 9.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CF residue 55 ASP Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 297 LEU Chi-restraints excluded: chain CH residue 338 LEU Chi-restraints excluded: chain CH residue 360 ARG Chi-restraints excluded: chain CH residue 378 THR Chi-restraints excluded: chain CK residue 118 SER Chi-restraints excluded: chain CL residue 68 GLN Chi-restraints excluded: chain CN residue 51 THR Chi-restraints excluded: chain CN residue 75 THR Chi-restraints excluded: chain CN residue 127 GLU Chi-restraints excluded: chain CN residue 233 ILE Chi-restraints excluded: chain CO residue 19 LYS Chi-restraints excluded: chain CQ residue 24 ASN Chi-restraints excluded: chain CQ residue 64 VAL Chi-restraints excluded: chain Cb residue 6 LYS Chi-restraints excluded: chain Cb residue 38 THR Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cd residue 16 ARG Chi-restraints excluded: chain Cd residue 86 ASP Chi-restraints excluded: chain Cd residue 123 LEU Chi-restraints excluded: chain Cd residue 381 ILE Chi-restraints excluded: chain Cf residue 16 LEU Chi-restraints excluded: chain Cf residue 87 MET Chi-restraints excluded: chain Cf residue 306 LEU Chi-restraints excluded: chain Ch residue 142 ILE Chi-restraints excluded: chain Ch residue 517 ASN Chi-restraints excluded: chain LA residue 80 GLU Chi-restraints excluded: chain LA residue 96 LEU Chi-restraints excluded: chain LA residue 114 SER Chi-restraints excluded: chain LA residue 161 SER Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LB residue 79 ILE Chi-restraints excluded: chain LB residue 90 VAL Chi-restraints excluded: chain LB residue 157 THR Chi-restraints excluded: chain LB residue 336 ILE Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 354 VAL Chi-restraints excluded: chain LD residue 93 THR Chi-restraints excluded: chain LD residue 181 ASN Chi-restraints excluded: chain LD residue 188 ILE Chi-restraints excluded: chain LE residue 16 THR Chi-restraints excluded: chain LE residue 31 GLU Chi-restraints excluded: chain LE residue 35 GLN Chi-restraints excluded: chain LE residue 165 ILE Chi-restraints excluded: chain LF residue 8 THR Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LG residue 86 ASP Chi-restraints excluded: chain LG residue 88 ASN Chi-restraints excluded: chain LH residue 109 ARG Chi-restraints excluded: chain LJ residue 13 LEU Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 112 ASP Chi-restraints excluded: chain LJ residue 147 SER Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LL residue 130 SER Chi-restraints excluded: chain LL residue 190 SER Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 10 SER Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LM residue 15 GLU Chi-restraints excluded: chain LM residue 86 GLU Chi-restraints excluded: chain LN residue 13 LYS Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LO residue 131 LEU Chi-restraints excluded: chain LO residue 160 GLU Chi-restraints excluded: chain LO residue 197 GLU Chi-restraints excluded: chain LP residue 75 GLN Chi-restraints excluded: chain LP residue 181 ARG Chi-restraints excluded: chain LQ residue 32 ILE Chi-restraints excluded: chain LQ residue 50 ASP Chi-restraints excluded: chain LQ residue 136 LYS Chi-restraints excluded: chain LR residue 107 VAL Chi-restraints excluded: chain LS residue 119 ARG Chi-restraints excluded: chain LT residue 33 THR Chi-restraints excluded: chain LT residue 93 ILE Chi-restraints excluded: chain LU residue 37 SER Chi-restraints excluded: chain LU residue 79 SER Chi-restraints excluded: chain LU residue 98 ASP Chi-restraints excluded: chain LV residue 98 GLU Chi-restraints excluded: chain LY residue 6 THR Chi-restraints excluded: chain LY residue 110 LEU Chi-restraints excluded: chain LZ residue 99 THR Chi-restraints excluded: chain La residue 58 MET Chi-restraints excluded: chain La residue 75 ILE Chi-restraints excluded: chain Lc residue 43 LYS Chi-restraints excluded: chain Ld residue 96 LYS Chi-restraints excluded: chain Lf residue 51 VAL Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lg residue 65 THR Chi-restraints excluded: chain Lg residue 105 VAL Chi-restraints excluded: chain Lh residue 19 GLU Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Lh residue 105 VAL Chi-restraints excluded: chain Lh residue 113 LEU Chi-restraints excluded: