Starting phenix.real_space_refine on Sun Mar 3 03:45:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv3_17952/03_2024/8pv3_17952_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv3_17952/03_2024/8pv3_17952.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv3_17952/03_2024/8pv3_17952_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv3_17952/03_2024/8pv3_17952_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv3_17952/03_2024/8pv3_17952_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv3_17952/03_2024/8pv3_17952.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv3_17952/03_2024/8pv3_17952.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv3_17952/03_2024/8pv3_17952_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pv3_17952/03_2024/8pv3_17952_updated.pdb" } resolution = 2.8 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= 0.017 sd= 0.147 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 3361 5.49 5 Mg 3 5.21 5 S 253 5.16 5 C 84896 2.51 5 N 28812 2.21 5 O 38113 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "CB PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF ASP 46": "OD1" <-> "OD2" Residue "CF TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF ASP 108": "OD1" <-> "OD2" Residue "CF TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF ASP 154": "OD1" <-> "OD2" Residue "CF TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH ASP 375": "OD1" <-> "OD2" Residue "CH GLU 431": "OE1" <-> "OE2" Residue "CH TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH GLU 486": "OE1" <-> "OE2" Residue "CH TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH GLU 505": "OE1" <-> "OE2" Residue "CH ASP 535": "OD1" <-> "OD2" Residue "CH GLU 585": "OE1" <-> "OE2" Residue "CH ASP 637": "OD1" <-> "OD2" Residue "CI TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CI GLU 309": "OE1" <-> "OE2" Residue "CJ PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ ASP 142": "OD1" <-> "OD2" Residue "CJ GLU 232": "OE1" <-> "OE2" Residue "CJ TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CK ASP 227": "OD1" <-> "OD2" Residue "CK TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CL GLU 30": "OE1" <-> "OE2" Residue "CL ASP 52": "OD1" <-> "OD2" Residue "CM GLU 26": "OE1" <-> "OE2" Residue "CM TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CM PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CM ASP 233": "OD1" <-> "OD2" Residue "CN TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CN PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CN ASP 44": "OD1" <-> "OD2" Residue "CN GLU 98": "OE1" <-> "OE2" Residue "CN ASP 120": "OD1" <-> "OD2" Residue "CN GLU 126": "OE1" <-> "OE2" Residue "CN ASP 131": "OD1" <-> "OD2" Residue "CN ASP 144": "OD1" <-> "OD2" Residue "CN ASP 171": "OD1" <-> "OD2" Residue "CO GLU 12": "OE1" <-> "OE2" Residue "CQ PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CQ GLU 119": "OE1" <-> "OE2" Residue "Cb TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cb GLU 90": "OE1" <-> "OE2" Residue "Cd TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cd ASP 119": "OD1" <-> "OD2" Residue "Cd ASP 173": "OD1" <-> "OD2" Residue "Cd PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cd ASP 312": "OD1" <-> "OD2" Residue "Cd GLU 424": "OE1" <-> "OE2" Residue "Cd GLU 428": "OE1" <-> "OE2" Residue "Ce GLU 228": "OE1" <-> "OE2" Residue "Ce GLU 247": "OE1" <-> "OE2" Residue "Ce GLU 313": "OE1" <-> "OE2" Residue "Ce PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ce ASP 387": "OD1" <-> "OD2" Residue "Ce ASP 440": "OD1" <-> "OD2" Residue "Cf TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cf TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cf GLU 270": "OE1" <-> "OE2" Residue "Cg ASP 77": "OD1" <-> "OD2" Residue "Cg GLU 135": "OE1" <-> "OE2" Residue "Cg GLU 154": "OE1" <-> "OE2" Residue "Ch PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ch ASP 175": "OD1" <-> "OD2" Residue "Ch TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ch ASP 380": "OD1" <-> "OD2" Residue "Ch PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ch ASP 483": "OD1" <-> "OD2" Residue "Ch GLU 488": "OE1" <-> "OE2" Residue "Ch ASP 509": "OD1" <-> "OD2" Residue "Cz GLU 94": "OE1" <-> "OE2" Residue "Cz TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB ASP 36": "OD1" <-> "OD2" Residue "LB ASP 59": "OD1" <-> "OD2" Residue "LB GLU 94": "OE1" <-> "OE2" Residue "LB PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB GLU 292": "OE1" <-> "OE2" Residue "LC GLU 148": "OE1" <-> "OE2" Residue "LC ASP 218": "OD1" <-> "OD2" Residue "LC ASP 266": "OD1" <-> "OD2" Residue "LC GLU 360": "OE1" <-> "OE2" Residue "LD PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD GLU 191": "OE1" <-> "OE2" Residue "LD GLU 209": "OE1" <-> "OE2" Residue "LD PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE ASP 110": "OD1" <-> "OD2" Residue "LE GLU 131": "OE1" <-> "OE2" Residue "LF GLU 31": "OE1" <-> "OE2" Residue "LF PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG ASP 86": "OD1" <-> "OD2" Residue "LG GLU 121": "OE1" <-> "OE2" Residue "LG GLU 126": "OE1" <-> "OE2" Residue "LG TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG ASP 210": "OD1" <-> "OD2" Residue "LG PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH GLU 65": "OE1" <-> "OE2" Residue "LH ASP 74": "OD1" <-> "OD2" Residue "LH TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH ASP 181": "OD1" <-> "OD2" Residue "LH TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LJ PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LJ TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LK ASP 91": "OD1" <-> "OD2" Residue "LK ASP 153": "OD1" <-> "OD2" Residue "LL ASP 118": "OD1" <-> "OD2" Residue "LM ASP 42": "OD1" <-> "OD2" Residue "LM TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LM ASP 91": "OD1" <-> "OD2" Residue "LM ASP 114": "OD1" <-> "OD2" Residue "LN GLU 9": "OE1" <-> "OE2" Residue "LN ASP 17": "OD1" <-> "OD2" Residue "LN GLU 103": "OE1" <-> "OE2" Residue "LN PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO ASP 11": "OD1" <-> "OD2" Residue "LO TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO GLU 108": "OE1" <-> "OE2" Residue "LO ASP 153": "OD1" <-> "OD2" Residue "LO GLU 159": "OE1" <-> "OE2" Residue "LP GLU 31": "OE1" <-> "OE2" Residue "LP ASP 53": "OD1" <-> "OD2" Residue "LP ASP 103": "OD1" <-> "OD2" Residue "LP GLU 147": "OE1" <-> "OE2" Residue "LQ PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LQ GLU 127": "OE1" <-> "OE2" Residue "LR TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS GLU 57": "OE1" <-> "OE2" Residue "LS PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS ASP 82": "OD1" <-> "OD2" Residue "LS ASP 109": "OD1" <-> "OD2" Residue "LS PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT ASP 38": "OD1" <-> "OD2" Residue "LT PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT ASP 145": "OD1" <-> "OD2" Residue "LU PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU GLU 40": "OE1" <-> "OE2" Residue "LU ASP 50": "OD1" <-> "OD2" Residue "LU GLU 71": "OE1" <-> "OE2" Residue "LU TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU GLU 111": "OE1" <-> "OE2" Residue "LV TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LV PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LV PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX GLU 91": "OE1" <-> "OE2" Residue "LX PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX ASP 142": "OD1" <-> "OD2" Residue "LY GLU 82": "OE1" <-> "OE2" Residue "LY ASP 113": "OD1" <-> "OD2" Residue "LZ TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ GLU 107": "OE1" <-> "OE2" Residue "LZ GLU 118": "OE1" <-> "OE2" Residue "La ASP 97": "OD1" <-> "OD2" Residue "La TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "La GLU 133": "OE1" <-> "OE2" Residue "La GLU 135": "OE1" <-> "OE2" Residue "La GLU 140": "OE1" <-> "OE2" Residue "Lc GLU 58": "OE1" <-> "OE2" Residue "Lc GLU 79": "OE1" <-> "OE2" Residue "Ld GLU 43": "OE1" <-> "OE2" Residue "Le ASP 24": "OD1" <-> "OD2" Residue "Le PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Le ASP 40": "OD1" <-> "OD2" Residue "Le GLU 84": "OE1" <-> "OE2" Residue "Lf TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lf ASP 39": "OD1" <-> "OD2" Residue "Lf PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lg TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lh ASP 84": "OD1" <-> "OD2" Residue "Lh ASP 101": "OD1" <-> "OD2" Residue "Li GLU 63": "OE1" <-> "OE2" Residue "Li PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lk ASP 70": "OD1" <-> "OD2" Residue "Ll TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lq ASP 49": "OD1" <-> "OD2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 155443 Number of models: 1 Model: "" Number of chains: 68 Chain: "C1" Number of atoms: 64177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2998, 64177 Classifications: {'RNA': 2998} Modifications used: {'rna2p': 1, 'rna2p_pur': 315, 'rna2p_pyr': 211, 'rna3p': 25, 'rna3p_pur': 1315, 'rna3p_pyr': 1123} Link IDs: {'rna2p': 527, 'rna3p': 2470} Chain breaks: 8 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 18 Chain: "C2" Number of atoms: 3319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3319 Classifications: {'RNA': 156} Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 12, 'rna3p_pur': 62, 'rna3p_pyr': 64} Link IDs: {'rna2p': 30, 'rna3p': 125} Chain: "C3" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1754 Classifications: {'RNA': 82} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 9, 'rna3p_pur': 31, 'rna3p_pyr': 31} Link IDs: {'rna2p': 19, 'rna3p': 62} Chain breaks: 1 Chain: "C4" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2536 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 54, 'rna3p_pyr': 53} Link IDs: {'rna2p': 12, 'rna3p': 106} Chain: "CB" Number of atoms: 2119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2119 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 246} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "CF" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1934 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 232} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "CH" Number of atoms: 5063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5063 Classifications: {'peptide': 627} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 600} Chain breaks: 2 Chain: "CI" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1234 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 142} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "CJ" Number of atoms: 3116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3116 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 356} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "CK" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1903 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 221} Chain breaks: 2 Chain: "CL" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 622 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 72} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "CM" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1773 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 205} Chain breaks: 2 Chain: "CN" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1853 Classifications: {'peptide': 246} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 237} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "CO" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 468 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain breaks: 2 Chain: "CQ" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1480 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "Cb" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 830 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "Cd" Number of atoms: 3691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3691 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Ce" Number of atoms: 2148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2148 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 246} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Cf" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2282 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "Cg" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1478 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 19, 'TRANS': 168} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Ch" Number of atoms: 3812 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 485, 3809 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 466} Conformer: "B" Number of residues, atoms: 485, 3809 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 466} bond proxies already assigned to first conformer: 3904 Chain: "Cz" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 869 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "LA" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1365 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 164} 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: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1181 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 142} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "LR" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1241 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 151} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "LS" Number of atoms: 1426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1426 Classifications: {'peptide': 174} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 163} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "LT" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1027 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 121} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "LU" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 846 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "LV" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 991 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 125} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "LX" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1133 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 136} Chain: "LY" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1056 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 6, 'TRANS': 126} Chain: "LZ" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1112 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "La" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 872 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain breaks: 1 Chain: "Lc" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 705 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Ld" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 105} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "Le" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1017 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "Lf" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 862 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "Lg" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 109} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Lh" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1003 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "Li" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 827 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 98} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS%COO:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Lj" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 698 Classifications: {'peptide': 88} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 83} Chain: "Lk" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 632 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 4, 'TRANS': 71} Chain: "Ll" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Lp" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 698 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "Lq" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1073 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 6, 'TRANS': 132} Chain: "CH" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "CQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Cb" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Cd" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 2, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Lg" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lj" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lp" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "CH" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Cd" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 91921 SG CYSCQ 6 146.372 179.609 99.851 1.00 21.35 S ATOM 91949 SG CYSCQ 9 149.984 180.687 100.478 1.00 21.22 S ATOM 92134 SG CYSCQ 32 149.342 177.427 98.663 1.00 16.07 S ATOM 92166 SG CYSCQ 36 148.611 177.863 102.391 1.00 17.66 S ATOM 93778 SG CYSCb 52 127.683 186.354 122.293 1.00 55.15 S ATOM 93801 SG CYSCb 55 131.036 184.696 122.578 1.00 56.77 S ATOM A125E SG CYSLg 45 142.562 159.502 198.184 1.00 29.10 S ATOM A125W SG CYSLg 48 139.951 161.292 196.111 1.00 33.85 S ATOM A12D4 SG CYSLg 82 142.105 163.299 198.577 1.00 32.55 S ATOM A12DM SG CYSLg 85 139.401 160.957 199.767 1.00 36.23 S ATOM A143J SG CYSLj 19 164.065 112.476 171.202 1.00 13.64 S ATOM A144B SG CYSLj 22 165.027 110.264 168.148 1.00 12.71 S ATOM A1471 SG CYSLj 34 161.512 111.395 168.621 1.00 13.62 S ATOM A147I SG CYSLj 37 162.940 108.909 171.091 1.00 15.19 S ATOM A15L8 SG CYSLp 39 123.882 162.295 191.510 1.00 40.87 S ATOM A15LW SG CYSLp 42 125.527 165.664 191.902 1.00 41.01 S ATOM A15P1 SG CYSLp 57 126.909 163.154 189.364 1.00 41.28 S ATOM A15PM SG CYSLp 60 127.368 162.414 192.993 1.00 45.84 S Time building chain proxies: 61.87, per 1000 atoms: 0.40 Number of scatterers: 155443 At special positions: 0 Unit cell: (235.125, 229.9, 317.68, 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 253 16.00 P 3361 15.00 Mg 3 11.99 O 38113 8.00 N 28812 7.00 C 84896 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: 56.85 Conformation dependent library (CDL) restraints added in 13.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNCQ1000 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 9 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 36 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 32 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 6 " pdb=" ZNCb1000 " pdb="ZN ZNCb1000 " - pdb=" ND1 HISCb 74 " pdb="ZN ZNCb1000 " - pdb=" NE2 HISCb 68 " pdb="ZN ZNCb1000 " - pdb=" SG CYSCb 52 " pdb="ZN ZNCb1000 " - pdb=" SG CYSCb 55 " pdb=" ZNLg1000 " pdb="ZN ZNLg1000 " - pdb=" SG CYSLg 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 34 " pdb="ZN ZNLj1000 " - pdb=" SG CYSLj 22 " pdb="ZN ZNLj1000 " - pdb=" SG CYSLj 19 " pdb="ZN ZNLj1000 " - pdb=" SG CYSLj 37 " pdb=" ZNLp 101 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 39 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 57 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 60 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 42 " Number of angles added : 26 20696 Ramachandran restraints generated. 