chain Lj residue 64 MET Chi-restraints excluded: chain Lj residue 84 LYS Chi-restraints excluded: chain Lk residue 7 ASP Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 41 GLN Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 70 THR Chi-restraints excluded: chain CC residue 396 TRP Chi-restraints excluded: chain CC residue 713 MET Chi-restraints excluded: chain CC residue 768 HIS Chi-restraints excluded: chain CJ residue 142 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 1291 optimal weight: 0.5980 chunk 151 optimal weight: 8.9990 chunk 763 optimal weight: 0.8980 chunk 978 optimal weight: 3.9990 chunk 758 optimal weight: 0.8980 chunk 1128 optimal weight: 5.9990 chunk 748 optimal weight: 0.9980 chunk 1334 optimal weight: 0.0370 chunk 835 optimal weight: 1.9990 chunk 813 optimal weight: 0.7980 chunk 616 optimal weight: 4.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 29 ASN CH 345 GLN CH 633 GLN CK 53 GLN CK 57 GLN CK 67 GLN CK 190 ASN CQ 87 GLN CQ 130 ASN ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 101 ASN Cf 54 GLN Cg 31 ASN Ch 56 ASN Ch 88 HIS Cz 56 GLN LA 115 ASN LB 379 GLN LC 264 GLN LD 17 GLN LE 53 GLN LE 78 GLN LE 162 GLN LE 172 ASN LF 10 ASN LF 163 ASN LG 27 ASN ** LG 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LH 179 GLN LH 201 GLN LJ 40 GLN LU 44 ASN ** LU 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 92 GLN LY 116 ASN Lh 77 ASN Lh 118 GLN Ll 11 GLN CD 286 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 165936 Z= 0.137 Angle : 0.602 16.854 240369 Z= 0.326 Chirality : 0.035 0.255 29364 Planarity : 0.005 0.126 18265 Dihedral : 22.386 179.195 63648 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.21 % Allowed : 11.34 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.08), residues: 10626 helix: 2.16 (0.08), residues: 3918 sheet: 0.26 (0.12), residues: 1745 loop : 0.31 (0.09), residues: 4963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRPCg 105 HIS 0.008 0.001 HISCd 252 PHE 0.020 0.001 PHECH 90 TYR 0.017 0.001 TYRLH 129 ARG 0.019 0.000 ARGCQ 161 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21252 Ramachandran restraints generated. 10626 Oldfield, 0 Emsley, 10626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21252 Ramachandran restraints generated. 10626 Oldfield, 0 Emsley, 10626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1124 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1019 time to evaluate : 9.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: CF 241 LYS cc_start: 0.8094 (mtpp) cc_final: 0.7845 (mmmt) REVERT: CH 362 GLN cc_start: 0.8137 (mt0) cc_final: 0.7830 (mt0) REVERT: CH 490 GLN cc_start: 0.7725 (tm-30) cc_final: 0.7355 (tm-30) REVERT: CQ 63 MET cc_start: 0.8545 (ttp) cc_final: 0.8201 (ttp) REVERT: Cb 6 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8513 (ttmp) REVERT: Ch 344 LYS cc_start: 0.8312 (mmmt) cc_final: 0.8049 (mptp) REVERT: Cz 76 ARG cc_start: 0.8108 (ttt-90) cc_final: 0.7888 (ttp-170) REVERT: LA 80 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: LA 199 THR cc_start: 0.7680 (OUTLIER) cc_final: 0.7383 (t) REVERT: LE 31 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7468 (mp0) REVERT: LE 162 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8439 (mm-40) REVERT: LJ 112 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7738 (p0) REVERT: LJ 132 MET cc_start: 0.8598 (mmm) cc_final: 0.8388 (mmm) REVERT: LM 15 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.7700 (pm20) REVERT: LM 103 GLN cc_start: 0.8445 (tt0) cc_final: 0.8199 (tt0) REVERT: LM 107 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7726 (mt-10) REVERT: LN 13 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8118 (mmtt) REVERT: LO 197 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: LP 182 ARG cc_start: 0.8076 (ttp-110) cc_final: 0.7545 (mtm-85) REVERT: LS 109 ASP cc_start: 0.8293 (t70) cc_final: 0.8046 (t0) REVERT: LS 119 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7289 (pmm150) REVERT: LT 111 GLU cc_start: 0.7616 (mp0) cc_final: 0.7368 (mp0) REVERT: LX 91 GLU cc_start: 0.7270 (mp0) cc_final: 0.6824 (mp0) REVERT: LY 30 MET cc_start: 0.9080 (mtp) cc_final: 0.8867 (mtp) REVERT: Lc 66 SER cc_start: 0.8636 (p) cc_final: 0.8427 (t) REVERT: Le 53 MET cc_start: 0.9033 (mtm) cc_final: 0.8706 (mtp) REVERT: Lk 41 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.7028 (tm-30) REVERT: CC 768 HIS cc_start: 0.8075 (OUTLIER) cc_final: 0.7659 (t-170) REVERT: CD 16 LYS cc_start: 0.8826 (mmmt) cc_final: 0.8594 (tppt) REVERT: CD 212 THR cc_start: 0.8989 (m) cc_final: 0.8653 (p) REVERT: CJ 611 LYS cc_start: 0.8919 (mtmm) cc_final: 0.8676 (mttt) REVERT: CJ 618 LYS cc_start: 0.8422 (mppt) cc_final: 0.8141 (mmtm) outliers start: 105 outliers final: 54 residues processed: 1066 average time/residue: 2.3964 time to fit residues: 3615.9574 Evaluate side-chains 1043 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 977 time to evaluate : 8.