10348 Oldfield, 0 Emsley, 10348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 19688 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: 379 helices and 105 sheets defined 45.2% alpha, 14.2% beta 1051 base pairs and 1863 stacking pairs defined. Time for finding SS restraints: 89.79 Creating SS restraints... Processing helix chain 'CB' and resid 19 through 40 removed outlier: 3.695A pdb=" N ALACB 40 " --> pdb=" O LYSCB 36 " (cutoff:3.500A) Processing helix chain 'CB' and resid 52 through 60 removed outlier: 4.582A pdb=" N GLUCB 59 " --> pdb=" O SERCB 55 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N THRCB 60 " --> pdb=" O THRCB 56 " (cutoff:3.500A) Processing helix chain 'CB' and resid 104 through 115 removed outlier: 4.440A pdb=" N TYRCB 108 " --> pdb=" O PROCB 104 " (cutoff:3.500A) Processing helix chain 'CB' and resid 117 through 125 removed outlier: 5.266A pdb=" N GLYCB 125 " --> pdb=" O ARGCB 121 " (cutoff:3.500A) Processing helix chain 'CB' and resid 129 through 137 Processing helix chain 'CB' and resid 139 through 151 removed outlier: 3.759A pdb=" N HISCB 150 " --> pdb=" O LEUCB 146 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASPCB 151 " --> pdb=" O PHECB 147 " (cutoff:3.500A) Processing helix chain 'CB' and resid 156 through 164 removed outlier: 5.100A pdb=" N ASNCB 161 " --> pdb=" O THRCB 157 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARGCB 162 " --> pdb=" O ARGCB 158 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEUCB 163 " --> pdb=" O ILECB 159 " (cutoff:3.500A) Proline residue: CB 164 - end of helix Processing helix chain 'CB' and resid 168 through 175 removed outlier: 3.646A pdb=" N TYRCB 172 " --> pdb=" O GLYCB 168 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N THRCB 174 " --> pdb=" O THRCB 170 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N THRCB 175 " --> pdb=" O PHECB 171 " (cutoff:3.500A) Processing helix chain 'CB' and resid 216 through 230 Processing helix chain 'CB' and resid 251 through 269 Processing helix chain 'CB' and resid 274 through 279 removed outlier: 3.677A pdb=" N VALCB 278 " --> pdb=" O LYSCB 274 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ARGCB 279 " --> pdb=" O TRPCB 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'CB' and resid 274 through 279' Processing helix chain 'CB' and resid 302 through 307 removed outlier: 4.607A pdb=" N VALCB 306 " --> pdb=" O ASPCB 302 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VALCB 307 " --> pdb=" O GLUCB 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'CB' and resid 302 through 307' Processing helix chain 'CF' and resid 19 through 37 removed outlier: 3.951A pdb=" N LYSCF 23 " --> pdb=" O GLYCF 19 " (cutoff:3.500A) Proline residue: CF 35 - end of helix Processing helix chain 'CF' and resid 51 through 61 removed outlier: 4.906A pdb=" N ASPCF 55 " --> pdb=" O ASNCF 51 " (cutoff:3.500A) removed outlier: 3.589A 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: 3.730A pdb=" N LEUCF 92 " --> pdb=" O GLYCF 88 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THRCF 93 " --> pdb=" O LEUCF 89 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ARGCF 94 " --> pdb=" O HISCF 90 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N TYRCF 95 " --> pdb=" O ARGCF 91 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEUCF 96 " --> pdb=" O LEUCF 92 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N THRCF 97 " --> pdb=" O THRCF 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'CF' and resid 88 through 97' Processing helix chain 'CF' and resid 108 through 119 Processing helix chain 'CF' and resid 161 through 169 Processing helix chain 'CF' and resid 202 through 213 Processing helix chain 'CF' and resid 237 through 243 removed outlier: 3.830A pdb=" N THRCF 242 " --> pdb=" O GLUCF 238 " (cutoff:3.500A) Processing helix chain 'CH' and resid 12 through 27 Processing helix chain 'CH' and resid 37 through 66 Processing helix chain 'CH' and resid 69 through 74 removed outlier: 6.072A pdb=" N HISCH 74 " --> pdb=" O LEUCH 70 " (cutoff:3.500A) Processing helix chain 'CH' and resid 75 through 85 Processing helix chain 'CH' and resid 86 through 118 removed outlier: 3.974A pdb=" N TYRCH 117 " --> pdb=" O ARGCH 113 " (cutoff:3.500A) Processing helix chain 'CH' and resid 120 through 143 removed outlier: 4.016A pdb=" N LEUCH 142 " --> pdb=" O LEUCH 138 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYSCH 143 " --> pdb=" O ILECH 139 " (cutoff:3.500A) Processing helix chain 'CH' and resid 144 through 159 Processing helix chain 'CH' and resid 178 through 187 Processing helix chain 'CH' and resid 227 through 232 removed outlier: 5.946A pdb=" N ASNCH 232 " --> pdb=" O LEUCH 228 " (cutoff:3.500A) 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: 4.045A pdb=" N ALACH 278 " --> pdb=" O LYSCH 274 " (cutoff:3.500A) Processing helix chain 'CH' and resid 293 through 298 removed outlier: 3.749A pdb=" N LEUCH 297 " --> pdb=" O LYSCH 293 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASPCH 298 " --> pdb=" O PHECH 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'CH' and resid 293 through 298' Processing helix chain 'CH' and resid 299 through 311 removed outlier: 3.781A pdb=" N THRCH 309 " --> pdb=" O ILECH 305 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYSCH 310 " --> pdb=" O ASNCH 306 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N SERCH 311 " --> pdb=" O ASPCH 307 " (cutoff:3.500A) Processing helix chain 'CH' and resid 326 through 351 removed outlier: 4.780A pdb=" N GLYCH 350 " --> pdb=" O LYSCH 346 " (cutoff:3.500A) removed outlier: 4.699A 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: 4.670A pdb=" N LYSCH 388 " --> pdb=" O PROCH 384 " (cutoff:3.500A) removed outlier: 3.945A 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 429 through 434 removed outlier: 4.431A pdb=" N LYSCH 433 " --> pdb=" O ASNCH 429 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N TYRCH 434 " --> pdb=" O PROCH 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'CH' and resid 429 through 434' Processing helix chain 'CH' and resid 445 through 450 Processing helix chain 'CH' and resid 453 through 472 removed outlier: 3.933A pdb=" N LYSCH 457 " --> pdb=" O ASPCH 453 " (cutoff:3.500A) Processing helix chain 'CH' and resid 482 through 510 Processing helix chain 'CH' and resid 519 through 524 removed outlier: 3.988A pdb=" N VALCH 523 " --> pdb=" O PROCH 519 " (cutoff:3.500A) removed outlier: 5.277A 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: 3.548A pdb=" N ILECH 544 " --> pdb=" O ASPCH 540 " (cutoff:3.500A) Processing helix chain 'CH' and resid 546 through 551 removed outlier: 5.474A pdb=" N GLNCH 551 " --> pdb=" O ARGCH 547 " (cutoff:3.500A) Processing helix chain 'CH' and resid 582 through 597 Processing helix chain 'CH' and resid 609 through 631 removed outlier: 4.027A pdb=" N GLNCH 624 " --> pdb=" O ALACH 620 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ARGCH 625 " --> pdb=" O LYSCH 621 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LYSCH 626 " --> pdb=" O LEUCH 622 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N METCH 627 " --> pdb=" O ALACH 623 " (cutoff:3.500A) Processing helix chain 'CH' and resid 645 through 650 Processing helix chain 'CI' and resid 199 through 211 removed outlier: 4.030A pdb=" N GLNCI 209 " --> pdb=" O GLYCI 205 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHECI 210 " --> pdb=" O TYRCI 206 " (cutoff:3.500A) Processing helix chain 'CI' and resid 237 through 249 Processing helix chain 'CI' and resid 284 through 295 Processing helix chain 'CI' and resid 298 through 322 removed outlier: 4.375A pdb=" N GLUCI 322 " --> pdb=" O GLUCI 318 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 11 through 16 Processing helix chain 'CJ' and resid 18 through 27 Processing helix chain 'CJ' and resid 29 through 41 Processing helix chain 'CJ' and resid 49 through 54 removed outlier: 3.894A pdb=" N VALCJ 53 " --> pdb=" O ASPCJ 49 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 65 through 75 removed outlier: 4.051A pdb=" N HISCJ 74 " --> pdb=" O GLNCJ 70 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLUCJ 75 " --> pdb=" O TYRCJ 71 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 76 through 98 Processing helix chain 'CJ' and resid 99 through 111 removed outlier: 3.919A pdb=" N ASNCJ 109 " --> pdb=" O ARGCJ 105 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALACJ 110 " --> pdb=" O LEUCJ 106 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASNCJ 111 " --> pdb=" O GLUCJ 107 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 112 through 117 Processing helix chain 'CJ' and resid 123 through 132 removed outlier: 3.608A pdb=" N ARGCJ 128 " --> pdb=" O ASNCJ 124 " (cutoff:3.500A) Proline residue: CJ 132 - end of helix Processing helix chain 'CJ' and resid 133 through 155 removed outlier: 4.404A pdb=" N ASPCJ 142 " --> pdb=" O LEUCJ 138 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ASPCJ 143 " --> pdb=" O ARGCJ 139 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASNCJ 153 " --> pdb=" O PHECJ 149 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEUCJ 154 " --> pdb=" O LEUCJ 150 " (cutoff:3.500A) Proline residue: CJ 155 - end of helix Processing helix chain 'CJ' and resid 161 through 183 Processing helix chain 'CJ' and resid 223 through 250 removed outlier: 3.654A pdb=" N PHECJ 240 " --> pdb=" O THRCJ 236 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 258 through 265 Processing helix chain 'CJ' and resid 362 through 367 removed outlier: 4.481A pdb=" N LEUCJ 366 " --> pdb=" O ASPCJ 362 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHECJ 367 " --> pdb=" O PROCJ 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'CJ' and resid 362 through 367' Processing helix chain 'CJ' and resid 379 through 391 Processing helix chain 'CJ' and resid 457 through 468 removed outlier: 4.407A pdb=" N VALCJ 461 " --> pdb=" O GLNCJ 457 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRPCJ 462 " --> pdb=" O PROCJ 458 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 472 through 477 removed outlier: 4.191A pdb=" N TYRCJ 476 " --> pdb=" O PROCJ 472 " (cutoff:3.500A) Processing helix chain 'CK' and resid 5 through 14 Processing helix chain 'CK' and resid 19 through 41 removed outlier: 4.929A pdb=" N GLYCK 32 " --> pdb=" O ALACK 28 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N HISCK 33 " --> pdb=" O ALACK 29 " (cutoff:3.500A) Processing helix chain 'CK' and resid 44 through 72 removed outlier: 5.066A pdb=" N ASNCK 72 " --> pdb=" O HISCK 68 " (cutoff:3.500A) Processing helix chain 'CK' and resid 128 through 133 Processing helix chain 'CK' and resid 174 through 179 removed outlier: 3.673A pdb=" N ARGCK 178 " --> pdb=" O PROCK 174 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYRCK 179 " --> pdb=" O METCK 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'CK' and resid 174 through 179' Processing helix chain 'CK' and resid 206 through 213 Processing helix chain 'CK' and resid 248 through 253 Processing helix chain 'CL' and resid 17 through 42 Processing helix chain 'CL' and resid 61 through 80 Processing helix chain 'CL' and resid 3 through 8 Proline residue: CL 8 - end of helix No H-bonds generated for 'chain 'CL' and resid 3 through 8' Processing helix chain 'CM' and resid 14 through 35 Processing helix chain 'CM' and resid 53 through 78 Processing helix chain 'CM' and resid 102 through 113 Processing helix chain 'CM' and resid 126 through 137 Processing helix chain 'CM' and resid 146 through 156 Processing helix chain 'CM' and resid 171 through 179 removed outlier: 4.856A pdb=" N ILECM 175 " --> pdb=" O ASPCM 171 " (cutoff:3.500A) Processing helix chain 'CM' and resid 186 through 197 Processing helix chain 'CM' and resid 200 through 209 removed outlier: 5.108A pdb=" N TRPCM 209 " --> pdb=" O ALACM 205 " (cutoff:3.500A) Processing helix chain 'CM' and resid 215 through 221 removed outlier: 4.351A pdb=" N GLYCM 219 " --> pdb=" O ASNCM 215 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHECM 220 " --> pdb=" O PROCM 216 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ARGCM 221 " --> pdb=" O ASNCM 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'CM' and resid 215 through 221' Processing helix chain 'CM' and resid 239 through 249 removed outlier: 4.760A pdb=" N ALACM 243 " --> pdb=" O GLUCM 239 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEUCM 244 " --> pdb=" O HISCM 240 " (cutoff:3.500A) Processing helix chain 'CN' and resid 12 through 17 removed outlier: 3.728A pdb=" N PHECN 16 " --> pdb=" O GLUCN 12 " (cutoff:3.500A) Processing helix chain 'CN' and resid 32 through 43 removed outlier: 3.708A pdb=" N PHECN 38 " --> pdb=" O PHECN 34 " (cutoff:3.500A) removed outlier: 3.669A 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: 4.484A pdb=" N ILECN 233 " --> pdb=" O GLYCN 229 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASNCN 234 " --> pdb=" O PROCN 230 " (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 42 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: 5.537A 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: 4.429A pdb=" N GLNCQ 70 " --> pdb=" O ASPCQ 66 " (cutoff:3.500A) removed outlier: 4.644A 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: 5.979A pdb=" N GLYCQ 114 " --> pdb=" O LYSCQ 110 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYSCQ 115 " --> pdb=" O ARGCQ 111 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ARGCQ 116 " --> pdb=" O METCQ 112 " (cutoff:3.500A) removed outlier: 5.245A 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: 4.724A pdb=" N LYSCQ 171 " --> pdb=" O LEUCQ 167 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 5 through 10 removed outlier: 3.636A pdb=" N METCb 9 " --> pdb=" O ALACb 5 " (cutoff:3.500A) removed outlier: 5.149A 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: 3.850A pdb=" N LYSCb 39 " --> pdb=" O TYRCb 35 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ALACb 40 " --> pdb=" O LYSCb 36 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 61 through 72 removed outlier: 3.832A pdb=" N LYSCb 70 " --> pdb=" O VALCb 66 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLYCb 71 " --> pdb=" O GLYCb 67 " (cutoff:3.500A) removed outlier: 5.275A 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: 3.687A 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: 3.870A pdb=" N LEUCd 41 " --> pdb=" O THRCd 37 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYSCd 42 " --> pdb=" O LEUCd 38 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 73 through 79 removed outlier: 4.650A pdb=" N PHECd 77 " --> pdb=" O ASNCd 73 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THRCd 78 " --> pdb=" O ARGCd 74 " (cutoff:3.500A) removed outlier: 5.918A 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: 3.514A pdb=" N ILECd 117 " --> pdb=" O PROCd 113 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 122 through 140 removed outlier: 3.827A pdb=" N HISCd 130 " --> pdb=" O GLYCd 126 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALACd 132 " --> pdb=" O LYSCd 128 " (cutoff:3.500A) removed outlier: 5.428A 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: 4.229A pdb=" N ASNCd 215 " --> pdb=" O GLUCd 211 " (cutoff:3.500A) removed outlier: 4.099A 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: 4.363A 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: 3.862A pdb=" N LYSCd 290 " --> pdb=" O ARGCd 286 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASPCd 291 " --> pdb=" O ILECd 287 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 306 through 322 Processing helix chain 'Cd' and resid 338 through 348 Processing helix chain 'Cd' and resid 389 through 397 Processing helix chain 'Cd' and resid 400 through 405 removed outlier: 3.937A pdb=" N VALCd 404 " --> pdb=" O ARGCd 400 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLUCd 405 " --> pdb=" O VALCd 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cd' and resid 400 through 405' Processing helix chain 'Cd' and resid 407 through 419 removed outlier: 4.036A pdb=" N ILECd 411 " --> pdb=" O PROCd 407 " (cutoff:3.500A) Proline residue: Cd 412 - end of helix removed outlier: 5.144A 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: 3.561A pdb=" N GLYCd 471 " --> pdb=" O ASPCd 467 " (cutoff:3.500A) Processing helix chain 'Ce' and resid 86 through 94 Processing helix chain 'Ce' and resid 186 through 192 removed outlier: 3.517A pdb=" N GLUCe 190 " --> pdb=" O PROCe 186 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N LYSCe 192 " --> pdb=" O THRCe 188 " (cutoff:3.500A) Processing helix chain 'Ce' and resid 218 through 269 Processing helix chain 'Ce' and resid 300 through 333 Processing helix chain 'Ce' and resid 334 through 353 Processing helix chain 'Ce' and resid 401 through 414 Processing helix chain 'Ce' and resid 435 through 441 Processing helix chain 'Cf' and resid 9 through 20 Processing helix chain 'Cf' and resid 39 through 54 Processing helix chain 'Cf' and resid 72 through 83 Processing helix chain 'Cf' and resid 125 through 130 removed outlier: 4.179A pdb=" N PHECf 129 " --> pdb=" O SERCf 125 " (cutoff:3.500A) removed outlier: 5.421A 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: 3.703A pdb=" N LYSCf 318 " --> pdb=" O METCf 314 " (cutoff:3.500A) removed outlier: 5.808A 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: 3.763A pdb=" N LEUCf 181 " --> pdb=" O VALCf 178 " (cutoff:3.500A) removed outlier: 4.816A 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: 3.665A pdb=" N ARGCg 123 " --> pdb=" O ARGCg 119 " (cutoff:3.500A) Processing helix chain 'Cg' and resid 156 through 164 Proline residue: Cg 164 - end of helix Processing helix chain 'Cg' and resid 168 through 198 removed outlier: 4.190A pdb=" N ASPCg 172 " --> pdb=" O SERCg 168 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LYSCg 173 " --> pdb=" O VALCg 169 " (cutoff:3.500A) removed outlier: 5.497A 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: 3.739A pdb=" N THRCh 337 " --> pdb=" O HISCh 333 " (cutoff:3.500A) Processing helix chain 'Ch' and resid 349 through 366 Processing helix chain 'Ch' and resid 388 through 393 Processing helix chain 'Cz' and resid 48 through 103 Processing helix chain 'Cz' and resid 104 through 121 Processing helix chain 'LA' and resid 33 through 38 Processing helix chain 'LA' and resid 103 through 108 removed outlier: 3.771A 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: 4.328A pdb=" N VALLA 191 " --> pdb=" O HISLA 187 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYSLA 192 " --> pdb=" O LYSLA 188 " (cutoff:3.500A) Processing helix chain 'LB' and resid 13 through 18 removed outlier: 5.029A pdb=" N LEULB 17 " --> pdb=" O SERLB 13 " (cutoff:3.500A) Proline residue: LB 18 - end of helix No H-bonds generated for 'chain 'LB' and resid 13 through 18' Processing helix chain 'LB' and resid 111 through 120 removed outlier: 4.013A pdb=" N ARGLB 117 " --> pdb=" O GLULB 113 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHELB 118 " --> pdb=" O VALLB 114 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYRLB 119 " --> pdb=" O LYSLB 115 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYSLB 120 " --> pdb=" O ARGLB 116 " (cutoff:3.500A) Processing helix chain 'LB' and resid 130 through 139 removed outlier: 3.759A pdb=" N LYSLB 135 " --> pdb=" O THRLB 131 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYSLB 136 " --> pdb=" O LYSLB 132 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TYRLB 137 " --> pdb=" O TYRLB 133 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALALB 138 " --> pdb=" O ALALB 134 " (cutoff:3.500A) Processing helix chain 'LB' and resid 142 through 155 Processing helix chain 'LB' and resid 166 through 171 removed outlier: 4.271A 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: 3.918A 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: 4.090A 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: 3.547A pdb=" N LEULB 388 " --> pdb=" O LEULB 384 " (cutoff:3.500A) Processing helix chain 'LC' and resid 24 through 29 removed outlier: 4.781A pdb=" N SERLC 28 " --> pdb=" O PROLC 24 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALALC 29 " --> pdb=" O LYSLC 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 24 through 29' Processing helix chain 'LC' and resid 32 through 47 removed outlier: 4.104A pdb=" N LYSLC 45 " --> pdb=" O THRLC 41 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASNLC 46 " --> pdb=" O GLYLC 42 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYSLC 47 " --> pdb=" O METLC 43 " (cutoff:3.500A) Processing helix chain 'LC' and resid 115 through 133 removed outlier: 3.693A pdb=" N ALALC 131 " --> pdb=" O LEULC 127 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VALLC 132 " --> pdb=" O ALALC 128 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ALALC 133 " --> pdb=" O ALALC 129 " (cutoff:3.500A) Processing helix chain 'LC' and resid 134 through 140 Processing helix chain 'LC' and resid 154 through 159 removed outlier: 3.991A 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: 4.053A pdb=" N LYSLC 189 " --> pdb=" O VALLC 185 " (cutoff:3.500A) Processing helix chain 'LC' and resid 194 through 200 removed outlier: 4.700A pdb=" N METLC 198 " --> pdb=" O GLYLC 194 " (cutoff:3.500A) Processing helix chain 'LC' and resid 220 through 228 removed outlier: 4.084A pdb=" N LYSLC 224 " --> pdb=" O LYSLC 220 " (cutoff:3.500A) removed outlier: 4.620A 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: 4.974A pdb=" N ASPLC 266 " --> pdb=" O ILELC 262 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALALC 267 " --> pdb=" O LYSLC 263 " (cutoff:3.500A) removed outlier: 3.684A 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: 4.482A pdb=" N VALLC 299 " --> pdb=" O GLULC 295 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEULC 300 " --> pdb=" O ILELC 296 " (cutoff:3.500A) Processing helix chain 'LC' and resid 318 through 323 removed outlier: 4.690A 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: 4.577A pdb=" N THRLC 335 " --> pdb=" O PROLC 331 " (cutoff:3.500A) Processing helix chain 'LC' and resid 355 through 364 removed outlier: 3.515A pdb=" N LYSLC 359 " --> pdb=" O PROLC 355 " (cutoff:3.500A) Processing helix chain 'LC' and resid 214 through 219 removed outlier: 3.896A 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: 3.708A pdb=" N ARGLD 35 " --> pdb=" O TYRLD 31 " (cutoff:3.500A) Processing helix chain 'LD' and resid 79 through 87 removed outlier: 3.996A pdb=" N LEULD 83 " --> pdb=" O TYRLD 79 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ARGLD 84 " --> pdb=" O SERLD 80 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ALALD 85 " --> pdb=" O HISLD 81 " (cutoff:3.500A) removed outlier: 4.329A 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: 3.679A 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: 4.071A pdb=" N LEULD 239 " --> pdb=" O GLULD 235 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLULD 240 " --> pdb=" O ALALD 236 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLULD 241 " --> pdb=" O ASPLD 237 " (cutoff:3.500A) Processing helix chain 'LD' and resid 266 through 278 removed outlier: 3.700A 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: 3.885A pdb=" N VALLE 102 " --> pdb=" O ASNLE 98 " (cutoff:3.500A) removed outlier: 5.799A 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: 4.742A pdb=" N ALALE 168 " --> pdb=" O ALALE 164 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEULE 169 " --> pdb=" O ILELE 165 " (cutoff:3.500A) Processing helix chain 'LE' and resid 178 through 186 removed outlier: 5.293A pdb=" N SERLE 186 " --> pdb=" O TYRLE 182 " (cutoff:3.500A) Processing helix chain 'LF' and resid 8 through 14 removed outlier: 3.522A pdb=" N ILELF 12 " --> pdb=" O THRLF 8 " (cutoff:3.500A) Processing helix chain 'LF' and resid 15 through 34 removed outlier: 5.091A pdb=" N GLULF 31 " --> pdb=" O LYSLF 27 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ARGLF 32 " --> pdb=" O ALALF 28 " (cutoff:3.500A) Processing helix chain 'LF' and resid 35 through 79 removed outlier: 3.755A pdb=" N GLULF 45 " --> pdb=" O GLNLF 41 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLNLF 48 " --> pdb=" O LYSLF 44 " (cutoff:3.500A) Processing helix chain 'LF' and resid 102 through 113 Processing helix chain 'LF' and resid 126 through 137 removed outlier: 3.923A pdb=" N METLF 132 " --> pdb=" O ALALF 128 " (cutoff:3.500A) Processing helix chain 'LF' and resid 146 through 157 Processing helix chain 'LF' and resid 171 through 179 removed outlier: 4.162A 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: 5.116A pdb=" N TRPLF 209 " --> pdb=" O ALALF 205 " (cutoff:3.500A) Processing helix chain 'LF' and resid 240 through 249 removed outlier: 3.819A 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: 5.086A pdb=" N PHELG 81 " --> pdb=" O ALALG 77 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLNLG 82 " --> pdb=" O ILELG 78 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYRLG 83 " --> pdb=" O ALALG 79 " (cutoff:3.500A) Processing helix chain 'LG' and resid 86 through 101 removed outlier: 4.156A pdb=" N LYSLG 99 " --> pdb=" O LYSLG 95 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TYRLG 100 " --> pdb=" O LEULG 96 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARGLG 101 " --> pdb=" O LEULG 97 " (cutoff:3.500A) Processing helix chain 'LG' and resid 104 through 122 Processing helix chain 'LG' and resid 124 through 129 removed outlier: 3.892A pdb=" N VALLG 128 " --> pdb=" O LYSLG 124 " (cutoff:3.500A) Processing helix chain 'LG' and resid 138 through 149 Processing helix chain 'LG' and resid 168 through 177 Processing helix chain 'LG' and resid 185 through 194 removed outlier: 3.557A pdb=" N LEULG 192 " --> pdb=" O ARGLG 188 " (cutoff:3.500A) Processing helix chain 'LG' and resid 207 through 230 removed outlier: 4.670A pdb=" N ASNLG 212 " --> pdb=" O SERLG 208 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N GLULG 213 " --> pdb=" O GLULG 209 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEULG 226 " --> pdb=" O LYSLG 222 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLULG 227 " --> pdb=" O GLULG 223 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LYSLG 228 " --> pdb=" O GLYLG 224 " (cutoff:3.500A) Processing helix chain 'LG' and resid 231 through 236 removed outlier: 4.218A pdb=" N ARGLG 235 " --> pdb=" O ASPLG 231 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N TRPLG 236 " --> pdb=" O THRLG 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'LG' and resid 231 through 236' Processing helix chain 'LG' and resid 242 through 259 Processing helix chain 'LH' and resid 98 through 121 removed outlier: 3.956A pdb=" N LEULH 105 " --> pdb=" O ASPLH 101 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARGLH 106 " --> pdb=" O VALLH 102 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THRLH 107 " --> pdb=" O ALALH 103 " (cutoff:3.500A) Processing helix chain 'LH' and resid 189 through 205 removed outlier: 3.870A pdb=" N CYSLH 204 " --> pdb=" O ILELH 200 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYSLH 205 " --> pdb=" O GLNLH 201 " (cutoff:3.500A) Processing helix chain 'LH' and resid 210 through 215 removed outlier: 4.990A 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: 4.172A pdb=" N LEULJ 113 " --> pdb=" O GLULJ 109 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLYLJ 114 " --> pdb=" O HISLJ 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'LJ' and resid 109 through 114' Processing helix chain 'LJ' and resid 136 through 142 removed outlier: 4.874A pdb=" N ALALJ 140 " --> pdb=" O GLYLJ 136 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYSLJ 141 " --> pdb=" O GLULJ 137 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 150 through 155 removed outlier: 5.871A pdb=" N ILELJ 155 " --> pdb=" O ALALJ 151 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 156 through 168 Processing helix chain 'LK' and resid 23 through 29 removed outlier: 4.755A pdb=" N ALALK 27 " --> pdb=" O GLYLK 23 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEULK 28 " --> pdb=" O ALALK 24 " (cutoff:3.500A) Processing helix chain 'LK' and resid 30 through 36 Proline residue: LK 34 - end of helix No H-bonds generated for 'chain 'LK' and resid 30 through 36' Processing helix chain 'LK' and resid 38 through 51 Processing helix chain 'LK' and resid 76 through 86 removed outlier: 3.981A pdb=" N LYSLK 86 " --> pdb=" O ILELK 82 " (cutoff:3.500A) Processing helix chain 'LK' and resid 105 through 117 Processing helix chain 'LK' and resid 124 through 140 Processing helix chain 'LK' and resid 147 through 158 Processing helix chain 'LL' and resid 17 through 22 removed outlier: 4.673A pdb=" N ARGLL 21 " --> pdb=" O HISLL 17 " (cutoff:3.500A) removed outlier: 3.718A 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: 3.795A pdb=" N GLYLL 94 " --> pdb=" O ALALL 90 " (cutoff:3.500A) Processing helix chain 'LL' and resid 105 through 123 removed outlier: 3.955A pdb=" N LEULL 109 " --> pdb=" O SERLL 105 " (cutoff:3.500A) Processing helix chain 'LL' and resid 139 through 144 removed outlier: 4.119A 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: 3.824A pdb=" N ALALM 62 " --> pdb=" O PROLM 58 " (cutoff:3.500A) removed outlier: 5.304A 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: 5.351A pdb=" N ASNLM 98 " --> pdb=" O TRPLM 94 " (cutoff:3.500A) Processing helix chain 'LM' and resid 99 through 112 removed outlier: 3.740A pdb=" N LEULM 112 " --> pdb=" O ARGLM 108 " (cutoff:3.500A) Processing helix chain 'LM' and resid 113 through 140 Processing helix chain 'LN' and resid 2 through 14 removed outlier: 4.701A pdb=" N TYRLN 6 " --> pdb=" O GLYLN 2 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYSLN 13 " --> pdb=" O GLULN 9 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYSLN 14 " --> pdb=" O LEULN 10 " (cutoff:3.500A) Processing helix chain 'LN' and resid 16 through 34 removed outlier: 4.740A 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: 3.701A 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: 4.467A pdb=" N CYSLN 152 " --> pdb=" O ILELN 148 " (cutoff:3.500A) removed outlier: 4.197A 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 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: 3.835A pdb=" N ALALO 51 " --> pdb=" O GLULO 47 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYSLO 61 " --> pdb=" O ALALO 57 " (cutoff:3.500A) Processing helix chain 'LO' and resid 77 through 91 removed outlier: 3.821A pdb=" N METLO 89 " --> pdb=" O ALALO 85 " (cutoff:3.500A) removed outlier: 3.616A 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: 3.643A pdb=" N ARGLO 103 " --> pdb=" O ALALO 99 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEULO 104 " --> pdb=" O ALALO 100 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LYSLO 105 " --> pdb=" O LEULO 101 " (cutoff:3.500A) Processing helix chain 'LO' and resid 112 through 118 removed outlier: 7.850A pdb=" N LYSLO 116 " --> pdb=" O PROLO 112 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYSLO 117 " --> pdb=" O PROLO 113 " (cutoff:3.500A) removed outlier: 5.538A 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 152 through 188 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: 4.826A 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: 3.959A pdb=" N LYSLQ 74 " --> pdb=" O ALALQ 70 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N SERLQ 83 " --> pdb=" O ARGLQ 79 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 91 through 100 removed outlier: 3.809A 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: 3.800A pdb=" N VALLR 22 " --> pdb=" O GLYLR 18 " (cutoff:3.500A) removed outlier: 6.055A 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: 3.627A pdb=" N ALALR 35 " --> pdb=" O GLULR 31 " (cutoff:3.500A) removed outlier: 5.493A 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: 5.634A 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: 6.703A 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: 3.687A pdb=" N ILELS 121 " --> pdb=" O ARGLS 117 " (cutoff:3.500A) removed outlier: 5.635A 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: 4.495A pdb=" N LEULS 143 " --> pdb=" O TYRLS 139 " (cutoff:3.500A) Processing helix chain 'LT' and resid 92 through 97 removed outlier: 3.990A pdb=" N VALLT 96 " --> pdb=" O ARGLT 92 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LYSLT 97 " --> pdb=" O ILELT 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'LT' and resid 92 through 97' Processing helix chain 'LT' and resid 102 through 123 Processing helix chain 'LT' and resid 155 through 160 Processing helix chain 'LU' and resid 25 through 32 Processing helix chain 'LU' and resid 35 through 47 Processing helix chain 'LU' and resid 79 through 95 Processing helix chain 'LV' and resid 68 through 73 removed outlier: 4.319A pdb=" N LYSLV 73 " --> pdb=" O PROLV 69 " (cutoff:3.500A) Processing helix chain 'LV' and resid 121 through 128 Processing helix chain 'LV' and resid 129 through 135 Processing helix chain 'LX' and resid 12 through 29 Processing helix chain 'LX' and resid 71 through 77 removed outlier: 4.899A pdb=" N ILELX 77 " --> pdb=" O HISLX 73 " (cutoff:3.500A) Processing helix chain 'LX' and resid 82 through 92 removed outlier: 3.686A 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: 3.593A pdb=" N VALLY 28 " --> pdb=" O SERLY 24 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SERLY 31 " --> pdb=" O ARGLY 27 " (cutoff:3.500A) Processing helix chain 'LY' and resid 35 through 43 Processing helix chain 'LY' and resid 99 through 104 removed outlier: 3.974A pdb=" N VALLY 103 " --> pdb=" O HISLY 99 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VALLY 104 " --> pdb=" O PROLY 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'LY' and resid 99 through 104' Processing helix chain 'LY' and resid 111 through 133 Processing helix chain 'LZ' and resid 57 through 66 removed outlier: 4.258A pdb=" N LYSLZ 66 " --> pdb=" O GLULZ 62 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 75 through 80 removed outlier: 3.532A pdb=" N LEULZ 79 " --> pdb=" O ASNLZ 75 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N METLZ 80 " --> pdb=" O TYRLZ 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'LZ' and resid 75 through 80' Processing helix chain 'LZ' and resid 96 through 103 removed outlier: 4.231A pdb=" N PHELZ 100 " --> pdb=" O ASNLZ 96 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSLZ 101 " --> pdb=" O ALALZ 97 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLULZ 102 " --> pdb=" O ASPLZ 98 " (cutoff:3.500A) Proline residue: LZ 103 - end of helix No H-bonds generated for 'chain 'LZ' and resid 96 through 103' Processing helix chain 'LZ' and resid 104 through 124 Processing helix chain 'LZ' and resid 126 through 132 removed outlier: 3.820A pdb=" N PHELZ 130 " --> pdb=" O ASNLZ 126 " (cutoff:3.500A) Proline residue: LZ 132 - end of helix Processing helix chain 'La' and resid 6 through 12 removed outlier: 3.847A pdb=" N LYSLa 10 " --> pdb=" O SERLa 6 " (cutoff:3.500A) Processing helix chain 'La' and resid 64 through 69 removed outlier: 4.472A pdb=" N TYRLa 68 " --> pdb=" O LEULa 64 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRPLa 69 " --> pdb=" O ARGLa 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'La' and resid 64 through 69' Processing helix chain 'La' and resid 74 through 83 removed outlier: 3.624A pdb=" N LEULa 78 " --> pdb=" O ASNLa 74 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TRPLa 79 " --> pdb=" O ILELa 75 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N SERLa 80 " --> pdb=" O ASPLa 76 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEULa 81 " --> pdb=" O LYSLa 77 " (cutoff:3.500A) removed outlier: 4.063A 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: 3.681A pdb=" N HISLa 107 " --> pdb=" O ASPLa 103 " (cutoff:3.500A) Processing helix chain 'La' and resid 131 through 142 Processing helix chain 'Lc' and resid 12 through 24 Processing helix chain 'Lc' and resid 29 through 40 Processing helix chain 'Lc' and resid 52 through 67 Processing helix chain 'Lc' and resid 76 through 85 Processing helix chain 'Ld' and resid 23 through 29 removed outlier: 4.001A 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: 4.892A pdb=" N LYSLe 27 " --> pdb=" O SERLe 23 " (cutoff:3.500A) Processing helix chain 'Le' and resid 41 through 46 Processing helix chain 'Le' and resid 79 through 87 removed outlier: 3.721A pdb=" N LEULe 85 " --> pdb=" O LYSLe 81 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEULe 86 " --> pdb=" O ASPLe 82 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEULe 87 " --> pdb=" O VALLe 83 " (cutoff:3.500A) Processing helix chain 'Le' and resid 102 through 117 Processing helix chain 'Lf' and resid 39 through 47 removed outlier: 4.086A pdb=" N PHELf 45 " --> pdb=" O ALALf 41 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TYRLf 46 " --> pdb=" O ALALf 42 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEULf 47 " --> pdb=" O ALALf 43 " (cutoff:3.500A) Processing helix chain 'Lg' and resid 59 through 67 removed outlier: 3.932A pdb=" N TYRLg 63 " --> pdb=" O ARGLg 59 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ALALg 64 " --> pdb=" O PROLg 60 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THRLg 65 " --> pdb=" O ARGLg 61 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILELg 66 " --> pdb=" O GLULg 62 " (cutoff:3.500A) removed outlier: 5.708A 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 68 through 73 removed outlier: 5.221A pdb=" N VALLg 73 " --> pdb=" O PROLg 69 " (cutoff:3.500A) Processing helix chain 'Lg' and resid 82 through 119 Processing helix chain 'Lh' and resid 8 through 16 removed outlier: 4.258A pdb=" N SERLh 14 " --> pdb=" O GLYLh 10 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYSLh 15 " --> pdb=" O GLNLh 11 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ASNLh 16 " --> pdb=" O LEULh 12 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 17 through 41 removed outlier: 3.688A pdb=" N ILELh 36 " --> pdb=" O SERLh 32 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 44 through 76 removed outlier: 4.029A pdb=" N LYSLh 48 " --> pdb=" O ALALh 44 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 82 through 87 Proline residue: Lh 87 - end of helix Processing helix chain 'Lh' and resid 90 through 96 Processing helix chain 'Lh' and resid 98 through 104 Processing helix chain 'Lh' and resid 106 through 116 Processing helix chain 'Li' and resid 34 through 39 removed outlier: 3.851A pdb=" N ARGLi 38 " --> pdb=" O ARGLi 34 " (cutoff:3.500A) removed outlier: 4.717A 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: 3.737A pdb=" N GLYLj 9 " --> pdb=" O THRLj 5 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYSLj 10 " --> pdb=" O SERLj 6 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARGLj 11 " --> pdb=" O SERLj 7 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 50 through 58 removed outlier: 3.765A pdb=" N LYSLj 57 " --> pdb=" O ALALj 53 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 65 through 77 removed outlier: 5.553A pdb=" N THRLj 69 " --> pdb=" O ARGLj 65 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VALLj 70 " --> pdb=" O TYRLj 66 " (cutoff:3.500A) Proline residue: Lj 71 - end of helix Processing helix chain 'Lk' and resid 7 through 17 Processing helix chain 'Lk' and resid 52 through 63 removed outlier: 4.213A pdb=" N LYSLk 59 " --> pdb=" O ALALk 55 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLNLk 60 " --> pdb=" O GLULk 56 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SERLk 61 " --> pdb=" O LYSLk 57 " (cutoff:3.500A) Proline residue: Lk 63 - end of helix Processing helix chain 'Ll' and resid 6 through 21 removed outlier: 5.401A pdb=" N ARGLl 21 " --> pdb=" O GLNLl 17 " (cutoff:3.500A) Processing helix chain 'Ll' and resid 24 through 30 removed outlier: 4.532A pdb=" N ARGLl 28 " --> pdb=" O PROLl 24 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEULl 29 " --> pdb=" O GLNLl 25 " (cutoff:3.500A) removed outlier: 3.917A 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: 4.047A pdb=" N LYSLp 28 " --> pdb=" O LYSLp 24 " (cutoff:3.500A) removed outlier: 4.359A 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: 5.409A pdb=" N ASPLq 49 " --> pdb=" O GLYLq 45 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 86 through 99 Processing helix chain 'Lq' and resid 104 through 124 removed outlier: 4.152A pdb=" N ARGLq 108 " --> pdb=" O ARGLq 104 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLNLq 109 " --> pdb=" O ALALq 105 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ALALq 110 " --> pdb=" O ASPLq 106 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARGLq 123 " --> pdb=" O LEULq 119 " (cutoff:3.500A) Proline residue: Lq 124 - end of helix Processing sheet with id= 1, first strand: chain 'CB' and resid 80 through 83 Processing sheet with id= 2, first strand: chain 'CB' and resid 97 through 100 Processing sheet with id= 3, first strand: chain 'CB' and resid 239 through 245 removed outlier: 5.714A pdb=" N THRCB 239 " --> pdb=" O THRCB 68 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILECB 62 " --> pdb=" O VALCB 245 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N PHECB 281 " --> pdb=" O ILECB 293 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'CF' and resid 63 through 67 removed outlier: 6.833A pdb=" N VALCF 42 " --> pdb=" O LEUCF 224 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'CF' and resid 135 through 138 removed outlier: 6.759A pdb=" N VALCF 135 " --> pdb=" O ILECF 194 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'CF' and resid 172 through 175 Processing sheet with id= 7, first strand: chain 'CF' and resid 232 through 236 removed outlier: 3.528A pdb=" N GLUCF 233 " --> pdb=" O SERCF 228 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'CF' and resid 38 through 42 removed outlier: 8.268A pdb=" N GLNCF 38 " --> pdb=" O SERCF 229 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLYCF 225 " --> pdb=" O VALCF 42 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'CH' and resid 203 through 209 removed outlier: 4.935A pdb=" N ARGCH 167 " --> pdb=" O ARGCH 214 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THRCH 220 " --> pdb=" O VALCH 171 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLYCH 173 " --> pdb=" O THRCH 220 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N METCH 281 " --> pdb=" O ALACH 247 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'CI' and resid 214 through 219 removed outlier: 4.914A pdb=" N ARGCI 230 " --> pdb=" O VALCI 219 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N VALCI 188 " --> pdb=" O VALCI 263 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'CJ' and resid 186 through 191 removed outlier: 3.748A pdb=" N GLYCJ 194 " --> pdb=" O SERCJ 191 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'CJ' and resid 394 through 397 Processing sheet with id= 13, first strand: chain 'CK' and resid 148 through 151 Processing sheet with id= 14, first strand: chain 'CK' and resid 190 through 195 removed outlier: 3.559A pdb=" N VALCK 191 " --> pdb=" O HISCK 186 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ASNCK 256 " --> pdb=" O THRCK 246 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N TYRCK 242 " --> pdb=" O LEUCK 260 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THRCK 219 " --> pdb=" O ILECK 245 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'CM' and resid 139 through 144 removed outlier: 5.721A pdb=" N TRPCM 139 " --> pdb=" O ILECM 95 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYSCM 88 " --> pdb=" O VALCM 125 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASNCM 119 " --> pdb=" O ARGCM 94 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ASNCM 118 " --> pdb=" O LEUCM 213 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'CN' and resid 1 through 4 Processing sheet with id= 17, first strand: chain 'CN' and resid 23 through 27 Processing sheet with id= 18, first strand: chain 'CN' and resid 69 through 73 Processing sheet with id= 19, first strand: chain 'CN' and resid 114 through 117 Processing sheet with id= 20, first strand: chain 'CN' and resid 158 through 161 Processing sheet with id= 21, first strand: chain 'CQ' and resid 3 through 6 removed outlier: 4.698A pdb=" N ARGCQ 11 " --> pdb=" O CYSCQ 6 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'CQ' and resid 18 through 23 removed outlier: 3.883A pdb=" N LYSCQ 27 " --> pdb=" O ARGCQ 23 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'Cb' and resid 50 through 53 removed outlier: 4.651A pdb=" N TYRCb 50 " --> pdb=" O PHECb 59 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'Cd' and resid 293 through 297 removed outlier: 3.936A pdb=" N CYSCd 378 " --> pdb=" O LEUCd 331 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLYCd 333 " --> pdb=" O CYSCd 378 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILECd 373 " --> pdb=" O LEUCd 369 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'Cf' and resid 56 through 60 removed outlier: 5.392A pdb=" N ARGCf 34 " --> pdb=" O PHECf 60 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N SERCf 92 " --> pdb=" O GLYCf 35 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N HISCf 98 " --> pdb=" O LEUCf 118 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N LEUCf 111 " --> pdb=" O PROCf 263 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ARGCf 259 " --> pdb=" O GLUCf 115 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'Cf' and resid 140 through 146 removed outlier: 6.771A pdb=" N VALCf 229 " --> pdb=" O HISCf 249 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'Cf' and resid 287 through 290 removed outlier: 4.802A pdb=" N ASPCf 294 " --> pdb=" O ASPCf 290 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'Cg' and resid 21 through 25 Processing sheet with id= 29, first strand: chain 'Cg' and resid 71 through 75 removed outlier: 4.237A pdb=" N THRCg 71 " --> pdb=" O THRCg 82 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'Cg' and resid 124 through 129 removed outlier: 8.744A pdb=" N ASNCg 124 " --> pdb=" O LYSCg 137 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LYSCg 137 " --> pdb=" O ASNCg 124 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'Ch' and resid 52 through 56 removed outlier: 4.136A pdb=" N THRCh 121 " --> pdb=" O HISCh 88 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LEUCh 94 " --> pdb=" O ILECh 89 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Ch' and resid 139 through 143 removed outlier: 5.080A pdb=" N ALACh 511 " --> pdb=" O GLYCh 507 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLYCh 507 " --> pdb=" O ALACh 511 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N LEUCh 502 " --> pdb=" O ALACh 497 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Ch' and resid 151 through 155 removed outlier: 6.358A pdb=" N ARGCh 161 " --> pdb=" O SERCh 155 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SERCh 160 " --> pdb=" O THRCh 176 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THRCh 170 " --> pdb=" O SERCh 166 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILECh 173 " --> pdb=" O LYSCh 182 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'Ch' and resid 193 through 198 removed outlier: 5.602A pdb=" N TYRCh 203 " --> pdb=" O SERCh 198 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THRCh 212 " --> pdb=" O SERCh 208 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'Ch' and resid 236 through 241 removed outlier: 5.855A pdb=" N ARGCh 252 " --> pdb=" O GLNCh 241 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ALACh 251 " --> pdb=" O VALCh 267 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THRCh 261 " --> pdb=" O SERCh 257 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILECh 264 " --> pdb=" O GLUCh 273 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARGCh 271 " --> pdb=" O LEUCh 266 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'Ch' and resid 284 through 289 removed outlier: 4.044A pdb=" N LEUCh 293 " --> pdb=" O GLYCh 289 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N ASPCh 292 " --> pdb=" O ALACh 308 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SERCh 302 " --> pdb=" O SERCh 298 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VALCh 305 " --> pdb=" O VALCh 314 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THRCh 312 " --> pdb=" O ASPCh 307 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'Ch' and resid 326 through 330 removed outlier: 3.715A pdb=" N HISCh 326 " --> pdb=" O ALACh 378 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARGCh 374 " --> pdb=" O SERCh 330 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THRCh 383 " --> pdb=" O SERCh 379 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'Ch' and resid 408 through 413 removed outlier: 5.737A pdb=" N LEUCh 418 " --> pdb=" O SERCh 413 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SERCh 427 " --> pdb=" O GLYCh 423 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYSCh 440 " --> pdb=" O LEUCh 430 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'Ch' and resid 451 through 455 removed outlier: 5.637A pdb=" N LEUCh 460 " --> pdb=" O SERCh 455 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ARGCh 459 " --> pdb=" O VALCh 475 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THRCh 469 " --> pdb=" O SERCh 465 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VALCh 472 " --> pdb=" O ALACh 481 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'Ch' and resid 170 through 173 Processing sheet with id= 41, first strand: chain 'Ch' and resid 261 through 264 removed outlier: 3.824A pdb=" N HISCh 274 " --> pdb=" O ILECh 264 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'Ch' and resid 302 through 305 Processing sheet with id= 43, first strand: chain 'Ch' and resid 469 through 472 Processing sheet with id= 44, first strand: chain 'LA' and resid 47 through 50 removed outlier: 3.530A pdb=" N GLULA 47 " --> pdb=" O ARGLA 60 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ARGLA 60 " --> pdb=" O LYSLA 46 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLNLA 86 " --> pdb=" O VALLA 45 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'LA' and resid 134 through 137 removed outlier: 6.431A pdb=" N ARGLA 147 " --> pdb=" O VALLA 137 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'LA' and resid 58 through 64 No H-bonds generated for sheet with id= 46 Processing sheet with id= 47, first strand: chain 'LA' and resid 145 through 150 removed outlier: 4.086A pdb=" N ALALA 154 " --> pdb=" O LEULA 150 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'LB' and resid 41 through 44 removed outlier: 6.322A pdb=" N GLNLB 183 " --> pdb=" O THRLB 44 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N HISLB 178 " --> pdb=" O THRLB 165 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N VALLB 159 " --> pdb=" O ILELB 184 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEULB 162 " --> pdb=" O VALLB 87 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYSLB 202 " --> pdb=" O VALLB 86 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'LB' and resid 53 through 58 removed outlier: 6.720A pdb=" N ILELB 78 " --> pdb=" O ALALB 51 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARGLB 335 " --> pdb=" O LYSLB 50 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILELB 336 " --> pdb=" O VALLB 221 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N VALLB 221 " --> pdb=" O ILELB 336 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N HISLB 274 " --> pdb=" O THRLB 222 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'LB' and resid 98 through 102 removed outlier: 6.983A pdb=" N GLYLB 91 " --> pdb=" O LEULB 102 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THRLB 103 " --> pdb=" O GLYLB 91 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'LB' and resid 285 through 289 removed outlier: 3.640A pdb=" N ARGLB 285 " --> pdb=" O METLB 324 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLYLB 289 " --> pdb=" O ASNLB 320 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASNLB 320 " --> pdb=" O GLYLB 289 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'LB' and resid 76 through 80 Processing sheet with id= 53, first strand: chain 'LB' and resid 88 through 93 No H-bonds generated for sheet with id= 53 Processing sheet with id= 54, first strand: chain 'LB' and resid 214 through 217 removed outlier: 4.425A pdb=" N GLULB 214 " --> pdb=" O ILELB 283 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'LC' and resid 5 through 9 removed outlier: 4.752A pdb=" N ALALC 19 " --> pdb=" O VALLC 9 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'LC' and resid 76 through 79 removed outlier: 4.364A pdb=" N GLNLC 88 " --> pdb=" O VALLC 78 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'LC' and resid 231 through 236 removed outlier: 5.257A pdb=" N PHELC 254 " --> pdb=" O GLYLC 208 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'LD' and resid 60 through 66 Processing sheet with id= 59, first strand: chain 'LE' and resid 5 through 9 Processing sheet with id= 60, first strand: chain 'LE' and resid 56 through 61 removed outlier: 4.052A pdb=" N THRLE 56 " --> pdb=" O LEULE 72 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYSLE 68 " --> pdb=" O LEULE 60 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'LF' and resid 139 through 144 removed outlier: 7.620A pdb=" N TRPLF 139 " --> pdb=" O ILELF 95 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYSLF 88 " --> pdb=" O VALLF 125 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASNLF 119 " --> pdb=" O ARGLF 94 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ASNLF 118 " --> pdb=" O LEULF 213 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'LF' and resid 158 through 162 removed outlier: 6.443A pdb=" N GLYLF 158 " --> pdb=" O LEULF 169 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'LG' and resid 179 through 184 Processing sheet with id= 64, first strand: chain 'LH' and resid 5 through 12 removed outlier: 5.921A pdb=" N GLYLH 88 " --> pdb=" O VALLH 12 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'LH' and resid 54 through 57 Processing sheet with id= 66, first strand: chain 'LH' and resid 137 through 144 removed outlier: 3.765A pdb=" N CYSLH 148 " --> pdb=" O ASNLH 143 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N TYRLH 149 " --> pdb=" O METLH 167 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'LH' and resid 171 through 176 removed outlier: 5.221A pdb=" N GLULH 182 " --> pdb=" O SERLH 176 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ASPLH 181 " --> pdb=" O TYRLH 129 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'LJ' and resid 46 through 50 removed outlier: 3.674A pdb=" N LYSLJ 17 " --> pdb=" O CYSLJ 131 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N SERLJ 23 " --> pdb=" O GLYLJ 125 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N GLYLJ 125 " --> pdb=" O SERLJ 23 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'LJ' and resid 90 through 93 Processing sheet with id= 70, first strand: chain 'LK' and resid 11 through 16 removed outlier: 4.370A pdb=" N THRLK 59 " --> pdb=" O VALLK 74 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'LL' and resid 56 through 59 Processing sheet with id= 72, first strand: chain 'LM' and resid 18 through 21 removed outlier: 4.680A pdb=" N ARGLM 18 " --> pdb=" O ILELM 30 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEULM 40 " --> pdb=" O VALLM 31 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'LN' and resid 35 through 39 removed outlier: 6.348A pdb=" N VALLN 35 " --> pdb=" O ARGLN 65 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILELN 61 " --> pdb=" O ALALN 39 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLYLN 58 " --> pdb=" O ASPLN 136 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILELN 133 " --> pdb=" O LEULN 116 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'LN' and resid 117 through 121 removed outlier: 3.639A pdb=" N ASNLN 117 " --> pdb=" O ILELN 133 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N TYRLN 129 " --> pdb=" O VALLN 121 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'LO' and resid 7 through 11 Processing sheet with id= 76, first strand: chain 'LP' and resid 14 through 20 Processing sheet with id= 77, first strand: chain 'LP' and resid 57 through 60 removed outlier: 5.351A pdb=" N ARGLP 80 " --> pdb=" O METLP 60 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'LP' and resid 124 through 131 removed outlier: 4.080A pdb=" N ARGLP 127 " --> pdb=" O TYRLP 139 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARGLP 135 " --> pdb=" O ARGLP 131 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'LQ' and resid 106 through 110 Processing sheet with id= 80, first strand: chain 'LQ' and resid 126 through 129 No H-bonds generated for sheet with id= 80 Processing sheet with id= 81, first strand: chain 'LS' and resid 24 through 30 removed outlier: 6.616A pdb=" N ILELS 10 " --> pdb=" O VALLS 59 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'LS' and resid 86 through 96 removed outlier: 5.120A pdb=" N ASNLS 74 " --> pdb=" O LEULS 129 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'LS' and resid 6 through 10 removed outlier: 4.706A pdb=" N GLULS 6 " --> pdb=" O ILELS 64 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'LT' and resid 38 through 43 removed outlier: 4.189A pdb=" N ASPLT 38 " --> pdb=" O VALLT 64 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYSLT 60 " --> pdb=" O ILELT 42 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALALT 71 " --> pdb=" O THRLT 68 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASNLT 66 " --> pdb=" O GLYLT 73 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'LT' and resid 72 through 80 Processing sheet with id= 86, first strand: chain 'LU' and resid 60 through 64 removed outlier: 5.390A pdb=" N GLYLU 108 " --> pdb=" O LYSLU 20 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'LV' and resid 22 through 26 removed outlier: 4.331A pdb=" N ALALV 23 " --> pdb=" O ILELV 38 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'LV' and resid 58 through 62 removed outlier: 4.239A pdb=" N ASPLV 58 " --> pdb=" O ILELV 80 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASPLV 99 " --> pdb=" O ALALV 84 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALALV 84 " --> pdb=" O ASPLV 99 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'LV' and resid 86 through 89 removed outlier: 3.842A pdb=" N VALLV 93 " --> pdb=" O ARGLV 89 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'LX' and resid 93 through 99 removed outlier: 6.822A pdb=" N ASNLX 93 " --> pdb=" O LEULX 139 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYSLX 133 " --> pdb=" O VALLX 99 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THRLX 132 " --> pdb=" O ARGLX 128 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYSLX 122 " --> pdb=" O ARGLX 138 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'LY' and resid 55 through 58 removed outlier: 4.217A pdb=" N LYSLY 65 " --> pdb=" O ILELY 57 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'LY' and resid 85 through 88 removed outlier: 4.633A pdb=" N GLNLY 92 " --> pdb=" O LYSLY 88 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'LZ' and resid 8 through 13 removed outlier: 4.472A pdb=" N ARGLZ 8 " --> pdb=" O ILELZ 24 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYSLZ 20 " --> pdb=" O VALLZ 12 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'LZ' and resid 41 through 44 Processing sheet with id= 95, first strand: chain 'La' and resid 99 through 102 Processing sheet with id= 96, first strand: chain 'Lc' and resid 25 through 28 removed outlier: 6.181A pdb=" N LYSLc 25 " --> pdb=" O LEULc 96 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'Ld' and resid 56 through 59 removed outlier: 5.057A pdb=" N ASPLd 56 " --> pdb=" O LEULd 97 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ALALd 17 " --> pdb=" O VALLd 117 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'Le' and resid 72 through 78 Processing sheet with id= 99, first strand: chain 'Lf' and resid 12 through 17 removed outlier: 5.967A pdb=" N LYSLf 12 " --> pdb=" O GLULf 35 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEULf 31 " --> pdb=" O LEULf 16 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARGLf 84 " --> pdb=" O THRLf 74 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYSLf 65 " --> pdb=" O ALALf 57 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYSLf 49 " --> pdb=" O ILELf 73 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARGLf 50 " --> pdb=" O METLf 103 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'Lf' and resid 10 through 16 removed outlier: 4.163A pdb=" N ALALf 98 " --> pdb=" O HISLf 15 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'Lg' and resid 20 through 25 removed outlier: 4.415A pdb=" N ARGLg 20 " --> pdb=" O ILELg 36 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'Lk' and resid 2 through 5 removed outlier: 4.711A pdb=" N VALLk 48 " --> pdb=" O VALLk 5 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SERLk 22 " --> pdb=" O ARGLk 39 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LYSLk 27 " --> pdb=" O VALLk 71 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 'Lp' and resid 47 through 50 removed outlier: 6.868A pdb=" N ILELp 54 " --> pdb=" O THRLp 50 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLYLp 53 " --> pdb=" O GLYLp 66 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYSLp 62 " --> pdb=" O CYSLp 57 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'Lq' and resid 19 through 22 removed outlier: 6.605A pdb=" N PHELq 19 " --> pdb=" O ARGLq 30 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain 'Lq' and resid 51 through 56 removed outlier: 5.226A pdb=" N ALALq 51 " --> pdb=" O LYSLq 66 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N SERLq 77 " --> pdb=" O LYSLq 67 " (cutoff:3.500A) 3741 hydrogen bonds defined for protein. 11115 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2665 hydrogen bonds 4458 hydrogen bond angles 0 basepair planarities 1051 basepair parallelities 1863 stacking parallelities Total time for adding SS restraints: 220.16 Time building geometry restraints manager: 62.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 23432 1.33 - 1.45: 61531 1.45 - 1.58: 73396 1.58 - 1.70: 6725 1.70 - 1.83: 419 Bond restraints: 165503 Sorted by residual: bond pdb=" C3' A2MC12289 " pdb=" C2' A2MC12289 " ideal model delta sigma weight residual 1.544 1.238 0.306 2.00e-02 2.50e+03 2.34e+02 bond pdb=" C3' A2MC11432 " pdb=" C2' A2MC11432 " ideal model delta sigma weight residual 1.544 1.241 0.303 2.00e-02 2.50e+03 2.30e+02 bond pdb=" C3' A2MC1 858 " pdb=" C2' A2MC1 858 " ideal model delta sigma weight residual 1.544 1.241 0.303 2.00e-02 2.50e+03 2.30e+02 bond pdb=" C3' A2MC1 389 " pdb=" C2' A2MC1 389 " ideal model delta sigma weight residual 1.544 1.241 0.303 2.00e-02 2.50e+03 2.29e+02 bond pdb=" C3' A2MC1 848 " pdb=" C2' A2MC1 848 " ideal model delta sigma weight residual 1.544 1.241 0.303 2.00e-02 2.50e+03 2.29e+02 ... (remaining 165498 not shown) Histogram of bond angle deviations from ideal: 97.18 - 106.93: 22396 106.93 - 116.68: 115631 116.68 - 126.42: 90747 126.42 - 136.17: 10930 136.17 - 145.92: 8 Bond angle restraints: 239712 Sorted by residual: angle pdb=" CA PROCJ 363 " pdb=" N PROCJ 363 " pdb=" CD PROCJ 363 " ideal model delta sigma weight residual 112.00 101.31 10.69 1.40e+00 5.10e-01 5.83e+01 angle pdb=" C1' OMGC1 385 " pdb=" N9 OMGC1 385 " pdb=" C4 OMGC1 385 " ideal model delta sigma weight residual 108.29 129.53 -21.24 3.00e+00 1.11e-01 5.01e+01 angle pdb=" C1' OMGC11433 " pdb=" N9 OMGC11433 " pdb=" C4 OMGC11433 " ideal model delta sigma weight residual 108.29 128.58 -20.29 3.00e+00 1.11e-01 4.57e+01 angle pdb=" C1' OMGC12578 " pdb=" N9 OMGC12578 " pdb=" C4 OMGC12578 " ideal model delta sigma weight residual 108.29 127.92 -19.63 3.00e+00 1.11e-01 4.28e+01 angle pdb=" C1' A2MC1 389 " pdb=" N9 A2MC1 389 " pdb=" C4 A2MC1 389 " ideal model delta sigma weight residual 126.51 145.92 -19.41 3.00e+00 1.11e-01 4.18e+01 ... (remaining 239707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 96145 35.99 - 71.98: 7929 71.98 - 107.97: 954 107.97 - 143.96: 19 143.96 - 179.95: 32 Dihedral angle restraints: 105079 sinusoidal: 74668 harmonic: 30411 Sorted by residual: dihedral pdb=" C4' CC13324 " pdb=" C3' CC13324 " pdb=" C2' CC13324 " pdb=" C1' CC13324 " ideal model delta sinusoidal sigma weight residual -35.00 34.03 -69.03 1 8.00e+00 1.56e-02 9.63e+01 dihedral pdb=" C5' CC13324 " pdb=" C4' CC13324 " pdb=" C3' CC13324 " pdb=" O3' CC13324 " ideal model delta sinusoidal sigma weight residual 147.00 78.90 68.10 1 8.00e+00 1.56e-02 9.40e+01 dihedral pdb=" O4' UC12100 " pdb=" C1' UC12100 " pdb=" N1 UC12100 " pdb=" C2 UC12100 " ideal model delta sinusoidal sigma weight residual 200.00 32.62 167.38 1 1.50e+01 4.44e-03 8.43e+01 ... (remaining 105076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 26933 0.074 - 0.147: 2144 0.147 - 0.221: 143 0.221 - 0.295: 22 0.295 - 0.368: 4 Chirality restraints: 29246 Sorted by residual: chirality pdb=" C3' CC13324 " pdb=" C4' CC13324 " pdb=" O3' CC13324 " pdb=" C2' CC13324 " both_signs ideal model delta sigma weight residual False -2.74 -2.38 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CB ILELF 101 " pdb=" CA ILELF 101 " pdb=" CG1 ILELF 101 " pdb=" CG2 ILELF 101 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.10e+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 2.66e+00 ... (remaining 29243 not shown) Planarity restraints: 18045 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMGC12578 " 0.066 2.00e-02 2.50e+03 6.03e-01 8.17e+03 pdb=" C4' OMGC12578 " 0.436 2.00e-02 2.50e+03 pdb=" O4' OMGC12578 " 0.639 2.00e-02 2.50e+03 pdb=" C3' OMGC12578 " -0.600 2.00e-02 2.50e+03 pdb=" O3' OMGC12578 " -0.644 2.00e-02 2.50e+03 pdb=" C2' OMGC12578 " -0.177 2.00e-02 2.50e+03 pdb=" O2' OMGC12578 " 0.983 2.00e-02 2.50e+03 pdb=" C1' OMGC12578 " 0.217 2.00e-02 2.50e+03 pdb=" N9 OMGC12578 " -0.920 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMGC1 627 " 0.076 2.00e-02 2.50e+03 5.86e-01 7.74e+03 pdb=" C4' OMGC1 627 " 0.419 2.00e-02 2.50e+03 pdb=" O4' OMGC1 627 " 0.566 2.00e-02 2.50e+03 pdb=" C3' OMGC1 627 " -0.606 2.00e-02 2.50e+03 pdb=" O3' OMGC1 627 " -0.636 2.00e-02 2.50e+03 pdb=" C2' OMGC1 627 " -0.172 2.00e-02 2.50e+03 pdb=" O2' OMGC1 627 " 0.994 2.00e-02 2.50e+03 pdb=" C1' OMGC1 627 " 0.227 2.00e-02 2.50e+03 pdb=" N9 OMGC1 627 " -0.868 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMGC12358 " -0.059 2.00e-02 2.50e+03 5.82e-01 7.63e+03 pdb=" C4' OMGC12358 " -0.429 2.00e-02 2.50e+03 pdb=" O4' OMGC12358 " -0.588 2.00e-02 2.50e+03 pdb=" C3' OMGC12358 " 0.596 2.00e-02 2.50e+03 pdb=" O3' OMGC12358 " 0.618 2.00e-02 2.50e+03 pdb=" C2' OMGC12358 " 0.182 2.00e-02 2.50e+03 pdb=" O2' OMGC12358 " -0.966 2.00e-02 2.50e+03 pdb=" C1' OMGC12358 " -0.226 2.00e-02 2.50e+03 pdb=" N9 OMGC12358 " 0.872 2.00e-02 2.50e+03 ... (remaining 18042 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 3464 2.65 - 3.21: 124005 3.21 - 3.77: 294062 3.77 - 4.34: 401238 4.34 - 4.90: 564637 Nonbonded interactions: 1387406 Sorted by model distance: nonbonded pdb=" O1B GTPCH 701 " pdb="MG MGCH 702 " model vdw 2.086 2.170 nonbonded pdb="MG MGCd1002 " pdb=" O HOHCd1102 " model vdw 2.089 2.170 nonbonded pdb=" OG SERCd 340 " pdb="MG MGCd1002 " model vdw 2.096 2.170 nonbonded pdb="MG MGCd1002 " pdb=" O2G GTPCd1003 " model vdw 2.097 2.170 nonbonded pdb="MG MGCd1001 " pdb=" O1G GTPCd1003 " model vdw 2.155 2.170 ... (remaining 1387401 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'CM' selection = (chain 'LF' and (resid 13 through 35 or resid 49 through 79 or resid 87 through \ 249)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.21 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.120 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: 0.150 Extract box with map and model: 29.760 Check model and map are aligned: 1.790 Set scattering table: 1.110 Process input model: 574.460 Find NCS groups from input model: 4.240 Set up NCS constraints: 0.510 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:10.