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CF residue 9 VAL Chi-restraints excluded: chain CF residue 55 ASP Chi-restraints excluded: chain CH residue 297 LEU Chi-restraints excluded: chain CH residue 357 ILE Chi-restraints excluded: chain CK residue 118 SER Chi-restraints excluded: chain CL residue 68 GLN Chi-restraints excluded: chain CN residue 51 THR Chi-restraints excluded: chain CN residue 127 GLU Chi-restraints excluded: chain CN residue 233 ILE Chi-restraints excluded: chain Cb residue 6 LYS Chi-restraints excluded: chain Cb residue 38 THR Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cb residue 79 LYS Chi-restraints excluded: chain Cd residue 86 ASP Chi-restraints excluded: chain Cd residue 123 LEU Chi-restraints excluded: chain Cf residue 16 LEU Chi-restraints excluded: chain Ch residue 142 ILE Chi-restraints excluded: chain Ch residue 517 ASN Chi-restraints excluded: chain LA residue 80 GLU Chi-restraints excluded: chain LA residue 114 SER Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LB residue 157 THR Chi-restraints excluded: chain LB residue 197 ARG Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 354 VAL Chi-restraints excluded: chain LD residue 188 ILE Chi-restraints excluded: chain LE residue 16 THR Chi-restraints excluded: chain LE residue 31 GLU Chi-restraints excluded: chain LE residue 162 GLN Chi-restraints excluded: chain LE residue 165 ILE Chi-restraints excluded: chain LG residue 88 ASN Chi-restraints excluded: chain LJ residue 13 LEU Chi-restraints excluded: chain LJ residue 112 ASP Chi-restraints excluded: chain LL residue 130 SER Chi-restraints excluded: chain LL residue 190 SER Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LM residue 15 GLU Chi-restraints excluded: chain LN residue 13 LYS Chi-restraints excluded: chain LN residue 15 GLN Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LO residue 175 LEU Chi-restraints excluded: chain LO residue 197 GLU Chi-restraints excluded: chain LQ residue 32 ILE Chi-restraints excluded: chain LQ residue 50 ASP Chi-restraints excluded: chain LQ residue 136 LYS Chi-restraints excluded: chain LR residue 142 ILE Chi-restraints excluded: chain LS residue 119 ARG Chi-restraints excluded: chain LU residue 79 SER Chi-restraints excluded: chain LU residue 98 ASP Chi-restraints excluded: chain LX residue 121 VAL Chi-restraints excluded: chain La residue 75 ILE Chi-restraints excluded: chain Lc residue 64 MET Chi-restraints excluded: chain Ld residue 96 LYS Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lg residue 65 THR Chi-restraints excluded: chain Lh residue 19 GLU Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Lh residue 105 VAL Chi-restraints excluded: chain Lh residue 113 LEU Chi-restraints excluded: chain Lk residue 7 ASP Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 41 GLN Chi-restraints excluded: chain CC residue 713 MET Chi-restraints excluded: chain CC residue 768 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 825 optimal weight: 6.9990 chunk 533 optimal weight: 0.8980 chunk 797 optimal weight: 0.9980 chunk 402 optimal weight: 9.9990 chunk 262 optimal weight: 10.0000 chunk 258 optimal weight: 5.9990 chunk 848 optimal weight: 0.0040 chunk 909 optimal weight: 0.8980 chunk 659 optimal weight: 0.1980 chunk 124 optimal weight: 6.9990 chunk 1049 optimal weight: 3.