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 632.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.306 165503 Z= 0.358 Angle : 0.736 21.239 239712 Z= 0.373 Chirality : 0.041 0.368 29246 Planarity : 0.019 0.603 18045 Dihedral : 20.941 179.954 85391 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.02 % Allowed : 0.17 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.23 (0.08), residues: 10348 helix: 0.59 (0.08), residues: 3991 sheet: 0.26 (0.13), residues: 1478 loop : -0.12 (0.08), residues: 4879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRPCQ 86 HIS 0.013 0.001 HISLX 66 PHE 0.036 0.002 PHECI 198 TYR 0.051 0.002 TYRCH 85 ARG 0.026 0.001 ARGCz 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20696 Ramachandran restraints generated. 10348 Oldfield, 0 Emsley, 10348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20696 Ramachandran restraints generated. 10348 Oldfield, 0 Emsley, 10348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 8932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1267 time to evaluate : 9.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CB 213 ASN cc_start: 0.8457 (t0) cc_final: 0.8062 (t0) REVERT: CH 509 ARG cc_start: 0.7746 (ttp-110) cc_final: 0.7535 (mtm110) REVERT: CI 274 LYS cc_start: 0.8879 (tttt) cc_final: 0.8613 (tttt) REVERT: Cb 79 LYS cc_start: 0.8107 (ttmt) cc_final: 0.7756 (pttt) REVERT: Cd 392 ASP cc_start: 0.7722 (m-30) cc_final: 0.7364 (m-30) REVERT: Ce 384 VAL cc_start: 0.9004 (m) cc_final: 0.8800 (m) REVERT: Cg 53 SER cc_start: 0.8589 (p) cc_final: 0.8163 (p) REVERT: LE 161 ASP cc_start: 0.8201 (m-30) cc_final: 0.7923 (m-30) REVERT: LH 127 MET cc_start: 0.8501 (mtp) cc_final: 0.8280 (mtp) REVERT: LJ 110 HIS cc_start: 0.7697 (p-80) cc_final: 0.7378 (p90) REVERT: LJ 124 TYR cc_start: 0.7649 (m-80) cc_final: 0.7201 (m-80) REVERT: LY 111 ASP cc_start: 0.7620 (p0) cc_final: 0.7384 (p0) outliers start: 1 outliers final: 7 residues processed: 1267 average time/residue: 2.4129 time to fit residues: 4334.6941 Evaluate side-chains 1015 residues out of total 8932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1008 time to evaluate : 8.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CI residue 213 ILE Chi-restraints excluded: chain CJ residue 468 GLU Chi-restraints excluded: chain CK residue 65 ILE Chi-restraints excluded: chain CN residue 234 ASN Chi-restraints excluded: chain LE residue 165 ILE Chi-restraints excluded: chain LN residue 92 LEU Chi-restraints excluded: chain Li residue 67 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1358 random chunks: chunk 1146 optimal weight: 8.9990 chunk 1029 optimal weight: 0.0070 chunk 571 optimal weight: 2.9990 chunk 351 optimal weight: 9.9990 chunk 694 optimal weight: 6.9990 chunk 549 optimal weight: 4.9990 chunk 1064 optimal weight: 0.7980 chunk 411 optimal weight: 0.0770 chunk 647 optimal weight: 6.9990 chunk 792 optimal weight: 0.9990 chunk 1233 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CB 73 HIS CB 132 HIS CF 29 ASN CF 159 HIS CH 389 ASN CH 499 HIS CH 641 HIS ** CI 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 79 GLN CK 53 GLN CK 72 ASN CQ 24 ASN ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cd 303 ASN Ce 216 ASN Ce 346 GLN Cf 26 ASN Cf 54 GLN Cf 279 GLN Cg 31 ASN Cg 34 ASN Cg 64 ASN Ch 64 ASN LC 38 HIS LD 249 GLN LF 48 GLN LG 62 GLN LG 194 HIS LH 5 HIS LH 139 ASN LH 155 ASN LJ 96 ASN LJ 102 ASN ** LK 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LK 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LL 159 GLN LM 24 ASN LM 106 GLN ** LN 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 111 ASN LP 121 GLN LR 3 ASN LY 43 ASN LY 127 GLN LZ 30 GLN Ld 108 ASN Lp 29 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 165503 Z= 0.128 Angle : 0.613 16.574 239712 Z= 0.329 Chirality : 0.035 0.248 29246 Planarity : 0.006 0.126 18045 Dihedral : 22.588 179.849 63920 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.09 % Allowed : 7.41 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.00 (0.08), residues: 10348 helix: 1.55 (0.08), residues: 4006 sheet: 0.26 (0.13), residues: 1490 loop : 0.16 (0.08), residues: 4852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRPCg 105 HIS 0.011 0.001 HISCF 159 PHE 0.021 0.001 PHELJ 58 TYR 0.020 0.001 TYRCH 85 ARG 0.011 0.000 ARGCe 267 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20696 Ramachandran restraints generated. 10348 Oldfield, 0 Emsley, 10348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20696 Ramachandran restraints generated. 10348 Oldfield, 0 Emsley, 10348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1168 residues out of total 8932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1073 time to evaluate : 9.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CB 105 GLN cc_start: 0.8617 (pt0) cc_final: 0.8373 (pt0) REVERT: CB 213 ASN cc_start: 0.8290 (t0) cc_final: 0.7880 (t0) REVERT: CH 509 ARG cc_start: 0.7738 (ttp-110) cc_final: 0.7489 (mtm110) REVERT: CI 274 LYS cc_start: 0.8860 (tttt) cc_final: 0.8625 (tttt) REVERT: CI 305 LYS cc_start: 0.7724 (pptt) cc_final: 0.6976 (pptt) REVERT: CM 110 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7923 (tm-30) REVERT: CM 225 PHE cc_start: 0.7172 (m-80) cc_final: 0.6902 (m-80) REVERT: CN 151 TYR cc_start: 0.8906 (m-80) cc_final: 0.8690 (m-80) REVERT: CN 219 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: Cb 24 ARG cc_start: 0.6172 (mmm-85) cc_final: 0.5941 (mtm110) REVERT: Cb 68 HIS cc_start: 0.7264 (OUTLIER) cc_final: 0.7049 (p90) REVERT: Cb 76 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8432 (ttm-80) REVERT: Cb 79 LYS cc_start: 0.8095 (ttmt) cc_final: 0.7856 (pttt) REVERT: Cd 392 ASP cc_start: 0.7684 (m-30) cc_final: 0.7341 (m-30) REVERT: Ce 384 VAL cc_start: 0.9012 (m) cc_final: 0.8787 (m) REVERT: Cf 253 MET cc_start: 0.8776 (mtt) cc_final: 0.8563 (mtt) REVERT: Cg 53 SER cc_start: 0.8565 (p) cc_final: 0.8294 (p) REVERT: LA 51 ASP cc_start: 0.8152 (t70) cc_final: 0.7903 (t70) REVERT: LF 171 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7353 (m-30) REVERT: LH 1 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7583 (ttt) REVERT: LH 109 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7596 (ttp-170) REVERT: LH 127 MET cc_start: 0.8472 (mtp) cc_final: 0.8269 (mtp) REVERT: LJ 110 HIS cc_start: 0.7734 (p-80) cc_final: 0.7394 (p90) REVERT: LJ 124 TYR cc_start: 0.7588 (m-80) cc_final: 0.7318 (m-80) REVERT: LK 117 ARG cc_start: 0.8157 (tpm-80) cc_final: 0.7943 (tpm-80) REVERT: LO 62 MET cc_start: 0.8557 (tpt) cc_final: 0.8340 (tpp) REVERT: LS 110 MET cc_start: 0.8990 (mmm) cc_final: 0.8636 (mmp) outliers start: 95 outliers final: 32 residues processed: 1113 average time/residue: 2.3566 time to fit residues: 3748.2954 Evaluate side-chains 1022 residues out of total 8932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 983 time to evaluate : 9.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CH residue 347 LEU Chi-restraints excluded: chain CH residue 424 ASP Chi-restraints excluded: chain CJ residue 164 MET Chi-restraints excluded: chain CJ residue 420 ILE Chi-restraints excluded: chain CK residue 234 SER Chi-restraints excluded: chain CM residue 110 GLN Chi-restraints excluded: chain CM residue 196 THR Chi-restraints excluded: chain CN residue 191 ASN Chi-restraints excluded: chain CN residue 219 GLU Chi-restraints excluded: chain CQ residue 67 SER Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cb residue 76 ARG Chi-restraints excluded: chain Cd residue 143 GLU Chi-restraints excluded: chain Cd residue 170 GLN Chi-restraints excluded: chain Ce residue 387 ASP Chi-restraints excluded: chain Cz residue 22 ASN Chi-restraints excluded: chain LA residue 161 SER Chi-restraints excluded: chain LC residue 277 LEU Chi-restraints excluded: chain LF residue 171 ASP Chi-restraints excluded: chain LH residue 1 MET Chi-restraints excluded: chain LH residue 9 THR Chi-restraints excluded: chain LH residue 109 ARG Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 49 SER Chi-restraints excluded: chain LJ residue 100 THR Chi-restraints excluded: chain LJ residue 133 THR Chi-restraints excluded: chain LO residue 47 GLU Chi-restraints excluded: chain LP residue 109 THR Chi-restraints excluded: chain LU residue 37 SER Chi-restraints excluded: chain LZ residue 32 THR Chi-restraints excluded: chain LZ residue 34 SER Chi-restraints excluded: chain LZ residue 53 THR Chi-restraints excluded: chain LZ residue 131 THR Chi-restraints excluded: chain Lc residue 51 THR Chi-restraints excluded: chain Lf residue 4 GLU Chi-restraints excluded: chain Li residue 102 ILE Chi-restraints excluded: chain Lj residue 82 VAL Chi-restraints excluded: chain Lp residue 28 LYS Chi-restraints excluded: chain Lp residue 70 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1358 random chunks: chunk 685 optimal weight: 0.9990 chunk 382 optimal weight: 4.9990 chunk 1026 optimal weight: 9.9990 chunk 839 optimal weight: 0.0970 chunk 340 optimal weight: 6.9990 chunk 1235 optimal weight: 6.9990 chunk 1334 optimal weight: 7.9990 chunk 1100 optimal weight: 3.9990 chunk 1225 optimal weight: 3.9990 chunk 421 optimal weight: 3.9990 chunk 991 optimal weight: 10.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 14 GLN CH 389 ASN CI 221 ASN ** CI 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CK 72 ASN CQ 24 ASN ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cf 26 ASN Cf 128 GLN Cg 31 ASN Cg 34 ASN Cg 64 ASN Cg 128 ASN Ch 64 ASN ** Ch 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 166 GLN LB 346 HIS LD 249 GLN LG 44 GLN LG 62 GLN LG 194 HIS LH 139 ASN LJ 96 ASN ** LK 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LK 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 170 HIS LQ 43 HIS LR 3 ASN LY 127 GLN LZ 30 GLN Lg 99 GLN Lh 77 ASN Lh 115 HIS Lk 32 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 165503 Z= 0.292 Angle : 0.650 17.834 239712 Z= 0.344 Chirality : 0.038 0.261 29246 Planarity : 0.006 0.137 18045 Dihedral : 22.490 179.193 63905 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.53 % Allowed : 8.46 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.20 (0.08), residues: 10348 helix: 1.78 (0.08), residues: 4013 sheet: 0.22 (0.13), residues: 1483 loop : 0.25 (0.09), residues: 4852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPCg 105 HIS 0.010 0.001 HISCF 39 PHE 0.021 0.002 PHECH 90 TYR 0.031 0.002 TYRCH 85 ARG 0.012 0.001 ARGCz 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20696 Ramachandran restraints generated. 10348 Oldfield, 0 Emsley, 10348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20696 Ramachandran restraints generated. 10348 Oldfield, 0 Emsley, 10348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1151 residues out of total 8932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1017 time to evaluate : 9.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CB 213 ASN cc_start: 0.8357 (t0) cc_final: 0.7982 (t0) REVERT: CH 301 MET cc_start: 0.7508 (mmm) cc_final: 0.7233 (mmp) REVERT: CH 303 GLN cc_start: 0.7704 (tp40) cc_final: 0.7427 (tp40) REVERT: CM 110 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7935 (tm-30) REVERT: CM 225 PHE cc_start: 0.7167 (m-80) cc_final: 0.6942 (m-80) REVERT: CN 219 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: CQ 22 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7831 (mmt) REVERT: Cb 23 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7653 (mt-10) REVERT: Cb 24 ARG cc_start: 0.6406 (mmm-85) cc_final: 0.6181 (mtm110) REVERT: Cb 68 HIS cc_start: 0.7677 (OUTLIER) cc_final: 0.7402 (p90) REVERT: Cb 79 LYS cc_start: 0.8108 (ttmt) cc_final: 0.7891 (pttt) REVERT: Cd 392 ASP cc_start: 0.7790 (m-30) cc_final: 0.7432 (m-30) REVERT: Ce 331 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: Ce 384 VAL cc_start: 0.8994 (m) cc_final: 0.8756 (m) REVERT: Cg 53 SER cc_start: 0.8567 (p) cc_final: 0.8305 (p) REVERT: LA 51 ASP cc_start: 0.8259 (t70) cc_final: 0.8023 (t70) REVERT: LA 135 THR cc_start: 0.8310 (m) cc_final: 0.7905 (t) REVERT: LE 110 ASP cc_start: 0.7222 (p0) cc_final: 0.6872 (p0) REVERT: LE 172 ASN cc_start: 0.8550 (m-40) cc_final: 0.8299 (m110) REVERT: LF 171 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.7231 (m-30) REVERT: LG 33 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7375 (mpt-90) REVERT: LH 1 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.7568 (ttt) REVERT: LJ 110 HIS cc_start: 0.7842 (p-80) cc_final: 0.7528 (p90) REVERT: LJ 124 TYR cc_start: 0.7750 (m-80) cc_final: 0.7500 (m-80) REVERT: LO 47 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.7016 (mp0) REVERT: LO 160 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6980 (pp20) REVERT: LP 111 ASN cc_start: 0.8065 (t0) cc_final: 0.7806 (t160) REVERT: LQ 50 ASP cc_start: 0.6775 (OUTLIER) cc_final: 0.6547 (m-30) REVERT: LQ 104 GLU cc_start: 0.7779 (mp0) cc_final: 0.7299 (mp0) REVERT: LS 27 MET cc_start: 0.8599 (mtp) cc_final: 0.8256 (mtp) REVERT: LV 110 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: LY 76 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8497 (mttp) REVERT: LY 111 ASP cc_start: 0.7696 (p0) cc_final: 0.7487 (p0) REVERT: Lg 103 LYS cc_start: 0.7945 (ttpt) cc_final: 0.7681 (mtpt) REVERT: Lp 30 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7282 (mp0) outliers start: 134 outliers final: 64 residues processed: 1078 average time/residue: 2.4030 time to fit residues: 3698.1480 Evaluate side-chains 1048 residues out of total 8932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 970 time to evaluate : 9.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 30 LEU Chi-restraints excluded: chain CF residue 159 HIS Chi-restraints excluded: chain CH residue 236 MET Chi-restraints excluded: chain CH residue 347 LEU Chi-restraints excluded: chain CI residue 311 GLN Chi-restraints excluded: chain CI residue 318 GLU Chi-restraints excluded: chain CJ residue 164 MET Chi-restraints excluded: chain CJ residue 420 ILE Chi-restraints excluded: chain CK residue 234 SER Chi-restraints excluded: chain CM residue 110 GLN Chi-restraints excluded: chain CM residue 196 THR Chi-restraints excluded: chain CN residue 191 ASN Chi-restraints excluded: chain CN residue 219 GLU Chi-restraints excluded: chain CO residue 25 VAL Chi-restraints excluded: chain CO residue 40 ILE Chi-restraints excluded: chain CQ residue 22 MET Chi-restraints excluded: chain CQ residue 67 SER Chi-restraints excluded: chain CQ residue 79 VAL Chi-restraints excluded: chain CQ residue 141 GLU Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cb residue 95 ILE Chi-restraints excluded: chain Cd residue 170 GLN Chi-restraints excluded: chain Cd residue 179 LEU Chi-restraints excluded: chain Ce residue 331 GLU Chi-restraints excluded: chain Ce residue 391 ASP Chi-restraints excluded: chain Cz residue 22 ASN Chi-restraints excluded: chain LA residue 105 SER Chi-restraints excluded: chain LA residue 161 SER Chi-restraints excluded: chain LB residue 84 MET Chi-restraints excluded: chain LC residue 277 LEU Chi-restraints excluded: chain LE residue 51 SER Chi-restraints excluded: chain LE residue 181 SER Chi-restraints excluded: chain LF residue 78 GLN Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 171 ASP Chi-restraints excluded: chain LF residue 233 ASP Chi-restraints excluded: chain LG residue 33 ARG Chi-restraints excluded: chain LH residue 1 MET Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 49 SER Chi-restraints excluded: chain LJ residue 71 THR Chi-restraints excluded: chain LJ residue 100 THR Chi-restraints excluded: chain LJ residue 108 SER Chi-restraints excluded: chain LJ residue 133 THR Chi-restraints excluded: chain LK residue 165 GLU Chi-restraints excluded: chain LO residue 47 GLU Chi-restraints excluded: chain LO residue 160 GLU Chi-restraints excluded: chain LP residue 109 THR Chi-restraints excluded: chain LP residue 152 GLU Chi-restraints excluded: chain LQ residue 50 ASP Chi-restraints excluded: chain LR residue 30 SER Chi-restraints excluded: chain LS residue 147 ASN Chi-restraints excluded: chain LT residue 142 SER Chi-restraints excluded: chain LU residue 37 SER Chi-restraints excluded: chain LU residue 83 LEU Chi-restraints excluded: chain LV residue 34 ARG Chi-restraints excluded: chain LV residue 110 GLU Chi-restraints excluded: chain LY residue 76 LYS Chi-restraints excluded: chain LZ residue 32 THR Chi-restraints excluded: chain LZ residue 53 THR Chi-restraints excluded: chain Lc residue 26 VAL Chi-restraints excluded: chain Lc residue 32 SER Chi-restraints excluded: chain Lc residue 45 ILE Chi-restraints excluded: chain Lc residue 51 THR Chi-restraints excluded: chain Lc residue 74 SER Chi-restraints excluded: chain Lc residue 76 THR Chi-restraints excluded: chain Le residue 31 SER Chi-restraints excluded: chain Lf residue 4 GLU Chi-restraints excluded: chain Lg residue 41 THR Chi-restraints excluded: chain Lg residue 99 GLN Chi-restraints excluded: chain Li residue 27 THR Chi-restraints excluded: chain Li residue 102 ILE Chi-restraints excluded: chain Lj residue 82 VAL Chi-restraints excluded: chain Lk residue 19 ASP Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 28 LYS Chi-restraints excluded: chain Lp residue 30 GLU Chi-restraints excluded: chain Lp residue 70 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1358 random chunks: chunk 1220 optimal weight: 8.9990 chunk 928 optimal weight: 1.9990 chunk 641 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 589 optimal weight: 4.9990 chunk 829 optimal weight: 0.9980 chunk 1239 optimal weight: 10.0000 chunk 1312 optimal weight: 10.0000 chunk 647 optimal weight: 7.9990 chunk 1175 optimal weight: 4.9990 chunk 353 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CH 389 ASN CH 639 HIS CH 641 HIS ** CI 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CK 72 ASN CQ 24 ASN ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ce 370 GLN Cf 54 GLN Cf 128 GLN Cg 31 ASN Cg 34 ASN Cg 64 ASN ** Ch 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cz 56 GLN ** LA 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LD 249 GLN LG 44 GLN LH 139 ASN LH 201 GLN LJ 96 ASN ** LK 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LK 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 110 GLN ** LN 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 153 GLN LR 3 ASN ** LT 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LY 127 GLN La 62 HIS Ld 108 ASN Lh 77 ASN Lk 32 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 165503 Z= 0.359 Angle : 0.685 17.647 239712 Z= 0.361 Chirality : 0.041 0.275 29246 Planarity : 0.007 0.142 18045 Dihedral : 22.508 179.529 63905 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.94 % Allowed : 9.18 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 10348 helix: 1.79 (0.08), residues: 4016 sheet: 0.18 (0.13), residues: 1466 loop : 0.23 (0.09), residues: 4866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPCg 105 HIS 0.013 0.001 HISLT 54 PHE 0.025 0.002 PHELJ 164 TYR 0.030 0.002 TYRCH 85 ARG 0.015 0.001 ARGCe 267 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20696 Ramachandran restraints generated. 10348 Oldfield, 0 Emsley, 10348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20696 Ramachandran restraints generated. 10348 Oldfield, 0 Emsley, 10348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1179 residues out of total 8932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1009 time to evaluate : 9.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CB 213 ASN cc_start: 0.8453 (t0) cc_final: 0.8083 (t0) REVERT: CH 301 MET cc_start: 0.7503 (mmm) cc_final: 0.7100 (mmt) REVERT: CH 303 GLN cc_start: 0.7734 (tp40) cc_final: 0.7458 (tp-100) REVERT: CI 274 LYS cc_start: 0.8830 (tttt) cc_final: 0.8627 (tttt) REVERT: CM 110 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7918 (tm-30) REVERT: CN 79 GLN cc_start: 0.8712 (mp10) cc_final: 0.8470 (mm-40) REVERT: CN 219 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: CQ 22 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7741 (mmp) REVERT: Cb 76 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.7353 (ttp-170) REVERT: Cb 79 LYS cc_start: 0.8088 (ttmt) cc_final: 0.7722 (pttt) REVERT: Ce 384 VAL cc_start: 0.8962 (m) cc_final: 0.8695 (m) REVERT: Cg 53 SER cc_start: 0.8627 (p) cc_final: 0.8393 (p) REVERT: Ch 43 ASP cc_start: 0.6674 (p0) cc_final: 0.6456 (p0) REVERT: LA 51 ASP cc_start: 0.8267 (t70) cc_final: 0.8034 (t70) REVERT: LA 135 THR cc_start: 0.8301 (m) cc_final: 0.8016 (t) REVERT: LB 386 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7920 (pttm) REVERT: LE 110 ASP cc_start: 0.7472 (p0) cc_final: 0.7217 (p0) REVERT: LE 124 GLN cc_start: 0.7304 (pp30) cc_final: 0.7072 (pp30) REVERT: LE 172 ASN cc_start: 0.8622 (m-40) cc_final: 0.8253 (m110) REVERT: LF 171 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7237 (m-30) REVERT: LF 238 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7597 (mt-10) REVERT: LH 1 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.7553 (ttt) REVERT: LJ 110 HIS cc_start: 0.7937 (p-80) cc_final: 0.7647 (p90) REVERT: LJ 124 TYR cc_start: 0.7827 (m-80) cc_final: 0.7623 (m-80) REVERT: LO 47 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.7002 (mp0) REVERT: LO 62 MET cc_start: 0.8701 (tpt) cc_final: 0.8434 (tpp) REVERT: LP 96 LYS cc_start: 0.8810 (mmpt) cc_final: 0.8599 (mmtm) REVERT: LP 111 ASN cc_start: 0.8224 (t0) cc_final: 0.7996 (t160) REVERT: LQ 50 ASP cc_start: 0.6791 (OUTLIER) cc_final: 0.6543 (m-30) REVERT: LY 76 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8562 (mttp) REVERT: LY 111 ASP cc_start: 0.7806 (p0) cc_final: 0.7593 (p0) REVERT: LZ 51 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7667 (ttpt) REVERT: LZ 98 ASP cc_start: 0.7440 (t70) cc_final: 0.7147 (t0) REVERT: Le 42 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7581 (mtm-85) REVERT: Le 81 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8174 (mtpt) REVERT: Lf 58 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7735 (mp10) REVERT: Lg 99 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.7111 (tp40) REVERT: Lq 131 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.7030 (tptp) outliers start: 170 outliers final: 76 residues processed: 1095 average time/residue: 2.3563 time to fit residues: 3702.3383 Evaluate side-chains 1063 residues out of total 8932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 970 time to evaluate : 9.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 30 LEU Chi-restraints excluded: chain CF residue 159 HIS Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 347 LEU Chi-restraints excluded: chain CH residue 370 VAL Chi-restraints excluded: chain CH residue 630 MET Chi-restraints excluded: chain CI residue 311 GLN Chi-restraints excluded: chain CI residue 318 GLU Chi-restraints excluded: chain CJ residue 420 ILE Chi-restraints excluded: chain CK residue 185 THR Chi-restraints excluded: chain CK residue 234 SER Chi-restraints excluded: chain CM residue 110 GLN Chi-restraints excluded: chain CM residue 196 THR Chi-restraints excluded: chain CN residue 42 LEU Chi-restraints excluded: chain CN residue 44 ASP Chi-restraints excluded: chain CN residue 136 GLU Chi-restraints excluded: chain CN residue 191 ASN Chi-restraints excluded: chain CN residue 219 GLU Chi-restraints excluded: chain CO residue 25 VAL Chi-restraints excluded: chain CO residue 95 ASP Chi-restraints excluded: chain CQ residue 22 MET Chi-restraints excluded: chain CQ residue 63 MET Chi-restraints excluded: chain CQ residue 67 SER Chi-restraints excluded: chain CQ residue 79 VAL Chi-restraints excluded: chain Cb residue 10 THR Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cb residue 76 ARG Chi-restraints excluded: chain Cb residue 95 ILE Chi-restraints excluded: chain Cd residue 170 GLN Chi-restraints excluded: chain Cd residue 179 LEU Chi-restraints excluded: chain Ce residue 387 ASP Chi-restraints excluded: chain Ce residue 391 ASP Chi-restraints excluded: chain Ce residue 430 THR Chi-restraints excluded: chain Cz residue 22 ASN Chi-restraints excluded: chain LA residue 105 SER Chi-restraints excluded: chain LA residue 161 SER Chi-restraints excluded: chain LB residue 147 ARG Chi-restraints excluded: chain LB residue 386 LYS Chi-restraints excluded: chain LC residue 277 LEU Chi-restraints excluded: chain LD residue 17 GLN Chi-restraints excluded: chain LE residue 51 SER Chi-restraints excluded: chain LE residue 181 SER Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 171 ASP Chi-restraints excluded: chain LF residue 233 ASP Chi-restraints excluded: chain LF residue 238 GLU Chi-restraints excluded: chain LH residue 1 MET Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 49 SER Chi-restraints excluded: chain LJ residue 71 THR Chi-restraints excluded: chain LJ residue 100 THR Chi-restraints excluded: chain LJ residue 108 SER Chi-restraints excluded: chain LJ residue 133 THR Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LO residue 47 GLU Chi-restraints excluded: chain LO residue 131 LEU Chi-restraints excluded: chain LO residue 160 GLU Chi-restraints excluded: chain LP residue 109 THR Chi-restraints excluded: chain LQ residue 50 ASP Chi-restraints excluded: chain LR residue 30 SER Chi-restraints excluded: chain LS residue 45 LEU Chi-restraints excluded: chain LT residue 142 SER Chi-restraints excluded: chain LU residue 37 SER Chi-restraints excluded: chain LU residue 83 LEU Chi-restraints excluded: chain LY residue 76 LYS Chi-restraints excluded: chain LZ residue 32 THR Chi-restraints excluded: chain LZ residue 51 LYS Chi-restraints excluded: chain LZ residue 53 THR Chi-restraints excluded: chain LZ residue 131 THR Chi-restraints excluded: chain Lc residue 26 VAL Chi-restraints excluded: chain Lc residue 32 SER Chi-restraints excluded: chain Lc residue 45 ILE Chi-restraints excluded: chain Lc residue 51 THR Chi-restraints excluded: chain Lc residue 74 SER Chi-restraints excluded: chain Lc residue 76 THR Chi-restraints excluded: chain Le residue 42 ARG Chi-restraints excluded: chain Le residue 81 LYS Chi-restraints excluded: chain Lf residue 4 GLU Chi-restraints excluded: chain Lf residue 58 GLN Chi-restraints excluded: chain Lg residue 41 THR Chi-restraints excluded: chain Lg residue 99 GLN Chi-restraints excluded: chain Li residue 27 THR Chi-restraints excluded: chain Li residue 55 GLU Chi-restraints excluded: chain Li residue 102 ILE Chi-restraints excluded: chain Lj residue 82 VAL Chi-restraints excluded: chain Lk residue 19 ASP Chi-restraints excluded: chain Lk residue 21 SER Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 6 LYS Chi-restraints excluded: chain Lp residue 70 THR Chi-restraints excluded: chain Lq residue 120 ARG Chi-restraints excluded: chain Lq residue 131 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1358 random chunks: chunk 1093 optimal weight: 5.9990 chunk 745 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 977 optimal weight: 0.8980 chunk 541 optimal weight: 5.9990 chunk 1120 optimal weight: 0.8980 chunk 907 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 670 optimal weight: 2.9990 chunk 1178 optimal weight: 6.9990 chunk 331 optimal weight: 20.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CH 216 GLN CH 389 ASN CI 301 GLN CK 72 ASN CQ 24 ASN ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ce 370 GLN Cf 54 GLN Cf 128 GLN Cg 31 ASN Cg 34 ASN Cg 64 ASN ** Ch 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 319 ASN ** LD 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 44 GLN LJ 96 ASN ** LK 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LK 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 110 GLN LN 32 GLN ** LN 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 153 GLN LR 3 ASN ** LY 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LZ 30 GLN Lg 99 GLN Lh 77 ASN Li 100 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 165503 Z= 0.281 Angle : 0.649 17.409 239712 Z= 0.345 Chirality : 0.038 0.273 29246 Planarity : 0.006 0.136 18045 Dihedral : 22.478 179.168 63905 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.87 % Allowed : 10.56 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.25 (0.08), residues: 10348 helix: 1.87 (0.08), residues: 4023 sheet: 0.15 (0.13), residues: 1480 loop : 0.26 (0.09), residues: 4845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPCg 105 HIS 0.008 0.001 HISCF 39 PHE 0.021 0.002 PHELJ 164 TYR 0.022 0.002 TYRLE 127 ARG 0.010 0.000 ARGLS 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20696 Ramachandran restraints generated. 10348 Oldfield, 0 Emsley, 10348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20696 Ramachandran restraints generated. 10348 Oldfield, 0 Emsley, 10348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1143 residues out of total 8932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 979 time to evaluate : 9.527 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: CB 213 ASN cc_start: 0.8437 (t0) cc_final: 0.8228 (t0) REVERT: CH 85 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.8104 (m-80) REVERT: CH 303 GLN cc_start: 0.7696 (tp40) cc_final: 0.7391 (tp-100) REVERT: CL 70 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6905 (mm-30) REVERT: CL 73 ARG cc_start: 0.7860 (mtm110) cc_final: 0.7634 (ttp80) REVERT: CN 219 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7314 (mp0) REVERT: CQ 22 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.7707 (mmp) REVERT: Cb 76 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7022 (ttp-170) REVERT: Cb 79 LYS cc_start: 0.8097 (ttmt) cc_final: 0.7783 (pttt) REVERT: Ce 384 VAL cc_start: 0.8958 (OUTLIER) cc_final: 0.8677 (m) REVERT: Cf 253 MET cc_start: 0.8857 (mtt) cc_final: 0.8479 (mtt) REVERT: Cg 53 SER cc_start: 0.8600 (p) cc_final: 0.8371 (p) REVERT: LA 51 ASP cc_start: 0.8252 (t70) cc_final: 0.8022 (t70) REVERT: LA 135 THR cc_start: 0.8256 (m) cc_final: 0.7996 (t) REVERT: LB 317 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7567 (mt-10) REVERT: LE 172 ASN cc_start: 0.8695 (m-40) cc_final: 0.8280 (m110) REVERT: LF 171 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.7205 (m-30) REVERT: LG 33 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6989 (mtt180) REVERT: LG 44 GLN cc_start: 0.8675 (mm-40) cc_final: 0.8264 (mm110) REVERT: LH 1 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7513 (ttt) REVERT: LJ 126 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7561 (ppp) REVERT: LO 47 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: LP 96 LYS cc_start: 0.8750 (mmpt) cc_final: 0.8523 (mmtm) REVERT: LQ 104 GLU cc_start: 0.7722 (mp0) cc_final: 0.7226 (mp0) REVERT: LT 122 GLU cc_start: 0.5816 (OUTLIER) cc_final: 0.5015 (pp20) REVERT: LV 110 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: LY 76 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8524 (mttp) REVERT: LZ 1 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.6822 (ppp) REVERT: LZ 51 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7482 (ttpt) REVERT: LZ 98 ASP cc_start: 0.7433 (t70) cc_final: 0.7136 (t0) REVERT: Le 42 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7553 (mtm-85) REVERT: Li 102 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8523 (mp) REVERT: Lq 131 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.7066 (tptp) outliers start: 164 outliers final: 90 residues processed: 1066 average time/residue: 2.3616 time to fit residues: 3610.6580 Evaluate side-chains 1067 residues out of total 8932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 958 time to evaluate : 9.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 30 LEU Chi-restraints excluded: chain CF residue 159 HIS Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 263 LEU Chi-restraints excluded: chain CH residue 347 LEU Chi-restraints excluded: chain CH residue 424 ASP Chi-restraints excluded: chain CH residue 600 THR Chi-restraints excluded: chain CH residue 615 LYS Chi-restraints excluded: chain CH residue 630 MET Chi-restraints excluded: chain CI residue 213 ILE Chi-restraints excluded: chain CI residue 311 GLN Chi-restraints excluded: chain CI residue 318 GLU Chi-restraints excluded: chain CJ residue 226 ILE Chi-restraints excluded: chain CK residue 185 THR Chi-restraints excluded: chain CK residue 234 SER Chi-restraints excluded: chain CM residue 196 THR Chi-restraints excluded: chain CN residue 42 LEU Chi-restraints excluded: chain CN residue 44 ASP Chi-restraints excluded: chain CN residue 91 ASP Chi-restraints excluded: chain CN residue 136 GLU Chi-restraints excluded: chain CN residue 191 ASN Chi-restraints excluded: chain CN residue 219 GLU Chi-restraints excluded: chain CN residue 234 ASN Chi-restraints excluded: chain CO residue 25 VAL Chi-restraints excluded: chain CO residue 95 ASP Chi-restraints excluded: chain CQ residue 22 MET Chi-restraints excluded: chain CQ residue 67 SER Chi-restraints excluded: chain CQ residue 79 VAL Chi-restraints excluded: chain CQ residue 141 GLU Chi-restraints excluded: chain Cb residue 10 THR Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cb residue 76 ARG Chi-restraints excluded: chain Cb residue 95 ILE Chi-restraints excluded: chain Cd residue 170 GLN Chi-restraints excluded: chain Cd residue 179 LEU Chi-restraints excluded: chain Ce residue 384 VAL Chi-restraints excluded: chain Ce residue 437 THR Chi-restraints excluded: chain Cz residue 22 ASN Chi-restraints excluded: chain LA residue 105 SER Chi-restraints excluded: chain LA residue 137 VAL Chi-restraints excluded: chain LA residue 161 SER Chi-restraints excluded: chain LB residue 47 MET Chi-restraints excluded: chain LB residue 84 MET Chi-restraints excluded: chain LB residue 147 ARG Chi-restraints excluded: chain LB residue 317 GLU Chi-restraints excluded: chain LC residue 277 LEU Chi-restraints excluded: chain LD residue 17 GLN Chi-restraints excluded: chain LE residue 16 THR Chi-restraints excluded: chain LE residue 35 GLN Chi-restraints excluded: chain LE residue 181 SER Chi-restraints excluded: chain LF residue 78 GLN Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LF residue 171 ASP Chi-restraints excluded: chain LF residue 233 ASP Chi-restraints excluded: chain LG residue 33 ARG Chi-restraints excluded: chain LH residue 1 MET Chi-restraints excluded: chain LH residue 115 MET Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 49 SER Chi-restraints excluded: chain LJ residue 71 THR Chi-restraints excluded: chain LJ residue 100 THR Chi-restraints excluded: chain LJ residue 108 SER Chi-restraints excluded: chain LJ residue 126 MET Chi-restraints excluded: chain LJ residue 133 THR Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LO residue 23 ILE Chi-restraints excluded: chain LO residue 47 GLU Chi-restraints excluded: chain LO residue 131 LEU Chi-restraints excluded: chain LO residue 160 GLU Chi-restraints excluded: chain LP residue 109 THR Chi-restraints excluded: chain LP residue 152 GLU Chi-restraints excluded: chain LR residue 30 SER Chi-restraints excluded: chain LS residue 45 LEU Chi-restraints excluded: chain LS residue 133 GLU Chi-restraints excluded: chain LT residue 122 GLU Chi-restraints excluded: chain LT residue 142 SER Chi-restraints excluded: chain LU residue 37 SER Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LU residue 60 ILE Chi-restraints excluded: chain LU residue 83 LEU Chi-restraints excluded: chain LV residue 110 GLU Chi-restraints excluded: chain LY residue 76 LYS Chi-restraints excluded: chain LZ residue 1 MET Chi-restraints excluded: chain LZ residue 32 THR Chi-restraints excluded: chain LZ residue 51 LYS Chi-restraints excluded: chain LZ residue 131 THR Chi-restraints excluded: chain La residue 84 SER Chi-restraints excluded: chain Lc residue 45 ILE Chi-restraints excluded: chain Lc residue 51 THR Chi-restraints excluded: chain Lc residue 66 SER Chi-restraints excluded: chain Lc residue 76 THR Chi-restraints excluded: chain Le residue 42 ARG Chi-restraints excluded: chain Lf residue 4 GLU Chi-restraints excluded: chain Lg residue 41 THR Chi-restraints excluded: chain Lg residue 99 GLN Chi-restraints excluded: chain Lh residue 70 GLN Chi-restraints excluded: chain Li residue 67 ILE Chi-restraints excluded: chain Li residue 102 ILE Chi-restraints excluded: chain Lj residue 82 VAL Chi-restraints excluded: chain Lk residue 18 LYS Chi-restraints excluded: chain Lk residue 19 ASP Chi-restraints excluded: chain Lk residue 21 SER Chi-restraints excluded: chain Lp residue 6 LYS Chi-restraints excluded: chain Lp residue 70 THR Chi-restraints excluded: chain Lq residue 120 ARG Chi-restraints excluded: chain Lq residue 131 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1358 random chunks: chunk 441 optimal weight: 1.9990 chunk 1182 optimal weight: 0.7980 chunk 259 optimal weight: 10.0000 chunk 770 optimal weight: 6.9990 chunk 324 optimal weight: 8.9990 chunk 1313 optimal weight: 6.9990 chunk 1090 optimal weight: 1.9990 chunk 608 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 434 optimal weight: 0.0980 chunk 689 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CH 389 ASN CH 641 HIS CK 72 ASN CM 25 GLN ** CM 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cf 54 GLN Cf 128 GLN Cg 31 ASN Cg 34 ASN Cg 64 ASN ** Ch 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LH 139 ASN LJ 96 ASN LJ 110 HIS ** LK 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LK 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 110 GLN LN 32 GLN ** LN 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 111 ASN LQ 153 GLN LR 3 ASN ** LY 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ld 108 ASN Lg 99 GLN Li 100 GLN Lk 32 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 165503 Z= 0.231 Angle : 0.628 17.341 239712 Z= 0.336 Chirality : 0.037 0.265 29246 Planarity : 0.006 0.133 18045 Dihedral : 22.435 178.867 63905 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.72 % Allowed : 11.51 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.34 (0.08), residues: 10348 helix: 1.96 (0.08), residues: 4020 sheet: 0.15 (0.13), residues: 1482 loop : 0.32 (0.09), residues: 4846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRPCg 105 HIS 0.007 0.001 HISCF 39 PHE 0.024 0.001 PHELJ 164 TYR 0.022 0.002 TYRLE 127 ARG 0.021 0.000 ARGCe 267 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20696 Ramachandran restraints generated. 10348 Oldfield, 0 Emsley, 10348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20696 Ramachandran restraints generated. 