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 29 ASN CH 633 GLN CK 57 GLN CK 67 GLN CK 190 ASN CQ 130 ASN ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cg 31 ASN Ch 88 HIS LA 115 ASN LB 379 GLN LC 264 GLN LD 17 GLN LE 53 GLN LE 78 GLN LE 162 GLN LE 172 ASN LF 163 ASN LG 27 ASN LG 212 ASN LH 179 GLN LH 201 GLN LJ 40 GLN LJ 44 GLN LS 147 ASN LU 27 GLN LU 44 ASN ** LU 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LY 116 ASN LY 127 GLN Lh 77 ASN ** Li 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ll 11 GLN ** CC 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CD 286 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 165936 Z= 0.129 Angle : 0.588 17.196 240369 Z= 0.318 Chirality : 0.034 0.242 29364 Planarity : 0.005 0.126 18265 Dihedral : 22.279 178.800 63648 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.59 % Favored : 98.40 % Rotamer: Outliers : 1.06 % Allowed : 11.97 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.08), residues: 10626 helix: 2.29 (0.08), residues: 3919 sheet: 0.26 (0.12), residues: 1738 loop : 0.40 (0.09), residues: 4969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRPCC 396 HIS 0.008 0.001 HISCd 252 PHE 0.028 0.001 PHECh 37 TYR 0.026 0.001 TYRCJ 196 ARG 0.013 0.000 ARGCQ 161 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21252 Ramachandran restraints generated. 10626 Oldfield, 0 Emsley, 10626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21252 Ramachandran restraints generated. 10626 Oldfield, 0 Emsley, 10626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1119 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1027 time to evaluate : 9.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CH 362 GLN cc_start: 0.8153 (mt0) cc_final: 0.7836 (mt0) REVERT: CH 490 GLN cc_start: 0.7690 (tm-30) cc_final: 0.7309 (tm-30) REVERT: CO 19 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8577 (ttmt) REVERT: CQ 63 MET cc_start: 0.8558 (ttp) cc_final: 0.8296 (ttp) REVERT: CQ 143 ARG cc_start: 0.8249 (ttp-110) cc_final: 0.8025 (ttm110) REVERT: Cb 6 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8485 (ttmp) REVERT: Cf 105 MET cc_start: 0.8394 (mtp) cc_final: 0.8022 (mmm) REVERT: Ch 344 LYS cc_start: 0.8293 (mmmt) cc_final: 0.8029 (mptp) REVERT: LA 199 THR cc_start: 0.7681 (OUTLIER) cc_final: 0.7381 (t) REVERT: LE 31 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7465 (mp0) REVERT: LJ 112 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7671 (p0) REVERT: LM 103 GLN cc_start: 0.8439 (tt0) cc_final: 0.8179 (tt0) REVERT: LM 121 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8544 (tmm) REVERT: LN 13 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.8065 (mmtt) REVERT: LO 197 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: LP 182 ARG cc_start: 0.8032 (ttp-110) cc_final: 0.7523 (mtm-85) REVERT: LS 109 ASP cc_start: 0.8225 (t70) cc_final: 0.7968 (t0) REVERT: LS 119 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7205 (pmm150) REVERT: LT 111 GLU cc_start: 0.7682 (mp0) cc_final: 0.7453 (mp0) REVERT: Le 53 MET cc_start: 0.9029 (mtm) cc_final: 0.8733 (mtp) REVERT: Lk 41 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.7003 (tm-30) REVERT: CC 768 HIS cc_start: 0.8051 (OUTLIER) cc_final: 0.7584 (t-170) REVERT: CD 19 PHE cc_start: 0.8969 (m-10) cc_final: 0.8741 (m-10) REVERT: CD 212 THR cc_start: 0.8998 (m) cc_final: 0.8649 (p) REVERT: CJ 611 LYS cc_start: 0.8899 (mtmm) cc_final: 0.8673 (mttt) REVERT: CJ 618 LYS cc_start: 0.8506 (mppt) cc_final: 0.8216 (mmtm) outliers start: 92 outliers final: 43 residues processed: 1069 average time/residue: 2.4147 time to fit residues: 3664.4059 Evaluate side-chains 1048 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 994 time to evaluate : 9.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CF residue 9 VAL Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 297 LEU Chi-restraints excluded: chain CH residue 357 ILE Chi-restraints excluded: chain CK residue 118 SER Chi-restraints excluded: chain CL residue 68 GLN Chi-restraints excluded: chain CN residue 42 LEU Chi-restraints excluded: chain CN residue 51 THR Chi-restraints excluded: chain CN residue 127 GLU Chi-restraints excluded: chain CN residue 233 ILE Chi-restraints excluded: chain CO residue 19 LYS Chi-restraints excluded: chain Cb residue 6 LYS Chi-restraints excluded: chain Cb residue 38 THR Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cd residue 86 ASP Chi-restraints excluded: chain Cd residue 123 LEU Chi-restraints excluded: chain Cg residue 172 ASP Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LB residue 157 THR Chi-restraints excluded: chain LB residue 197 ARG Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 354 VAL Chi-restraints excluded: chain LE residue 16 THR