10348 Oldfield, 0 Emsley, 10348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1138 residues out of total 8932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 987 time to evaluate : 9.648 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: CB 213 ASN cc_start: 0.8386 (t0) cc_final: 0.8181 (t0) REVERT: CH 85 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.8168 (m-80) REVERT: CH 303 GLN cc_start: 0.7678 (tp40) cc_final: 0.7392 (tp-100) REVERT: CH 509 ARG cc_start: 0.7816 (ttp-110) cc_final: 0.7602 (mtm110) REVERT: CM 110 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7933 (tm-30) REVERT: CM 189 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7934 (m-30) REVERT: CN 219 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: CQ 22 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7667 (mmp) REVERT: Cb 76 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.6961 (ttp-170) REVERT: Cb 79 LYS cc_start: 0.8077 (ttmt) cc_final: 0.7734 (pttt) REVERT: Ce 384 VAL cc_start: 0.8931 (OUTLIER) cc_final: 0.8660 (m) REVERT: Cg 31 ASN cc_start: 0.8584 (m-40) cc_final: 0.8292 (m110) REVERT: Cg 53 SER cc_start: 0.8618 (p) cc_final: 0.8394 (p) REVERT: LA 51 ASP cc_start: 0.8247 (t70) cc_final: 0.8019 (t70) REVERT: LA 135 THR cc_start: 0.8243 (m) cc_final: 0.7975 (t) REVERT: LC 181 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7384 (t0) REVERT: LE 124 GLN cc_start: 0.7282 (pp30) cc_final: 0.7054 (pp30) REVERT: LE 172 ASN cc_start: 0.8451 (m-40) cc_final: 0.8229 (m110) REVERT: LF 53 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7908 (mtt180) REVERT: LF 171 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7222 (m-30) REVERT: LG 33 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7119 (mtt180) REVERT: LH 1 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7503 (ttt) REVERT: LH 109 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7349 (tmm-80) REVERT: LJ 18 LEU cc_start: 0.8885 (tp) cc_final: 0.8675 (tp) REVERT: LJ 126 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7460 (ppp) REVERT: LN 73 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7430 (mtm-85) REVERT: LO 47 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: LO 160 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6860 (pp20) REVERT: LP 96 LYS cc_start: 0.8733 (mmpt) cc_final: 0.8526 (mmtm) REVERT: LQ 104 GLU cc_start: 0.7712 (mp0) cc_final: 0.7215 (mp0) REVERT: LV 110 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: LY 66 GLU cc_start: 0.8002 (tt0) cc_final: 0.7741 (mt-10) REVERT: LY 76 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8497 (mttp) REVERT: LZ 1 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.6808 (ppp) REVERT: LZ 51 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7501 (ttpt) REVERT: LZ 98 ASP cc_start: 0.7461 (t70) cc_final: 0.7177 (t0) REVERT: Lf 58 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7749 (mp10) REVERT: Lg 102 VAL cc_start: 0.8345 (t) cc_final: 0.8092 (p) REVERT: Li 102 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8522 (mp) REVERT: Lp 30 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: Lq 131 LYS cc_start: 0.7344 (OUTLIER) cc_final: 0.7073 (tptp) outliers start: 151 outliers final: 82 residues processed: 1065 average time/residue: 2.3340 time to fit residues: 3564.6065 Evaluate side-chains 1078 residues out of total 8932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 971 time to evaluate : 9.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 30 LEU Chi-restraints excluded: chain CF residue 159 HIS Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 191 THR Chi-restraints excluded: chain CH residue 347 LEU Chi-restraints excluded: chain CH residue 370 VAL Chi-restraints excluded: chain CH residue 424 ASP Chi-restraints excluded: chain CH residue 600 THR Chi-restraints excluded: chain CH residue 630 MET Chi-restraints excluded: chain CI residue 213 ILE Chi-restraints excluded: chain CI residue 311 GLN Chi-restraints excluded: chain CI residue 318 GLU Chi-restraints excluded: chain CJ residue 226 ILE Chi-restraints excluded: chain CK residue 166 VAL Chi-restraints excluded: chain CK residue 185 THR Chi-restraints excluded: chain CK residue 234 SER Chi-restraints excluded: chain CM residue 110 GLN Chi-restraints excluded: chain CM residue 189 ASP Chi-restraints excluded: chain CM residue 196 THR Chi-restraints excluded: chain CN residue 42 LEU Chi-restraints excluded: chain CN residue 44 ASP Chi-restraints excluded: chain CN residue 191 ASN Chi-restraints excluded: chain CN residue 219 GLU Chi-restraints excluded: chain CO residue 25 VAL Chi-restraints excluded: chain CO residue 95 ASP Chi-restraints excluded: chain CQ residue 22 MET Chi-restraints excluded: chain CQ residue 63 MET Chi-restraints excluded: chain CQ residue 67 SER Chi-restraints excluded: chain CQ residue 79 VAL Chi-restraints excluded: chain CQ residue 141 GLU Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cb residue 76 ARG Chi-restraints excluded: chain Cb residue 95 ILE Chi-restraints excluded: chain Cd residue 170 GLN Chi-restraints excluded: chain Cd residue 179 LEU Chi-restraints excluded: chain Ce residue 384 VAL Chi-restraints excluded: chain Ce residue 387 ASP Chi-restraints excluded: chain Ce residue 437 THR Chi-restraints excluded: chain Cz residue 22 ASN Chi-restraints excluded: chain LA residue 105 SER Chi-restraints excluded: chain LA residue 161 SER Chi-restraints excluded: chain LB residue 47 MET Chi-restraints excluded: chain LB residue 84 MET Chi-restraints excluded: chain LB residue 147 ARG Chi-restraints excluded: chain LC residue 181 ASP Chi-restraints excluded: chain LC residue 277 LEU Chi-restraints excluded: chain LD residue 17 GLN Chi-restraints excluded: chain LE residue 16 THR Chi-restraints excluded: chain LE residue 35 GLN Chi-restraints excluded: chain LE residue 181 SER Chi-restraints excluded: chain LF residue 53 ARG Chi-restraints excluded: chain LF residue 78 GLN Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LF residue 171 ASP Chi-restraints excluded: chain LF residue 233 ASP Chi-restraints excluded: chain LG residue 33 ARG Chi-restraints excluded: chain LH residue 1 MET Chi-restraints excluded: chain LH residue 109 ARG Chi-restraints excluded: chain LH residue 115 MET Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 49 SER Chi-restraints excluded: chain LJ residue 71 THR Chi-restraints excluded: chain LJ residue 100 THR Chi-restraints excluded: chain LJ residue 108 SER Chi-restraints excluded: chain LJ residue 126 MET Chi-restraints excluded: chain LJ residue 133 THR Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 73 ARG Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LO residue 23 ILE Chi-restraints excluded: chain LO residue 47 GLU Chi-restraints excluded: chain LO residue 131 LEU Chi-restraints excluded: chain LO residue 160 GLU Chi-restraints excluded: chain LP residue 109 THR Chi-restraints excluded: chain LP residue 152 GLU Chi-restraints excluded: chain LR residue 30 SER Chi-restraints excluded: chain LS residue 45 LEU Chi-restraints excluded: chain LS residue 133 GLU Chi-restraints excluded: chain LU residue 37 SER Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LU residue 83 LEU Chi-restraints excluded: chain LV residue 110 GLU Chi-restraints excluded: chain LX residue 146 LEU Chi-restraints excluded: chain LY residue 76 LYS Chi-restraints excluded: chain LZ residue 1 MET Chi-restraints excluded: chain LZ residue 32 THR Chi-restraints excluded: chain LZ residue 51 LYS Chi-restraints excluded: chain La residue 15 VAL Chi-restraints excluded: chain Lc residue 45 ILE Chi-restraints excluded: chain Lc residue 51 THR Chi-restraints excluded: chain Lc residue 66 SER Chi-restraints excluded: chain Lc residue 76 THR Chi-restraints excluded: chain Lf residue 4 GLU Chi-restraints excluded: chain Lf residue 58 GLN Chi-restraints excluded: chain Lg residue 41 THR Chi-restraints excluded: chain Lh residue 70 GLN Chi-restraints excluded: chain Li residue 55 GLU Chi-restraints excluded: chain Li residue 67 ILE Chi-restraints excluded: chain Li residue 102 ILE Chi-restraints excluded: chain Lj residue 82 VAL Chi-restraints excluded: chain Lk residue 18 LYS Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 30 GLU Chi-restraints excluded: chain Lp residue 70 THR Chi-restraints excluded: chain Lq residue 131 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1358 random chunks: chunk 1266 optimal weight: 0.5980 chunk 148 optimal weight: 7.9990 chunk 748 optimal weight: 5.9990 chunk 959 optimal weight: 0.7980 chunk 743 optimal weight: 7.9990 chunk 1106 optimal weight: 4.9990 chunk 733 optimal weight: 30.0000 chunk 1308 optimal weight: 0.4980 chunk 819 optimal weight: 0.7980 chunk 797 optimal weight: 10.0000 chunk 604 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CH 389 ASN CH 641 HIS CK 72 ASN CM 25 GLN ** CM 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cf 54 GLN Cf 128 GLN Cg 34 ASN Cg 64 ASN ** Ch 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cz 58 GLN LA 79 ASN ** LD 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 62 GLN LJ 96 ASN LJ 110 HIS ** LK 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LK 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 110 GLN LN 32 GLN ** LN 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 111 ASN LQ 153 GLN LR 3 ASN ** LY 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LZ 30 GLN Li 100 GLN Lk 32 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 165503 Z= 0.150 Angle : 0.600 16.975 239712 Z= 0.324 Chirality : 0.034 0.254 29246 Planarity : 0.005 0.126 18045 Dihedral : 22.384 178.904 63905 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.37 % Allowed : 12.05 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.08), residues: 10348 helix: 2.08 (0.08), residues: 4030 sheet: 0.18 (0.13), residues: 1476 loop : 0.38 (0.09), residues: 4842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRPCg 105 HIS 0.009 0.001 HISCF 58 PHE 0.025 0.001 PHELJ 164 TYR 0.022 0.001 TYRLE 127 ARG 0.015 0.000 ARGCQ 144 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20696 Ramachandran restraints generated. 10348 Oldfield, 0 Emsley, 10348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20696 Ramachandran restraints generated. 10348 Oldfield, 0 Emsley, 10348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1114 residues out of total 8932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 994 time to evaluate : 9.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CH 85 TYR cc_start: 0.8473 (OUTLIER) cc_final: 0.8111 (m-80) REVERT: CH 303 GLN cc_start: 0.7680 (tp40) cc_final: 0.7394 (tp-100) REVERT: CH 509 ARG cc_start: 0.7788 (ttp-110) cc_final: 0.7572 (mtm110) REVERT: CI 274 LYS cc_start: 0.8801 (tttt) cc_final: 0.8541 (tttt) REVERT: CQ 22 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.7759 (mmt) REVERT: Cb 76 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.6869 (ttp-170) REVERT: Cb 79 LYS cc_start: 0.8050 (ttmt) cc_final: 0.7824 (pttt) REVERT: Cd 392 ASP cc_start: 0.7787 (m-30) cc_final: 0.7536 (m-30) REVERT: Cf 105 MET cc_start: 0.7725 (mmm) cc_final: 0.7459 (mtt) REVERT: Cf 253 MET cc_start: 0.8800 (mtt) cc_final: 0.8420 (mtt) REVERT: Cg 53 SER cc_start: 0.8642 (p) cc_final: 0.8411 (p) REVERT: LA 51 ASP cc_start: 0.8236 (t70) cc_final: 0.8008 (t70) REVERT: LA 135 THR cc_start: 0.8222 (m) cc_final: 0.7955 (t) REVERT: LE 172 ASN cc_start: 0.8460 (m-40) cc_final: 0.8230 (m110) REVERT: LF 53 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7920 (mtt180) REVERT: LG 33 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7283 (mtt180) REVERT: LH 1 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.7515 (ttt) REVERT: LH 109 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7337 (tmm-80) REVERT: LJ 18 LEU cc_start: 0.8860 (tp) cc_final: 0.8654 (tp) REVERT: LN 73 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7427 (mtm-85) REVERT: LO 160 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6738 (pp20) REVERT: LQ 104 GLU cc_start: 0.7704 (mp0) cc_final: 0.7235 (mp0) REVERT: LS 109 ASP cc_start: 0.8499 (t0) cc_final: 0.8280 (t0) REVERT: LV 110 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: LY 66 GLU cc_start: 0.7958 (tt0) cc_final: 0.7686 (mt-10) REVERT: LY 76 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8449 (mttp) REVERT: Li 102 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8501 (mp) REVERT: Lp 30 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7312 (mp0) outliers start: 120 outliers final: 73 residues processed: 1050 average time/residue: 2.3992 time to fit residues: 3641.9970 Evaluate side-chains 1050 residues out of total 8932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 964 time to evaluate : 9.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 30 LEU Chi-restraints excluded: chain CF residue 159 HIS Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 191 THR Chi-restraints excluded: chain CH residue 263 LEU Chi-restraints excluded: chain CH residue 347 LEU Chi-restraints excluded: chain CH residue 370 VAL Chi-restraints excluded: chain CH residue 424 ASP Chi-restraints excluded: chain CH residue 630 MET Chi-restraints excluded: chain CI residue 213 ILE Chi-restraints excluded: chain CI residue 311 GLN Chi-restraints excluded: chain CI residue 318 GLU Chi-restraints excluded: chain CJ residue 164 MET Chi-restraints excluded: chain CK residue 166 VAL Chi-restraints excluded: chain CK residue 234 SER Chi-restraints excluded: chain CM residue 196 THR Chi-restraints excluded: chain CM residue 234 LEU Chi-restraints excluded: chain CN residue 191 ASN Chi-restraints excluded: chain CO residue 95 ASP Chi-restraints excluded: chain CQ residue 22 MET Chi-restraints excluded: chain CQ residue 63 MET Chi-restraints excluded: chain CQ residue 67 SER Chi-restraints excluded: chain CQ residue 141 GLU Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cb residue 76 ARG Chi-restraints excluded: chain Cb residue 95 ILE Chi-restraints excluded: chain Cd residue 170 GLN Chi-restraints excluded: chain Ce residue 437 THR Chi-restraints excluded: chain Cz residue 22 ASN Chi-restraints excluded: chain Cz residue 79 ARG Chi-restraints excluded: chain LA residue 105 SER Chi-restraints excluded: chain LA residue 161 SER Chi-restraints excluded: chain LB residue 47 MET Chi-restraints excluded: chain LB residue 84 MET Chi-restraints excluded: chain LB residue 147 ARG Chi-restraints excluded: chain LD residue 17 GLN Chi-restraints excluded: chain LE residue 16 THR Chi-restraints excluded: chain LE residue 181 SER Chi-restraints excluded: chain LF residue 53 ARG Chi-restraints excluded: chain LF residue 78 GLN Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LG residue 33 ARG Chi-restraints excluded: chain LH residue 1 MET Chi-restraints excluded: chain LH residue 109 ARG Chi-restraints excluded: chain LH residue 115 MET Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 49 SER Chi-restraints excluded: chain LJ residue 71 THR Chi-restraints excluded: chain LJ residue 133 THR Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 73 ARG Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LO residue 160 GLU Chi-restraints excluded: chain LP residue 109 THR Chi-restraints excluded: chain LP residue 152 GLU Chi-restraints excluded: chain LQ residue 122 GLN Chi-restraints excluded: chain LR residue 30 SER Chi-restraints excluded: chain LS residue 45 LEU Chi-restraints excluded: chain LS residue 133 GLU Chi-restraints excluded: chain LT residue 142 SER Chi-restraints excluded: chain LU residue 37 SER Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LU residue 83 LEU Chi-restraints excluded: chain LU residue 106 SER Chi-restraints excluded: chain LU residue 117 ILE Chi-restraints excluded: chain LV residue 110 GLU Chi-restraints excluded: chain LX residue 146 LEU Chi-restraints excluded: chain LY residue 76 LYS Chi-restraints excluded: chain LZ residue 32 THR Chi-restraints excluded: chain Lc residue 26 VAL Chi-restraints excluded: chain Lc residue 45 ILE Chi-restraints excluded: chain Lc residue 51 THR Chi-restraints excluded: chain Lc residue 66 SER Chi-restraints excluded: chain Lc residue 74 SER Chi-restraints excluded: chain Lf residue 4 GLU Chi-restraints excluded: chain Lf residue 51 VAL Chi-restraints excluded: chain Lg residue 99 GLN Chi-restraints excluded: chain Li residue 102 ILE Chi-restraints excluded: chain Lj residue 82 VAL Chi-restraints excluded: chain Lk residue 18 LYS Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 30 GLU Chi-restraints excluded: chain Lp residue 70 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1358 random chunks: chunk 809 optimal weight: 4.9990 chunk 522 optimal weight: 6.9990 chunk 781 optimal weight: 7.9990 chunk 394 optimal weight: 3.9990 chunk 257 optimal weight: 10.0000 chunk 253 optimal weight: 4.9990 chunk 832 optimal weight: 6.9990 chunk 891 optimal weight: 3.9990 chunk 647 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 1028 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CH 362 GLN CH 389 ASN CH 641 HIS CK 72 ASN CM 25 GLN ** CM 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cf 54 GLN Cf 128 GLN Cg 31 ASN Cg 34 ASN Cg 64 ASN ** Ch 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 79 ASN ** LA 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LD 249 GLN LG 62 GLN LH 139 ASN LJ 16 GLN LJ 96 ASN LJ 110 HIS ** LK 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LK 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 110 GLN LN 32 GLN ** LN 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 153 GLN LR 3 ASN ** LY 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LZ 30 GLN ** Lg 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Li 100 GLN Lk 32 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.126 165503 Z= 0.420 Angle : 0.711 17.987 239712 Z= 0.371 Chirality : 0.042 0.270 29246 Planarity : 0.007 0.143 18045 Dihedral : 22.418 179.864 63905 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.63 % Allowed : 12.20 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.24 (0.08), residues: 10348 helix: 1.88 (0.08), residues: 4018 sheet: 0.14 (0.13), residues: 1457 loop : 0.26 (0.09), residues: 4873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPCg 105 HIS 0.009 0.001 HISCF 39 PHE 0.025 0.002 PHELJ 164 TYR 0.024 0.002 TYRCN 151 ARG 0.015 0.001 ARGCz 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20696 Ramachandran restraints generated. 10348 Oldfield, 0 Emsley, 10348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20696 Ramachandran restraints generated. 10348 Oldfield, 0 Emsley, 10348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1126 residues out of total 8932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 983 time to evaluate : 9.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CH 85 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.8113 (m-80) REVERT: CH 303 GLN cc_start: 0.7719 (tp-100) cc_final: 0.7425 (tp-100) REVERT: CM 110 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7935 (tm-30) REVERT: CM 189 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.7957 (m-30) REVERT: CQ 22 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.7723 (mmp) REVERT: Cb 76 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7144 (ttp-170) REVERT: Cb 79 LYS cc_start: 0.8091 (ttmt) cc_final: 0.7858 (pttt) REVERT: Cf 105 MET cc_start: 0.7815 (mmm) cc_final: 0.7474 (mtt) REVERT: Cg 53 SER cc_start: 0.8618 (p) cc_final: 0.8400 (p) REVERT: LA 51 ASP cc_start: 0.8261 (t70) cc_final: 0.8028 (t70) REVERT: LA 135 THR cc_start: 0.8261 (m) cc_final: 0.8003 (t) REVERT: LA 147 ARG cc_start: 0.6672 (mtm-85) cc_final: 0.6450 (mtm-85) REVERT: LB 317 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7571 (mt-10) REVERT: LE 172 ASN cc_start: 0.8555 (m-40) cc_final: 0.8277 (m110) REVERT: LF 53 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7929 (mtt180) REVERT: LG 33 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7182 (mtt180) REVERT: LG 36 ASN cc_start: 0.8207 (t0) cc_final: 0.7974 (t0) REVERT: LH 1 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.7532 (ttt) REVERT: LH 109 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7411 (tmm-80) REVERT: LJ 18 LEU cc_start: 0.8901 (tp) cc_final: 0.8691 (tp) REVERT: LQ 104 GLU cc_start: 0.7767 (mp0) cc_final: 0.7349 (mp0) REVERT: LV 110 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: LX 72 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6733 (pt0) REVERT: LY 66 GLU cc_start: 0.8008 (tt0) cc_final: 0.7763 (mt-10) REVERT: LY 76 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8578 (mttp) REVERT: LZ 51 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7631 (ttpt) REVERT: LZ 98 ASP cc_start: 0.7448 (t70) cc_final: 0.7171 (t0) REVERT: Lf 58 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7790 (mp10) REVERT: Li 102 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8456 (mp) REVERT: Ll 45 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8260 (ttt180) outliers start: 143 outliers final: 88 residues processed: 1059 average time/residue: 2.3703 time to fit residues: 3591.6684 Evaluate side-chains 1067 residues out of total 8932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 962 time to evaluate : 9.