Chi-restraints excluded: chain LE residue 31 GLU Chi-restraints excluded: chain LG residue 88 ASN Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 112 ASP Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LL residue 130 SER Chi-restraints excluded: chain LL residue 144 THR Chi-restraints excluded: chain LL residue 190 SER Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LM residue 121 MET Chi-restraints excluded: chain LN residue 13 LYS Chi-restraints excluded: chain LO residue 175 LEU Chi-restraints excluded: chain LO residue 197 GLU Chi-restraints excluded: chain LR residue 142 ILE Chi-restraints excluded: chain LS residue 119 ARG Chi-restraints excluded: chain LU residue 79 SER Chi-restraints excluded: chain LX residue 147 ASP Chi-restraints excluded: chain La residue 75 ILE Chi-restraints excluded: chain Lc residue 64 MET Chi-restraints excluded: chain Ld residue 96 LYS Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lg residue 65 THR Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Lh residue 105 VAL Chi-restraints excluded: chain Lk residue 7 ASP Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 41 GLN Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain CC residue 713 MET Chi-restraints excluded: chain CC residue 768 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 1214 optimal weight: 8.9990 chunk 1278 optimal weight: 10.0000 chunk 1166 optimal weight: 6.9990 chunk 1243 optimal weight: 9.9990 chunk 748 optimal weight: 3.9990 chunk 541 optimal weight: 1.9990 chunk 976 optimal weight: 9.9990 chunk 381 optimal weight: 5.9990 chunk 1124 optimal weight: 0.8980 chunk 1176 optimal weight: 8.9990 chunk 1239 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 29 ASN CH 345 GLN CH 536 GLN CH 633 GLN CK 57 GLN CK 67 GLN CK 190 ASN CQ 130 ASN ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cf 26 ASN Cf 54 GLN Cg 128 ASN Ch 88 HIS Cz 56 GLN LB 379 GLN LC 264 GLN ** LD 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 25 GLN LE 53 GLN LE 78 GLN ** LE 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 172 ASN LF 10 ASN LF 163 ASN LG 64 GLN LH 179 GLN LH 201 GLN LJ 40 GLN LJ 110 HIS ** LL 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 91 GLN LS 147 ASN ** LU 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LU 95 GLN LX 92 GLN LY 116 ASN Ld 62 GLN ** Li 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 165936 Z= 0.409 Angle : 0.726 18.916 240369 Z= 0.378 Chirality : 0.043 0.269 29364 Planarity : 0.007 0.142 18265 Dihedral : 22.375 179.955 63648 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.17 % Allowed : 12.24 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.08), residues: 10626 helix: 1.98 (0.08), residues: 3925 sheet: 0.28 (0.12), residues: 1745 loop : 0.25 (0.09), residues: 4956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRPCC 396 HIS 0.011 0.002 HISLR 125 PHE 0.021 0.002 PHECD 65 TYR 0.025 0.002 TYRLC 269 ARG 0.013 0.001 ARGLG 114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21252 Ramachandran restraints generated. 10626 Oldfield, 0 Emsley, 10626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21252 Ramachandran restraints generated. 10626 Oldfield, 0 Emsley, 10626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1102 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1000 time to evaluate : 9.348 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: CH 300 GLU cc_start: 0.7443 (pm20) cc_final: 0.7007 (pm20) REVERT: CH 362 GLN cc_start: 0.8156 (mt0) cc_final: 0.7810 (mt0) REVERT: CH 490 GLN cc_start: 0.7782 (tm-30) cc_final: 0.7398 (tm-30) REVERT: CL 21 ARG cc_start: 0.8409 (mtm-85) cc_final: 0.8171 (mtt90) REVERT: CO 19 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8693 (ttmt) REVERT: CQ 63 MET cc_start: 0.8641 (ttp) cc_final: 0.8238 (ttp) REVERT: CQ 95 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8047 (tmt-80) REVERT: CQ 143 ARG cc_start: 0.8239 (ttp-110) cc_final: 0.8010 (ttm110) REVERT: Cb 6 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8523 (ttmp) REVERT: Ch 344 LYS cc_start: 0.8382 (mmmt) cc_final: 0.8119 (mptp) REVERT: LA 165 MET cc_start: 0.8642 (ttm) cc_final: 0.8284 (ttm) REVERT: LA 199 THR cc_start: 0.7776 (OUTLIER) cc_final: 0.7443 (t) REVERT: LE 31 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: LJ 112 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7770 (p0) REVERT: LM 103 GLN cc_start: 0.8481 (tt0) cc_final: 0.8281 (tt0) REVERT: LN 13 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8150 (mmtt) REVERT: LO 197 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7993 (mp0) REVERT: LP 182 ARG cc_start: 0.8090 (ttp-110) cc_final: 0.7538 (mtm-85) REVERT: LS 119 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7294 (pmm150) REVERT: LT 111 GLU cc_start: 0.7672 (mp0) cc_final: 0.7453 (mp0) REVERT: Le 53 MET cc_start: 0.9064 (mtm) cc_final: 0.8714 (mtp) REVERT: Lk 41 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.7086 (tm-30) REVERT: CC 768 HIS cc_start: 0.8304 (OUTLIER) cc_final: 0.7642 (t70) outliers start: 102 outliers final: 57 residues processed: 1053 average time/residue: 2.4696 time to fit residues: 3691.6277 Evaluate side-chains 1048 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 980 time to evaluate : 9.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CF residue 9 VAL Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 297 LEU Chi-restraints excluded: chain CH residue 357 ILE Chi-restraints excluded: chain CK residue 118 SER Chi-restraints excluded: chain CL residue 68 GLN Chi-restraints excluded: chain CN residue 42 LEU Chi-restraints excluded: chain CN residue 75 THR Chi-restraints excluded: chain CN residue 114 THR Chi-restraints excluded: chain CN residue 127 GLU Chi-restraints excluded: chain CN residue 233 ILE Chi-restraints excluded: chain CO residue 19 LYS Chi-restraints excluded: chain CQ residue 95 ARG Chi-restraints excluded: chain Cb residue 6 LYS Chi-restraints excluded: chain Cb residue 38 THR Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cb residue 79 LYS Chi-restraints excluded: chain Cd residue 86 ASP Chi-restraints excluded: chain Cd residue 123 LEU Chi-restraints excluded: chain Cf residue 17 GLU Chi-restraints excluded: chain Ch residue 142 ILE Chi-restraints excluded: chain LA residue 96 LEU Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LB residue 336 ILE Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 354 VAL Chi-restraints excluded: chain LD residue 188 ILE Chi-restraints excluded: chain LE residue 16 THR Chi-restraints excluded: chain LE residue 31 GLU Chi-restraints excluded: chain LE residue 165 ILE Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 112 ASP Chi-restraints excluded: chain LJ residue 127 ASP Chi-restraints excluded: chain LJ residue 147 SER Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LL residue 130 SER Chi-restraints excluded: chain LL residue 144 THR Chi-restraints excluded: chain LL residue 190 SER Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LN residue 13 LYS Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LO residue 197 GLU Chi-restraints excluded: chain LP residue 75 GLN Chi-restraints excluded: chain LS residue 119 ARG Chi-restraints excluded: chain LT residue 33 THR Chi-restraints excluded: chain LU residue 79 SER Chi-restraints excluded: chain LV residue 98 GLU Chi-restraints excluded: chain LX residue 147 ASP Chi-restraints excluded: chain La residue 75 ILE Chi-restraints excluded: chain Lc residue 35 LYS Chi-restraints excluded: chain Lc residue 64 MET Chi-restraints excluded: chain Ld residue 96 LYS Chi-restraints excluded: chain Lf residue 51 VAL Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lg residue 65 THR Chi-restraints excluded: chain Lg residue 105 VAL Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Lh residue 105 VAL Chi-restraints excluded: chain Lk residue 7 ASP Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 41 GLN Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 70 THR Chi-restraints excluded: chain CC residue 713 MET Chi-restraints excluded: chain CC residue 768 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 816 optimal weight: 0.6980 chunk 1315 optimal weight: 6.9990 chunk 802 optimal weight: 3.9990 chunk 624 optimal weight: 3.9990 chunk 914 optimal weight: 1.9990 chunk 1379 optimal weight: 10.0000 chunk 1269 optimal weight: 4.9990 chunk 1098 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 848 optimal weight: 0.5980 chunk 673 optimal weight: 20.