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 30 LEU Chi-restraints excluded: chain CF residue 159 HIS Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 263 LEU Chi-restraints excluded: chain CH residue 347 LEU Chi-restraints excluded: chain CH residue 630 MET Chi-restraints excluded: chain CI residue 213 ILE Chi-restraints excluded: chain CI residue 311 GLN Chi-restraints excluded: chain CI residue 318 GLU Chi-restraints excluded: chain CK residue 166 VAL Chi-restraints excluded: chain CK residue 185 THR Chi-restraints excluded: chain CK residue 234 SER Chi-restraints excluded: chain CM residue 110 GLN Chi-restraints excluded: chain CM residue 189 ASP Chi-restraints excluded: chain CM residue 196 THR Chi-restraints excluded: chain CN residue 42 LEU Chi-restraints excluded: chain CN residue 44 ASP Chi-restraints excluded: chain CN residue 91 ASP Chi-restraints excluded: chain CN residue 136 GLU Chi-restraints excluded: chain CN residue 191 ASN Chi-restraints excluded: chain CO residue 25 VAL Chi-restraints excluded: chain CO residue 40 ILE Chi-restraints excluded: chain CO residue 95 ASP Chi-restraints excluded: chain CQ residue 22 MET Chi-restraints excluded: chain CQ residue 63 MET Chi-restraints excluded: chain CQ residue 67 SER Chi-restraints excluded: chain CQ residue 79 VAL Chi-restraints excluded: chain Cb residue 10 THR Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cb residue 76 ARG Chi-restraints excluded: chain Cb residue 95 ILE Chi-restraints excluded: chain Cd residue 170 GLN Chi-restraints excluded: chain Ce residue 384 VAL Chi-restraints excluded: chain Ce residue 387 ASP Chi-restraints excluded: chain Ce residue 437 THR Chi-restraints excluded: chain Cz residue 22 ASN Chi-restraints excluded: chain Cz residue 79 ARG Chi-restraints excluded: chain LA residue 105 SER Chi-restraints excluded: chain LA residue 161 SER Chi-restraints excluded: chain LB residue 84 MET Chi-restraints excluded: chain LB residue 147 ARG Chi-restraints excluded: chain LB residue 317 GLU Chi-restraints excluded: chain LC residue 277 LEU Chi-restraints excluded: chain LD residue 17 GLN Chi-restraints excluded: chain LE residue 16 THR Chi-restraints excluded: chain LE residue 35 GLN Chi-restraints excluded: chain LE residue 181 SER Chi-restraints excluded: chain LF residue 53 ARG Chi-restraints excluded: chain LF residue 78 GLN Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LG residue 33 ARG Chi-restraints excluded: chain LG residue 203 ILE Chi-restraints excluded: chain LH residue 1 MET Chi-restraints excluded: chain LH residue 109 ARG Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 49 SER Chi-restraints excluded: chain LJ residue 71 THR Chi-restraints excluded: chain LJ residue 100 THR Chi-restraints excluded: chain LJ residue 108 SER Chi-restraints excluded: chain LJ residue 133 THR Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LO residue 23 ILE Chi-restraints excluded: chain LO residue 131 LEU Chi-restraints excluded: chain LO residue 160 GLU Chi-restraints excluded: chain LP residue 109 THR Chi-restraints excluded: chain LQ residue 122 GLN Chi-restraints excluded: chain LR residue 30 SER Chi-restraints excluded: chain LS residue 45 LEU Chi-restraints excluded: chain LS residue 133 GLU Chi-restraints excluded: chain LT residue 142 SER Chi-restraints excluded: chain LU residue 37 SER Chi-restraints excluded: chain LU residue 83 LEU Chi-restraints excluded: chain LU residue 106 SER Chi-restraints excluded: chain LV residue 110 GLU Chi-restraints excluded: chain LX residue 72 GLU Chi-restraints excluded: chain LY residue 76 LYS Chi-restraints excluded: chain LZ residue 32 THR Chi-restraints excluded: chain LZ residue 51 LYS Chi-restraints excluded: chain LZ residue 131 THR Chi-restraints excluded: chain La residue 15 VAL Chi-restraints excluded: chain La residue 84 SER Chi-restraints excluded: chain Lc residue 45 ILE Chi-restraints excluded: chain Lc residue 51 THR Chi-restraints excluded: chain Lc residue 66 SER Chi-restraints excluded: chain Lc residue 74 SER Chi-restraints excluded: chain Lf residue 4 GLU Chi-restraints excluded: chain Lf residue 22 ARG Chi-restraints excluded: chain Lf residue 51 VAL Chi-restraints excluded: chain Lf residue 58 GLN Chi-restraints excluded: chain Lg residue 41 THR Chi-restraints excluded: chain Lg residue 99 GLN Chi-restraints excluded: chain Lh residue 70 GLN Chi-restraints excluded: chain Lh residue 103 SER Chi-restraints excluded: chain Li residue 102 ILE Chi-restraints excluded: chain Lj residue 82 VAL Chi-restraints excluded: chain Lk residue 19 ASP Chi-restraints excluded: chain Lk residue 21 SER Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Ll residue 45 ARG Chi-restraints excluded: chain Lp residue 70 THR Chi-restraints excluded: chain Lq residue 120 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1358 random chunks: chunk 1190 optimal weight: 0.9990 chunk 1253 optimal weight: 0.7980 chunk 1144 optimal weight: 4.9990 chunk 1219 optimal weight: 1.9990 chunk 734 optimal weight: 8.9990 chunk 531 optimal weight: 3.9990 chunk 957 optimal weight: 0.6980 chunk 374 optimal weight: 0.0170 chunk 1102 optimal weight: 0.7980 chunk 1153 optimal weight: 3.9990 chunk 1215 optimal weight: 5.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CH 389 ASN CK 72 ASN CM 25 GLN ** CM 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cf 54 GLN Cf 128 GLN Cg 31 ASN Cg 34 ASN Cg 64 ASN ** Ch 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 79 ASN ** LD 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 62 GLN LJ 96 ASN LJ 110 HIS ** LK 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LK 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 110 GLN ** LN 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 111 ASN LQ 153 GLN ** LY 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Li 100 GLN Lk 32 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 165503 Z= 0.135 Angle : 0.607 16.769 239712 Z= 0.327 Chirality : 0.034 0.255 29246 Planarity : 0.005 0.124 18045 Dihedral : 22.369 178.914 63905 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.19 % Allowed : 12.94 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.08), residues: 10348 helix: 2.09 (0.08), residues: 4038 sheet: 0.18 (0.13), residues: 1476 loop : 0.39 (0.09), residues: 4834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRPCg 105 HIS 0.007 0.001 HISCd 252 PHE 0.028 0.001 PHELJ 164 TYR 0.026 0.001 TYRLE 127 ARG 0.017 0.000 ARGCz 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20696 Ramachandran restraints generated. 10348 Oldfield, 0 Emsley, 10348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20696 Ramachandran restraints generated. 10348 Oldfield, 0 Emsley, 10348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1099 residues out of total 8932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 995 time to evaluate : 10.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CH 85 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: CH 509 ARG cc_start: 0.7788 (ttp-110) cc_final: 0.7572 (mtm110) REVERT: CI 281 LYS cc_start: 0.8479 (ptmm) cc_final: 0.8123 (ptmm) REVERT: CM 110 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7910 (tm-30) REVERT: CQ 22 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7708 (mmt) REVERT: Cb 76 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.6773 (ttp-170) REVERT: Cb 79 LYS cc_start: 0.8035 (ttmt) cc_final: 0.7813 (pttt) REVERT: Cd 95 MET cc_start: 0.7850 (tpt) cc_final: 0.7578 (tpt) REVERT: Cd 392 ASP cc_start: 0.7769 (m-30) cc_final: 0.7486 (m-30) REVERT: Cf 105 MET cc_start: 0.7731 (mmm) cc_final: 0.7450 (mtt) REVERT: Cg 53 SER cc_start: 0.8632 (p) cc_final: 0.8413 (p) REVERT: LA 51 ASP cc_start: 0.8230 (t70) cc_final: 0.7993 (t70) REVERT: LA 135 THR cc_start: 0.8206 (m) cc_final: 0.7961 (t) REVERT: LA 147 ARG cc_start: 0.6580 (mtm-85) cc_final: 0.6271 (mtm-85) REVERT: LE 172 ASN cc_start: 0.8460 (m-40) cc_final: 0.8218 (m110) REVERT: LF 53 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7901 (mtt180) REVERT: LG 33 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7158 (mtt180) REVERT: LG 36 ASN cc_start: 0.8171 (t0) cc_final: 0.7909 (t0) REVERT: LH 1 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7485 (ttt) REVERT: LH 109 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7359 (tmm-80) REVERT: LN 73 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7456 (mtm-85) REVERT: LO 160 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6680 (pp20) REVERT: LQ 104 GLU cc_start: 0.7739 (mp0) cc_final: 0.7278 (mp0) REVERT: LV 110 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: LV 139 MET cc_start: 0.8183 (ttt) cc_final: 0.7850 (ttm) REVERT: LY 66 GLU cc_start: 0.7947 (tt0) cc_final: 0.7663 (mt-10) REVERT: LY 76 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8399 (mttp) REVERT: LZ 51 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7455 (ttpt) REVERT: Li 102 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8494 (mp) REVERT: Lq 120 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.8016 (tpp-160) outliers start: 104 outliers final: 52 residues processed: 1050 average time/residue: 2.3770 time to fit residues: 3576.0327 Evaluate side-chains 1036 residues out of total 8932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 969 time to evaluate : 9.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 30 LEU Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 191 THR Chi-restraints excluded: chain CH residue 263 LEU Chi-restraints excluded: chain CH residue 600 THR Chi-restraints excluded: chain CI residue 213 ILE Chi-restraints excluded: chain CI residue 311 GLN Chi-restraints excluded: chain CI residue 318 GLU Chi-restraints excluded: chain CK residue 60 GLN Chi-restraints excluded: chain CK residue 234 SER Chi-restraints excluded: chain CM residue 110 GLN Chi-restraints excluded: chain CM residue 196 THR Chi-restraints excluded: chain CM residue 234 LEU Chi-restraints excluded: chain CN residue 42 LEU Chi-restraints excluded: chain CN residue 191 ASN Chi-restraints excluded: chain CQ residue 22 MET Chi-restraints excluded: chain CQ residue 67 SER Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cb residue 76 ARG Chi-restraints excluded: chain Cd residue 170 GLN Chi-restraints excluded: chain Ce residue 384 VAL Chi-restraints excluded: chain LA residue 105 SER Chi-restraints excluded: chain LA residue 137 VAL Chi-restraints excluded: chain LA residue 161 SER Chi-restraints excluded: chain LB residue 84 MET Chi-restraints excluded: chain LB residue 147 ARG Chi-restraints excluded: chain LE residue 102 VAL Chi-restraints excluded: chain LE residue 181 SER Chi-restraints excluded: chain LF residue 53 ARG Chi-restraints excluded: chain LF residue 78 GLN Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LG residue 33 ARG Chi-restraints excluded: chain LH residue 1 MET Chi-restraints excluded: chain LH residue 109 ARG Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 49 SER Chi-restraints excluded: chain LJ residue 133 THR Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 73 ARG 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 LP residue 169 SER Chi-restraints excluded: chain LQ residue 122 GLN Chi-restraints excluded: chain LS residue 45 LEU Chi-restraints excluded: chain LS residue 133 GLU Chi-restraints excluded: chain LU residue 37 SER Chi-restraints excluded: chain LU residue 83 LEU Chi-restraints excluded: chain LU residue 106 SER Chi-restraints excluded: chain LU residue 117 ILE Chi-restraints excluded: chain LV residue 110 GLU Chi-restraints excluded: chain LY residue 76 LYS Chi-restraints excluded: chain LZ residue 32 THR Chi-restraints excluded: chain LZ residue 51 LYS Chi-restraints excluded: chain Lc residue 45 ILE Chi-restraints excluded: chain Lc residue 51 THR Chi-restraints excluded: chain Lc residue 65 MET Chi-restraints excluded: chain Lf residue 4 GLU Chi-restraints excluded: chain Lf residue 51 VAL Chi-restraints excluded: chain Lg residue 99 GLN Chi-restraints excluded: chain Li residue 67 ILE Chi-restraints excluded: chain Li residue 102 ILE Chi-restraints excluded: chain Lj residue 82 VAL Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 70 THR Chi-restraints excluded: chain Lq residue 120 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1358 random chunks: chunk 800 optimal weight: 0.6980 chunk 1289 optimal weight: 4.9990 chunk 787 optimal weight: 0.5980 chunk 611 optimal weight: 4.9990 chunk 896 optimal weight: 2.9990 chunk 1352 optimal weight: 5.9990 chunk 1245 optimal weight: 0.8980 chunk 1077 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 832 optimal weight: 6.9990 chunk 660 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CH 362 GLN CH 389 ASN CK 72 ASN CM 25 GLN ** CM 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CQ 130 ASN ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cf 128 GLN ** Cg 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cg 64 ASN ** Ch 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 79 ASN ** LD 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 62 GLN LH 139 ASN LJ 96 ASN LJ 110 HIS ** LK 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LK 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 110 GLN ** LN 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 153 GLN LR 3 ASN ** LY 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LZ 30 GLN Ld 102 GLN Lg 30 GLN ** Lg 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Li 100 GLN Lk 32 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 165503 Z= 0.158 Angle : 0.602 17.155 239712 Z= 0.324 Chirality : 0.034 0.248 29246 Planarity : 0.006 0.127 18045 Dihedral : 22.299 178.752 63905 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.93 % Allowed : 13.38 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.08), residues: 10348 helix: 2.13 (0.08), residues: 4045 sheet: 0.24 (0.13), residues: 1463 loop : 0.42 (0.09), residues: 4840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRPCg 105 HIS 0.011 0.001 HISCF 39 PHE 0.029 0.001 PHELJ 164 TYR 0.026 0.001 TYRCf 117 ARG 0.023 0.000 ARGCI 295 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20696 Ramachandran restraints generated. 10348 Oldfield, 0 Emsley, 10348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20696 Ramachandran restraints generated. 10348 Oldfield, 0 Emsley, 10348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1064 residues out of total 8932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 983 time to evaluate : 9.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CH 85 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.8039 (m-80) REVERT: CH 362 GLN cc_start: 0.8208 (tp40) cc_final: 0.7978 (tm-30) REVERT: CH 509 ARG cc_start: 0.7779 (ttp-110) cc_final: 0.7565 (mtm110) REVERT: CI 281 LYS cc_start: 0.8382 (ptmm) cc_final: 0.7977 (ptmm) REVERT: CM 110 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7918 (tm-30) REVERT: CQ 22 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7596 (mmp) REVERT: Cb 33 GLN cc_start: 0.7829 (mm110) cc_final: 0.7383 (mm-40) REVERT: Cb 37 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6759 (mm-30) REVERT: Cb 76 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.6803 (ttp-170) REVERT: Cb 79 LYS cc_start: 0.8029 (ttmt) cc_final: 0.7806 (pttt) REVERT: Cd 392 ASP cc_start: 0.7777 (m-30) cc_final: 0.7536 (m-30) REVERT: Cf 105 MET cc_start: 0.7749 (mmm) cc_final: 0.7470 (mtt) REVERT: Cf 253 MET cc_start: 0.8789 (mtt) cc_final: 0.8509 (mtt) REVERT: Cg 53 SER cc_start: 0.8644 (p) cc_final: 0.8422 (p) REVERT: LA 51 ASP cc_start: 0.8222 (t70) cc_final: 0.7982 (t70) REVERT: LA 135 THR cc_start: 0.8188 (m) cc_final: 0.7899 (t) REVERT: LE 172 ASN cc_start: 0.8466 (m-40) cc_final: 0.8225 (m110) REVERT: LG 33 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7117 (mtt180) REVERT: LG 36 ASN cc_start: 0.8164 (t0) cc_final: 0.7913 (t0) REVERT: LH 1 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7549 (ttt) REVERT: LH 109 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7342 (tmm-80) REVERT: LO 160 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6706 (pp20) REVERT: LQ 104 GLU cc_start: 0.7722 (mp0) cc_final: 0.7259 (mp0) REVERT: LV 139 MET cc_start: 0.8185 (ttt) cc_final: 0.7866 (ttm) REVERT: LY 66 GLU cc_start: 0.7930 (tt0) cc_final: 0.7659 (mt-10) REVERT: LY 76 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8431 (mttp) REVERT: LZ 51 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7408 (ttpt) REVERT: Lf 103 MET cc_start: 0.8881 (mmm) cc_final: 0.8616 (mmt) REVERT: Li 102 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8483 (mp) outliers start: 81 outliers final: 50 residues processed: 1028 average time/residue: 2.3646 time to fit residues: 3484.0060 Evaluate side-chains 1017 residues out of total 8932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 956 time to evaluate : 9.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 30 LEU Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 191 THR Chi-restraints excluded: chain CH residue 263 LEU Chi-restraints excluded: chain CH residue 370 VAL Chi-restraints excluded: chain CH residue 600 THR Chi-restraints excluded: chain CH residue 630 MET Chi-restraints excluded: chain CI residue 213 ILE Chi-restraints excluded: chain CI residue 311 GLN Chi-restraints excluded: chain CI residue 318 GLU Chi-restraints excluded: chain CJ residue 164 MET Chi-restraints excluded: chain CK residue 234 SER Chi-restraints excluded: chain CM residue 110 GLN Chi-restraints excluded: chain CM residue 196 THR Chi-restraints excluded: chain CM residue 234 LEU Chi-restraints excluded: chain CN residue 42 LEU Chi-restraints excluded: chain CN residue 191 ASN Chi-restraints excluded: chain CQ residue 22 MET Chi-restraints excluded: chain CQ residue 67 SER Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cb residue 76 ARG Chi-restraints excluded: chain Cd residue 170 GLN Chi-restraints excluded: chain LA residue 105 SER Chi-restraints excluded: chain LA residue 137 VAL Chi-restraints excluded: chain LA residue 161 SER Chi-restraints excluded: chain LB residue 47 MET Chi-restraints excluded: chain LB residue 147 ARG Chi-restraints excluded: chain LE residue 181 SER Chi-restraints excluded: chain LF residue 78 GLN Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LG residue 33 ARG Chi-restraints excluded: chain LG residue 203 ILE Chi-restraints excluded: chain LH residue 1 MET Chi-restraints excluded: chain LH residue 109 ARG Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 49 SER Chi-restraints excluded: chain LJ residue 133 THR Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LO residue 160 GLU Chi-restraints excluded: chain LS residue 45 LEU Chi-restraints excluded: chain LS residue 133 GLU Chi-restraints excluded: chain LU residue 37 SER Chi-restraints excluded: chain LU residue 83 LEU Chi-restraints excluded: chain LU residue 106 SER Chi-restraints excluded: chain LY residue 76 LYS Chi-restraints excluded: chain LZ residue 32 THR Chi-restraints excluded: chain LZ residue 51 LYS Chi-restraints excluded: chain Lc residue 45 ILE Chi-restraints excluded: chain Lc residue 51 THR Chi-restraints excluded: chain Lc residue 65 MET Chi-restraints excluded: chain Lf residue 4 GLU Chi-restraints excluded: chain Lf residue 51 VAL Chi-restraints excluded: chain Lg residue 99 GLN Chi-restraints excluded: chain Li residue 102 ILE Chi-restraints excluded: chain Lj residue 82 VAL Chi-restraints excluded: chain Lk residue 18 LYS Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 70 THR Chi-restraints excluded: chain Lq residue 120 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1358 random chunks: chunk 855 optimal weight: 5.9990 chunk 1147 optimal weight: 4.9990 chunk 330 optimal weight: 40.0000 chunk 993 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 299 optimal weight: 6.9990 chunk 1079 optimal weight: 4.9990 chunk 451 optimal weight: 1.9990 chunk 1108 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CH 389 ASN CM 25 GLN ** CM 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cf 54 GLN Cf 128 GLN Cg 31 ASN ** Cg 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cg 64 ASN ** Ch 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LD 249 GLN LJ 16 GLN LJ 96 ASN LJ 110 HIS ** LK 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LK 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 110 GLN ** LN 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 153 GLN LT 54 HIS ** LY 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lg 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Li 100 GLN Lk 32 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.089055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.062244 restraints weight = 300874.154| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 1.12 r_work: 0.2646 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2538 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2532 r_free = 0.2532 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2531 r_free = 0.2531 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.128 165503 Z= 0.418 Angle : 0.720 17.928 239712 Z= 0.375 Chirality : 0.042 0.270 29246 Planarity : 0.007 0.144 18045 Dihedral : 22.373 179.942 63905 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.19 % Allowed : 13.28 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.27 (0.08), residues: 10348 helix: 1.88 (0.08), residues: 4033 sheet: 0.14 (0.13), residues: 1457 loop : 0.29 (0.09), residues: 4858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPCg 105 HIS 0.011 0.001 HISCF 39 PHE 0.028 0.002 PHELJ 164 TYR 0.029 0.002 TYRCf 117 ARG 0.017 0.001 ARGCz 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 51504.35 seconds wall clock time: 895 minutes 30.46 seconds (53730.46 seconds total)