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 29 ASN CH 345 GLN CH 633 GLN CK 57 GLN CK 67 GLN CK 190 ASN CQ 87 GLN CQ 130 ASN ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cf 54 GLN Cg 128 ASN Ch 88 HIS Cz 56 GLN LA 115 ASN LB 379 GLN LC 264 GLN LD 17 GLN LE 53 GLN LE 78 GLN ** LE 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 172 ASN LF 10 ASN LF 163 ASN LG 212 ASN LH 179 GLN LH 201 GLN LJ 40 GLN LP 42 GLN LS 147 ASN ** LU 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 92 GLN LY 116 ASN LY 127 GLN Lg 30 GLN Lh 77 ASN Lh 118 GLN ** Li 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ll 11 GLN ** CC 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CD 286 GLN CD 483 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 165936 Z= 0.254 Angle : 0.656 18.054 240369 Z= 0.349 Chirality : 0.038 0.294 29364 Planarity : 0.006 0.135 18265 Dihedral : 22.373 179.519 63648 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.99 % Allowed : 12.62 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.08), residues: 10626 helix: 2.03 (0.08), residues: 3928 sheet: 0.29 (0.12), residues: 1720 loop : 0.24 (0.09), residues: 4978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRPCC 396 HIS 0.009 0.001 HISCd 252 PHE 0.021 0.002 PHECD 65 TYR 0.021 0.002 TYRLC 269 ARG 0.014 0.000 ARGLG 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21252 Ramachandran restraints generated. 10626 Oldfield, 0 Emsley, 10626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21252 Ramachandran restraints generated. 10626 Oldfield, 0 Emsley, 10626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1085 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 999 time to evaluate : 9.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CH 362 GLN cc_start: 0.8162 (mt0) cc_final: 0.7816 (mt0) REVERT: CH 490 GLN cc_start: 0.7744 (tm-30) cc_final: 0.7373 (tm-30) REVERT: CL 21 ARG cc_start: 0.8370 (mtm-85) cc_final: 0.8085 (mtm110) REVERT: CO 19 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8658 (ttmt) REVERT: CQ 63 MET cc_start: 0.8604 (ttp) cc_final: 0.8276 (ttp) REVERT: CQ 95 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7974 (tmt-80) REVERT: CQ 138 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.6629 (mtm-85) REVERT: CQ 143 ARG cc_start: 0.8262 (ttp-110) cc_final: 0.8036 (ttm110) REVERT: Cb 6 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8522 (ttmp) REVERT: Ch 344 LYS cc_start: 0.8373 (mmmt) cc_final: 0.8112 (mptp) REVERT: Cz 76 ARG cc_start: 0.8147 (ttt-90) cc_final: 0.7894 (ttp-170) REVERT: LA 165 MET cc_start: 0.8642 (ttm) cc_final: 0.8272 (ttm) REVERT: LA 199 THR cc_start: 0.7790 (OUTLIER) cc_final: 0.7458 (t) REVERT: LE 31 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: LH 109 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7632 (ttp-170) REVERT: LJ 86 LYS cc_start: 0.8342 (tppp) cc_final: 0.8063 (tppt) REVERT: LJ 112 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7738 (p0) REVERT: LN 13 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8092 (mmtt) REVERT: LP 182 ARG cc_start: 0.8032 (ttp-110) cc_final: 0.7502 (mtm-85) REVERT: LS 3 ARG cc_start: 0.6604 (tpp-160) cc_final: 0.6275 (tpp-160) REVERT: LS 119 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7266 (pmm150) REVERT: LT 111 GLU cc_start: 0.7676 (mp0) cc_final: 0.7442 (mp0) REVERT: LY 112 LYS cc_start: 0.8035 (ttpt) cc_final: 0.7811 (ttpt) REVERT: Le 53 MET cc_start: 0.9051 (mtm) cc_final: 0.8742 (mtp) REVERT: Lk 41 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.7053 (tm-30) REVERT: CC 768 HIS cc_start: 0.8267 (OUTLIER) cc_final: 0.7790 (t70) REVERT: CD 483 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8497 (mt0) outliers start: 86 outliers final: 55 residues processed: 1041 average time/residue: 2.4624 time to fit residues: 3624.5759 Evaluate side-chains 1048 residues out of total 9177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 980 time to evaluate : 8.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CF residue 9 VAL Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 297 LEU Chi-restraints excluded: chain CH residue 357 ILE Chi-restraints excluded: chain CK residue 118 SER Chi-restraints excluded: chain CL residue 68 GLN Chi-restraints excluded: chain CN residue 114 THR Chi-restraints excluded: chain CN residue 127 GLU Chi-restraints excluded: chain CN residue 233 ILE Chi-restraints excluded: chain CO residue 19 LYS Chi-restraints excluded: chain CQ residue 95 ARG Chi-restraints excluded: chain CQ residue 138 ARG Chi-restraints excluded: chain Cb residue 6 LYS Chi-restraints excluded: chain Cb residue 38 THR Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cd residue 86 ASP Chi-restraints excluded: chain Cd residue 123 LEU Chi-restraints excluded: chain Cf residue 17 GLU Chi-restraints excluded: chain Ch residue 142 ILE Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LB residue 336 ILE Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 354 VAL Chi-restraints excluded: chain LD residue 188 ILE Chi-restraints excluded: chain LE residue 16 THR Chi-restraints excluded: chain LE residue 31 GLU Chi-restraints excluded: chain LE residue 165 ILE Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LH residue 109 ARG Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 100 THR Chi-restraints excluded: chain LJ residue 112 ASP Chi-restraints excluded: chain LJ residue 127 ASP Chi-restraints excluded: chain LJ residue 147 SER Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LL residue 130 SER Chi-restraints excluded: chain LL residue 190 SER Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LN residue 13 LYS Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LO residue 197 GLU Chi-restraints excluded: chain LP residue 75 GLN Chi-restraints excluded: chain LQ residue 32 ILE Chi-restraints excluded: chain LQ residue 50 ASP Chi-restraints excluded: chain LS residue 119 ARG Chi-restraints excluded: chain LU residue 79 SER Chi-restraints excluded: chain LV residue 91 ASP Chi-restraints excluded: chain LY residue 6 THR Chi-restraints excluded: chain La residue 75 ILE Chi-restraints excluded: chain Lc residue 64 MET Chi-restraints excluded: chain Ld residue 96 LYS Chi-restraints excluded: chain Lf residue 51 VAL Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lg residue 65 THR Chi-restraints excluded: chain Lg residue 105 VAL Chi-restraints excluded: chain Lh residue 84 ASP Chi-restraints excluded: chain Lh residue 105 VAL Chi-restraints excluded: chain Lh residue 113 LEU Chi-restraints excluded: chain Lk residue 7 ASP Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 41 GLN Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 70 THR Chi-restraints excluded: chain CC residue 713 MET Chi-restraints excluded: chain CC residue 768 HIS Chi-restraints excluded: chain CD residue 483 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1385 random chunks: chunk 872 optimal weight: 0.0570 chunk 1170 optimal weight: 0.8980 chunk 336 optimal weight: 0.0060 chunk 1013 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 305 optimal weight: 7.9990 chunk 1100 optimal weight: 0.2980 chunk 460 optimal weight: 1.9990 chunk 1130 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 202 optimal weight: 20.0000 overall best weight: 0.6516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 29 ASN CH 536 GLN CH 633 GLN CK 57 GLN CK 190 ASN CQ 130 ASN ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 101 ASN Cf 54 GLN Ch 88 HIS LA 115 ASN LB 379 GLN LC 264 GLN LE 53 GLN LE 78 GLN ** LE 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 172 ASN LF 10 ASN LF 163 ASN ** LG 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LH 179 GLN LH 201 GLN LJ 40 GLN LN 123 GLN LP 42 GLN LS 147 ASN ** LU 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 92 GLN LY 116 ASN Lh 77 ASN Lh 118 GLN ** Li 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ll 11 GLN CD 286 GLN CD 483 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.091403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.064117 restraints weight = 295421.828| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.09 r_work: 0.2764 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 165936 Z= 0.143 Angle : 0.625 17.688 240369 Z= 0.337 Chirality : 0.035 0.276 29364 Planarity : 0.006 0.127 18265 Dihedral : 22.382 179.709 63648 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.81 % Allowed : 12.88 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.08), residues: 10626 helix: 2.16 (0.08), residues: 3919 sheet: 0.23 (0.12), residues: 1737 loop : 0.31 (0.09), residues: 4970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRPCC 396 HIS 0.008 0.001 HISCh 342 PHE 0.036 0.001 PHECh 37 TYR 0.019 0.001 TYRLC 269 ARG 0.013 0.000 ARGLG 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 54016.52 seconds wall clock time: 937 minutes 56.30 seconds (56276.30 seconds total)